bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal patterns in single cell immune profile of tuberculosis lung granulomas
Authors: Gideon Hannah Priyadarshini , Hughes Travis K. , Wadsworth Marc H. , Nyquist Sarah , Lin Philana Ling , Fortune Sarah , Shalek Alex K , Flynn JoAnne L 
Published: January 2023

Abstract
Infection with Mycobacterium tuberculosis results in the formation of tuberculosis lung granulomas, which are complex structures with a network of multiple immune cells closely intertwined and function together. Within a given host, granulomas have unique trajectories and outcomes resulting in bacterial control or persistent bacterial replication and dissemination. The timing of establishment and immune composition of the granuloma in the lung plays a crucial role in the control of bacterial burden. Using high-throughput single-cell mRNA sequencing (SeqWell) on individual TB lung granulomas and computational algorithms, we are generating models to understand infection dynamics that incorporate timing of establishment, immune cell composition, its functional interactions; bacterial burden and trajectories of the granulomas to identify robust drivers of bacterial control. We evaluated original and new lung granulomas identified by PET CT scan from 15 cynomolgus macaques infected with M. tuberculosis (Erdman strain) for 4, 6 or 10 weeks. We identified over 30 functional clusters of cells spanning multiple immune and non-immune cells types including T cells, B cells, plasma cells, dendritic cells, mast cells, macrophages, neutrophils, pneumocytes, fibroblasts and endothelial cells. We observe differential cellular composition associated with temporal patterns (original vs. new) in granulomas that are associated with bacterial burden. By understanding these immune features associated with temporal patterns that limit bacterial replication, we hope to identify novel targets for host-directed immune therapies and prophylactics in M. tuberculosis infection and other granulomatous diseases.
Continuous generation of effector (Teff) and effector memory (Tem) T cells with mouse cytomegalovirus (MCMV) vaccination to prolong malaria immunity
Authors: Gbedande Komi , Ibitokou Samad , Brown Michael G. , Degli-Esposti Mariapia , Stephens Robin 
Published: January 2023

Abstract
Immunity to Plasmodium infection or vaccination decays without continuous exposure. This decay correlates with loss of malaria-specific T cells, not antibody. We recently demonstrated that Teff protect better than memory T cells, and that Ifng+ Teff are responsible for the protection provided by persistent P. chabaudi infection. Based on this data, we have reverse-engineered a vaccine strategy that first induces a long-lived antibody response, and then boosts the Teff and Tem response to prolong protection. We chose live vaccination with “infection and drug cure”, which generates protection that decays over 200 days. The boost uses MCMV as it is an excellent T cell-inducing vector with promise against SIV, tuberculosis and liver-stage malaria. First, we observed that MCMV infection strongly reduced parasite growth, as previously shown for Leishmania, suggesting a useful adjuvant effect. To promote continuous induction of specific T cells, we generated MCMV expressing the P. chabaudi T cell epitope B5. Vaccination with MCMV-B5 activated both adoptively transferred B5 TCR Tg T cells and MCMV-specific CD4 T cells, generating protective Teff and Tem phenotypes for over 2.5 months. Importantly, we show that boosting with the MCMV vector prolongs protection generated by the live vaccine, as shown by better protection from re-infection at day 200. We are currently investigating the contribution of activated Plasmodium-specific T cells in prolonging protective immunity by MCMV-B5, and mechanisms of protection. Our findings suggest that chronic vaccination can redress the problem of short-lived protection to malaria infection and vaccines, which would be beneficial for any efficacious but short-term vaccine strategy.
T cell-derived interferon-γ is required for host defense to Toxoplasma gondii
Authors: Sasai Miwa , Pradipta Ariel , Yamamoto Masahiro 
Published: January 2023

