bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiomic and spatial immunophenotyping reveals a prominent Runx3+ resident T cell population in the healthy human breast
Authors: Longworth Aaron J , Mallya Sharmila , Lev Tatyana , Pein Maren , Adam Isam , Lincy Antony , Naef Pascal , McMullen Timothy P , Halas Paige , Kessenbrock Kai , Lawson Devon A 
Published: August 2023

Abstract
The role of Runt-domain related transcription factor 3 (Runx3) in the early development of T cells is well established, however recent work has implicated Runx3 as a driver of residency in barrier tissues such as the lung and intestinal epithelium, as well as in the tumor infiltrating lymphocytes of murine and human melanomas. We have identified a subpopulation of resident T cells in the healthy human breast exhibiting constitutive expression of Runx3. Employing single-cell RNA sequencing paired with concurrent sequencing of T cell receptors (TCRseq, 10× Genomics) and oligo-tagged antibodies (Totalseq, BioLegend) specific to canonical markers of memory and effector T cells, we compared the clonality and transcriptome of T lymphocytes isolated from reduction mammoplasty or tumor-patient-derived contralateral mastectomies to those obtained from matched patient peripheral blood. We subsequently utilized highly-multiplexed spatial immunophenotyping through Co-detection by indexing (CODEX, Akoya Biosciences) to infer the role of Runx3+ resident T cells in the healthy human breast based on informatic analysis of the associated cellular neighborhoods. Our analysis finds an abundant population of highly clonal CD8+ Runx3+ cytotoxic T lymphocytes consistently located in the milk-producing lobular and secretory ductal regions of the healthy adult breast, postulating roles in barrier immunity and tissue reconstruction. Furthermore, marked presence of these cells in the contralateral mastectomies of tumor-bearing patients suggests a protective antitumoral role in nonaffected or cleared tissue.
Supported by NIH grant R01 (5R01CACA237376-03), T32 (T32-NS121727-01)
RGC-32 facilitates reactive astrocytosis by modulating the expression of axonal guidance molecules
Authors: Rus Horea G , Tatomir Alexandru , Cuevas Jacob , Nguyen Vinh , Cudrici Cornelia , Badea Tudor , Rus Violeta 
Published: August 2023

Abstract
Response Gene to Complement (RGC)-32 modulates TGF-β-induced extracellular matrix secretion and the ability of astrocytes to undergo reactive changes in vivo during experimental autoimmune encephalomyelitis (EAE). However, the molecular pathways underlying these effects are still not well understood. In this study, we investigated how lack of RGC-32 affects the transcriptomic profile and the expression of axonal guidance molecules (AGM) in astrocytes during EAE. We performed next-generation RNA sequencing on brain neonatal astrocytes isolated from wild type (WT) and RGC-32 knock-out (KO) mice, either unstimulated or stimulated with TGF-β. Results were then validated by using Real-Time PCR. Spinal cords from WT and RGC-32 KO mice with EAE (at days 0 and 14) were stained by immunohistochemistry for the astrocyte marker GFAP, AGM, and for nuclear factor IA (NFIA), a gliogenic factor and transcriptional regulator of AGM. Lack of RGC-32 had a significant impact on the transcriptomic programs normally associated with brain development whose re-expression is usually seen in reactive astrocytes. Connectivity analysis revealed that genes coding for AGM were particularly affected. We found lower transcript levels of ephrin receptor A type 7 (Epha7), plexin A1 and Slit guidance ligand 2 in RGC-32 KO astrocytes. Moreover, our results showed that NFIA and EPHA7 are expressed by astrocytes during EAE. We found a lower number of astrocytes expressing EPHA7 and NFIA in RGC-32 KO mice with acute EAE when compared with WT mice. These results suggest that RGC-32 might facilitate reactive astrogliosis during acute EAE through regulating the expression of AGM and NFIA.
Veterans Administration Merit Award I01BX001458 (to HR)
Interferon-alpha plays an important role in glial-mediated symptoms of neuropsychiatric systemic lupus erythematosus
Authors: Lin Stacie L , Aw Ernest , Zhang Yingying , Carroll Michael C 
Published: August 2023

Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease that leads to clinical pathology across organs, including the central nervous system (CNS). In up to 80% of patients with SLE, CNS manifestations can range from anxiety and fatigue to overt psychosis. While studies have demonstrated a hallmark increase in circulating interferon alpha (IFNα) in the peripheral blood and cerebrospinal fluid, the cellular mechanisms leading to neuropsychiatric lupus (NPSLE) remain unclear (Crow et. al., 2014). Using a mouse model of lupus which expresses an elevated IFNα signature and exhibits behaviors of NPSLE, we found a spatial pattern of interferon-stimulated genes (ISGs) in the brain parenchyma utilizing the multiplexed spatial transcriptomics platform MERFISH (Moffitt et. al., 2016). Guided by unbiased single nucleus sequencing highlighting astrocytes and oligodendrocytes as major glial cells enriched in ISG expression, we hypothesized that this spatial distribution implicates IFNα-driven glial activity against neuron function, thus disrupting regions of the CNS that manifests as NPSLE. We also investigated the role of IFNα on microglia activity and behavior changes using a cell-specific Cre mouse model. Further functional assays reveal increased synapse engulfment by microglia upon IFNα activation. Despite waning ISGs levels in the periphery, levels in the brain persist along with behavior severity, pointing to a CNS source of IFNα. This body of work demonstrates how IFNα released locally by glial cells can mediate NPSLE development via disruption of neuron function. Deeper understanding of targetable pathways in IFNα signaling will expand the therapeutic potential of type 1 interferon-driven neuropsychiatric diseases.
Hepatic regulatory T-cells promote colorectal liver metastasis in NASH
Authors: Hu Jiannan , Wang Han , Zhang Hongji , Ren Jinghua , Cheng Xiang , Yao Yonghong , Tsung Allan , Huang Hai 
Published: August 2023

Abstract

Background
Non-alcoholic steatohepatitis (NASH), a progressive inflammatory form of NAFLD, underlies an extremely versatile and dynamic inflammatory microenvironment along with aberrant metabolism and ongoing liver regeneration. Regulatory T cells (Tregs), as essential immune regulatory cells, are critical for the inhibition of tumor-promoting inflammation and cancer cell escape. Our recent study found that Tregs were selectively increased in both mouse models and patients with NAFLD, which promotes us to study the role of Tregs in NASH-HCC. However, the role of Tregs in the development of hepatic metastasis in NASH liver remains unknown.

Methods
A Western diet mouse model and the STAM mouse model were utilized for NASH development. MC38 murine colorectal tumor cells were injected via portal vein at 12 weeks of feeding or orthotopically injected into cecum subserosa. Tumor development will be determined 3 or 4 weeks after injection. Depletion of Tregs by FoxP3-DTR mice or CD25 antibody treatment. Transcriptomic profiling of leucocytes in hepatic immune microenvironment was determined by scRNA-seq.

Results
There is a positive correlation between increased Tregs and hepatic tumor growth in NASH liver. Depleting Tregs inhibits the development of hepatic metastasis in NASH liver compared with control liver. NASH development led to a significant transcriptomic shift in hepatic immune cells, such as Kupffer cells, Tregs and MDSCs. Blocking the interaction of Tregs and PMN-MDSCs in the TME prevents tumor growth in the NASH liver.

Conclusions
Tregs can suppress immunosurveillance in the premalignant stages of NASH. Therapies targeting Tregs could offer a potential strategy for preventing hepatic metastasis in patients with NASH.

RO1GM137203
T Follicular Helper Cells Restrain Obesity-Related Metabolic Disease by Damping Intestinal Inflammation
Authors: Wang Haiguang , Barrow Fanta , Florczak Kira , Abujamra Maya , Parthiban Preethy , Fredrickson Gavin , Revelo Xavier S 
Published: August 2023

Abstract
The intestinal immune system is a central modulator of obesity-associated metabolic disease. Particularly, high-affinity intestinal IgA maintains gut homeostasis after its generation in a germinal center (GC) response that requires functional T follicular helper (Tfh) cells in Peyer’s patches (PP). The objective of this study was to determine how obesity affects Tfh function leading to metabolic disease. We investigated the phenotype of Tfh cells in diet-induced obese mice. Obese mice showed enlarged PP featured by an expansion of CXCR5high ICOShigh Tfh cells. Surprisingly, intestinal Tfh cells in obese mice showed evidence of dysfunction as they expressed substantially lower PD1 and BCL6 but higher CCR7. As a result, the GC response and the generation of IgA+ B cells are also defective in obese mice. To determine if Tfh directly regulate intestinal inflammation and metabolic disease during obesity, we fed Tfh-deficient (Cd4Cre Bcl6flox) mice a western diet and investigated their microbiota composition, barrier integrity, and inflammatory status. In the gut, Tfh-deficient obese mice showed a disturbed microbiota, reduced regulatory T cells (Tregs), compromised intestinal barrier, and a loss of the microbiota-derived short-chain fatty acid butyrate. Moreover, we observed exacerbated liver inflammation in Tfh-deficient mice, suggesting a fundamental role for Tfh in dampening inflammation in the gut-liver axis. Mechanistically, Tfh cells express lower levels of insulin receptors and increased Foxo1, suggesting that reduced insulin signaling underlies the dysfunction of Tfh cells during obesity. Overall, our findings highlight an unexpected role for Tfh cells as essential regulators of obesity-related metabolic disease.
IL-2 producing T Follicular Helper cells self restricts entry of T follicular helper cells in the germinal centers
Authors: Dave Shivangi 
Published: August 2023

Abstract
Upon infection or immunization, dendritic cells (DCs) present antigens (Ags) to naïve CD4+ T cells. As a result, a fraction of the responding CD4+ T cells upregulate Bcl6 and differentiate into T follicular helper (Tfh) cells, which migrate into the B cell follicles. Once in the B cell follicles, Tfh cells help promote the development and maintenance of the germinal centers (GC). Importantly, limiting the number of Tfh cells is critical for maintaining the selective pressure in the GC, thereby allowing the Darwinian selection that leads to affinity maturation. However, the mechanisms that regulate Tfh cell numbers and prevent excessive Tfh help remains unknown. Using an influenza virus infection model, we show here that Tfh cell differentiation is limited to the first 72h of the infection. After this time, whereas DCs continue to present viral antigens and efficiently prime naïve T cells, responding CD4+ T cells fail to upregulate Bcl6 and preferentially differentiate into effector Th1 cells. Mechanistically, we demonstrate that the lack of Tfh cell differentiation after day three was due to the presence of the early-primed Tfh cells. Our results indicate that early-primed Tfh cells produce large amounts of IL-2 in the proximity of the B cell follicles, thereby limiting the differentiation of new Tfh cells after day three. Collectively, our data demonstrate that early-primed Tfh cells act as a self-regulating factor that shields the B cell follicles early after infection, thereby preventing the continuous differentiation of Tfh cells regardless of the presence of viral antigens. These data demonstrate a new self-competitive mechanism that critically contributes to limiting Tfh cell expansion after infection.
This work was supported by The University of Alabama at Birmingham (UAB) and the National Institutes of Health grant 1R01AI162698-01A1 to A.B.-T
Opposing functions of circadian protein DBP and atypical E2F family E2F8 in anti-tumor Th9 cell differentiation
Authors: Lim Yun-Ji , Park Sang-A , Ku Wai Lim , Zhang Dunfang , Cui Kairong , Tang Liu-Ya , Zanvit Peter , Chen Zuojia , Jin Wenwen , Xu Junji , Wu Chuan , Zhang Ying E , Zhao Keji , Chen WanJun 
Published: August 2023

Abstract
Interleukin-9 (IL-9)-producing CD4+ T helper cells (Th9) have been implicated in allergy/asthma and anti-tumor immunity, yet molecular insights on their differentiation from activated T cells, driven by IL-4 and transforming growth factor-beta (TGF-β), is still lacking. Here we show opposing functions of two transcription factors, D-binding protein (DBP) and E2F8, in controlling Th9 differentiation. Specifically, TGF-β and IL-4 signaling induces phosphorylation of the serine 213 site in the linker region of the Smad3 (pSmad3L-Ser213) via phosphorylated p38, which is necessary and sufficient for Il9 gene transcription. We identify DBP and E2F8 as an activator and repressor, respectively, for Il9 transcription by pSmad3L-Ser213. Notably, Th9 cells with siRNA-mediated knockdown for Dbp or E2f8 promote and suppress tumor growth, respectively, in mouse tumor models. Importantly, DBP and E2F8 also exhibit opposing functions in regulating human TH9 differentiation in vitro. Thus, our data uncover a molecular mechanism of Smad3 linker region-mediated, opposing functions of DBP and E2F8 in Th9 differentiation.
Open Access funding provided by the National Institutes of Health (NIH).
A method for in vitro polarization of pathogenic ST2-expressing memory Th2 cells
Authors: Liu Caini , Xiao Jianxin , Qian Wen 
Published: August 2023

Abstract
IL-33 and its receptor subunit ST2 (IL1RL1) have been linked to type 2 eosinophilic asthma in multiple human and mouse studies. In particular, recent clinical trials demonstrate that monoclonal antibodies targeting IL-33/ST2 are beneficial to subsets of asthma patients. ST2+ memory Th2 cells (mTh2) are important effector cells in IL-33-mediated type 2 eosinophilic asthma. Herein we describe a unique method for polarizing a subset of pathogenic ST2+ mTh2 (ST2+ mTh2p) cells from naïve mouse CD4 T cells in vitro, which does not require multi-round activation/resting or co-culturing with antigen-presenting cells as reported in prior studies. The ST2+ mTh2p cells proliferate and produce large amounts of type 2 cytokines upon IL-33 treatment [without involving T-cell receptor (TCR) ligation]. IL-33 stimulation induces metabolic reprogramming of ST2+ mTh2p, as indicated by the increased mitochondrial respiration and glycolytic rate in Seahorse assays as well as upregulated key metabolites and metabolic genes involved in these two bioenergetic pathways. Interestingly, IL-33 stimulation also increases the metabolites and the expression of key enzymes for the production of polyamines (the important regulators of cell proliferation). Moreover, ST2+ mTh2p cells are highly pathogenic, as they are capable of propagating and producing type 2 cytokines in the lung, resulting in strong eosinophilic inflammation induced by intranasal IL-33 administration alone after adoptive transfer to Rag2−/−IL2r−/− mice (lacking both innate and adaptive lymphocytes). In summary, the current study provides useful tools to investigate IL-33/ST2-regulated molecular mechanisms and immunological functions of ST2+ mTh2p cells both in vitro and in vivo.
R0 1HL144497
Gut microbiome and metabolites relate diabetes risk among Native Hawaiians and Pacific Islanders
Authors: Peres-David Rafael Aniu , Kunihiro Braden P , Wells Riley K , Phankitnirundorn Krit Aniu , Umeda Lesley P , Lee Rosa Aniu , Juarez Ruben , Maunakea Alika K 
Published: August 2023

Abstract
Native Hawaiians and Pacific Islanders (NHPIs) suffer higher rates of type 2 diabetes mellitus (T2DM) prevalence and mortality compared to other racial-ethnic groups in Hawaii. Gut microbiome is recognized as a partial determinant of T2DM progression, the role of its associated metabolome is not well understood in the context of immunometabolic health disparity. We employed community-based research strategies among Oahu, Hawaii residents to form a cohort enriched with NHPIs (N=98). Gut microbiome profiling was achieved via 16s rDNA metagenomic sequencing from stool. Plasma inflammation factors were measured using magnetic bead-based multiplex assays. Stool metabolites were identified using mass spectrometry. T2D individuals had reduced relative abundance of gut bacteria belonging to Bacteroidetes (P&lt;0.05). Similar reduction was observed for known butyrate-producers, including Roseburia sp. (P&lt;0.05), Faecalibacterium sp.(P=0.01), and Eubacterium sp (P=0.03). Metabolomic data revealed that phenylbutyric acid (PBA), a short-chain fatty acid (SCFA) derivative of butyrate, was differentially present between diabetics and control (P=0.001). Furthermore, PBA concentrations correlated negatively with A1c (%; R=−0.34, P&lt;0.01), CRP(ng/mL; R=−0.32, P&lt;0.01), and positively with Adiponectin (ng/mL; R=0.38, P&lt;0.01) and IL-10 (ng/mL; R=0.47, P&lt;0.01). Higher stool levels of PBA were associated with lower levels of IL-1 (P=0.03), MCP-1 (P=0.01), and IFN-g (P=0.02). Further elucidation of biological mechanisms underlying gut bacterial modulation of systemic inflammation through SCFA metabolites may allow for future development of mitigative strategies for T2DM risk in such health-disparate communities as NHPIs.
This project was supported in part by the National Institutes of Health (NIH), National Institute on Minority Health and Health Disparities (NIMHD) under grant numbers R56MD014630, U54MD007601-35, and R01MD016593 and by the National Institute of General Medical Sciences (NIGMS) under the IDeA Networks of Biomedical Research Excellence (INBRE) program (P20GM103466).
IL21 Receptor-Deficient Regulatory T Cells Promote Resolution of Intestinal Inflammation by Resisting Metabolic Disturbance
Authors: Bamidele Adebowale , Klatt Emily , Hirsova Petra , Mishra Shravan , Fehrenbach Patrick , Sagstetter Mary , Valenzuela-Perez Lucia , Lee Hyun Se Kim , Faubion William 
Published: August 2023

Abstract

Background
Inflammatory regulatory T cells (Tregs) are one of the hallmarks of therapy resistance. Yet mechanisms leading to inflammatory Treg development and its contribution to inflammatory bowel disease (IBD) are unexplored.

Methods
Tregs derived from healthy PBMCS were characterized by immune and mitochondrial phenotyping. Transcripts were validated in dataset from IBD intestinal lesions. Wildtype (WT) and IL21 receptor-deleted (Il21r−/−) Tregs were examined in murine models of CD4+ T cell-induced colitis.

Results
Through in vitro cytokine challenge of Tregs and subsequent analysis, we found that IL21 induces Tregs co-expressing TNF, IFNγ and IL17. Transcriptomic and metabolomic integration revealed upregulation of mRNA and metabolites associated with glycolysis, and amino acid, nucleotide and lipid metabolism. Moreover, IL21-induced metabolic transcripts were more enriched in Treg cluster within scRNA-seq dataset from intestinal lesions of anti-TNF non-responders vs. non-responders. Mechanistically, cell imaging and real-time bioenergetic analysis revealed disruption to mitochondria-ER ultrastructure and function, coinciding with glycogen synthase kinase 3β (GSK3β) activation and glycolytic switch rather than pyruvate-mediated oxidative phosphorylation. GSK3β inhibition or methyl pyruvate supplementation rescued IL21-induced metabolic and inflammatory phenotypes. In contrast to WT Tregs, murine Il21r−/− Treg transfer efficiently prevented and rescued CD4+CD45Rbhigh T cell-induced colitis.

Conclusions
IL21-induced metabolic dysfunction can incapacitate Treg immunosuppressive function. Desensitizing Tregs to IL21 through various therapeutic approaches can alleviate IBD.

This work was supported by National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) K01DK124358, the Pilot & Feasibility Award by the Center for Cell Signaling in Gastroenterology (P30DK084567), and the Mayo Clinic Center for Biomedical Discovery Career Development Award, and David F. and Margaret T. Grohne Cancer Immunology and Immunotherapy (to AOB).
Targeting Multiple Costimulatory Molecules Prevents Persistence of Lung Tissue-resident Memory T cells and Leads to Airway Tolerance
Authors: Sethi Gurupreet Singh , Croft Michael 
Published: August 2023

Abstract
Pools of tissue-resident memory T (Trm) cells are thought to maintain and contribute to exacerbations of inflammatory or autoimmune disease. We hypothesized that several costimulatory molecules would control the expansion and maintenance of these populations when responding to antigen, and tested the potential of targeting OX40L, CD30L, and ICOSL, using a house dust mite (HDM) allergen-based mouse model of asthmatic lung inflammation. We found that allergen induced persisting CD4+CD44hiCD62Llo CD69+ and CD69− lung-localized Trm cells and RNA-seq revealed the heterogeneity of these memory pools, containing Th2, Tfh, Th17, and Th1 clusters. Showing their reliance on costimulation for recall activity to allergen, blocking CD30L and OX40L together, or blocking ICOSL alone, resulted in ~50% reduction in the expansion of both CD69+ and CD69− tissue-resident effector T cells during a secondary allergen exposure or a tertiary allergen exposure. Blocking all three molecules at once further inhibited T cell accumulation by ~90%, corresponding to a similar reduction in lung tissue inflammation, including eosinophilia. Moreover, triple costimulation blockade resulted in a diminished persisting lung tissue-resident memory T cell pool, which failed to expand to normal levels and drive further exacerbations of lung inflammation upon subsequent exposure to allergen, resulting in a state of airway tolerance. Overall, our data suggest that the concurrent inhibition of OX40, CD30, and ICOS signaling, can impair the expansion and persistence of lung-localized Trm cells and could engender long-lasting tolerance in asthma and similar autoimmune or inflammatory diseases that are maintained by tissue-resident memory T cells.
Deletion of protein kinase D1 in myeloid lineage cells suppresses development of IFNγ+IL-17A+ CD4 T cells and ameliorates hypersensitivity pneumonitis
Authors: Yi Ae-Kyung , Snyder John D , Yoon Tae Won , Fitzpatrick Elizabeth A 
Published: August 2023

Abstract
Hypersensitivity pneumonitis (HP) is an extrinsic allergic alveolitis characterized by inflammation of the interstitium, bronchioles, and alveoli of the lung that leads to granuloma formation and ultimately irreversible fibrosis. Previous studies found that exposure to HP inciting antigen S. rectivirgula (SR) leads to the activation of protein kinase D1 (PKD1) in the mouse lung in vivo and that PKD1 contributes to the acute pulmonary inflammation, IL-17A expression in the lungs, and development of HP caused by repeated exposure to SR. In the present study, we investigated whether PKD1 in myeloid cells affects the pathogenic course of the SR-induced HP. Compared to control PKD1-sufficient mice, mice with deficiency of PKD1 in myeloid cells (PKD1mKO) showed significantly suppressed expression of IL-6, TNFα, IFNγ, CCL2, CCL3, CCL4, CXCL1, CXCL2, and CXCL10 and neutrophilic alveolitis after single intranasal exposure to SR. Substantially reduced levels of alveolitis and granuloma formation were observed in the PKD1mKO mice repeatedly exposed to SR. Surface expression of MHC-II and CD86 on myeloid cells, and expression of IFNγ, IL-17A, CCL20, CXCL9, and CXCL10 in lungs were significantly reduced in the PKD1mKO mice repeatedly exposed to SR. In addition, surface expression of CD69, CXCR3, and CCR6 on CD4 T cells and frequency of IFNγ+IL-17A+ CD4 T cells in the lungs were significantly reduced in PKD1mKO mice repeatedly exposed to SR. Our results demonstrate PKD1 in myeloid lineage cells plays an essential role in the initial proinflammatory responses and neutrophil influx in the lung after exposed to SR and contributes to the development of IFNγ+IL-17A+ CD4 T cells and HP caused by repeated exposure to SR.
Supported by grants from NIH (R01 AR064723, R01 AR069010) and UTHSC.