Abstract
Interferon-γ (IFN-γ) is important for host defense against various intracellular organisms including a protozoan pathogen Toxoplasma gondii. Various immune cells are recently shown to produce IFN-γ in T. gondii infection, however, it remains elusive which cell types are important for anti-T. gondii host defense so far. Here we generate a new IFN-γ reporter mouse line in which a fusion protein of Venus and NanoLuc to analyze IFN-γ producing cells during T. gondii infection and find that CD4+, CD8+, γδ T cells and natural killer cells express Venus in a time dependent manner. Furthermore, Lck-Cre/Ifngfl/fl mice are highly susceptible to T. gondii infection. Taken together, our results demonstrate that T cell-derived IFN-γ plays an important role in anti-T. gondii host defense.
The role of Axl in bacterial infection-mediated inflammatory responses
Authors: Kim Minjae , Choi Harim , Kim Su-Man , Kang Hyung-Sik 
Published: January 2023

Abstract
Salmonella Typhimurium (S. Typhimurium), one of the most common infectious bacteria, triggers an inflammatory reaction in epithelial cells of the intestine and migrates into the spleen and liver to colonize. To elucidate the role of Axl in bacterial infection-mediated inflammatory responses, Axl-depleted mice and WT mice were infected with S. Typhimurium, and the systemic dissemination caused by the infection was evaluated. The Axl-depleted mice shows better histological scores and increased intraepithelial T cells. The colony number and CFU of S. typhimurium were also lower in the liver of Axl-depleted mice than in that of WT mice. Thus, lack of Axl results in better resistance to S. Typhimurium, suggesting that downregulation of Axl is essential for bacterial resistance by inducing increased number and activity of intraepithelial T cells.
Epithelial STAT6 O-GlcNAcylation drives type 2 mucosal immunity against helminth infection
Authors: Zhao Ming , Ren Kaiqun , Ruan Hai-Bin 
Published: January 2023

Abstract
The tuft cell-type 2 innate lymphoid cell circuit has emerged as a critical component of mucosal type 2 immunity against helminth, which infects more than 1 billion people worldwide. However, little is known regarding the molecular mechanisms underlying type 2 cytokine-induced tuft cell hyperplasia. O-linked N-Acetylglucosamine (O-GlcNAc), a posttranslational modification on intracellular proteins at serine and threonine residues, plays a central role in many biological processes such as gene transcription, protein stability, and cell signaling. We have previously reported that depletion of intestinal epithelial O-GlcNAcylation by knocking out O-GlcNAc transferase (OGT) leads to epithelial cell dysfunction. Here, we specifically studied the role of protein O-GlcNAcylation in tuft cell development. O-GlcNAcylation in the intestinal epithelium was transiently elevated upon helminth infection, while genetic deletion of OGT impaired tuft cell hyperplasia and type 2 immune responses. Intriguingly, such defects were not observed in mice that OGT was specifically deleted in committed tuft cells, suggesting that O-GlcNAcylation is required for the differentiation of intestinal progenitors toward the tuft cell lineage. Mechanistically, STAT6, a type 2 cytokine-responsive transcriptional factor essential for tuft cell development, is O-GlcNAcylated. O-GlcNAcylation enhanced STAT6 transcriptional activity, while O-GlcNAc-deficient STAT6 blunted its transcriptional activity and tuft cell differentiation. Taken together, our data demonstrate that protein O-GlcNAcylation, by modifying STAT6 signaling, is indispensable for tuft cell-involved mucosal type 2 immune responses against helminth infections.
Differential phenotypes and localization of CD8 T cell responses to acute and chronic viral infections
Authors: Hardman Blair K , Osborne Lisa C 
Published: January 2023

Abstract
Norovirus is the most common viral cause of gastroenteritis globally. Most infections are either acute, symptomatic, and rapidly cleared or persist asymptomatically. However, the mechanisms underlying these outcomes are unknown. MNV-CW3 and -CR6 are murine noroviruses which demonstrate immune correlates of acute and chronic infection respectively. This research interrogates the mechanisms underlying strain-specific differential antiviral CD8 T cell responses to acute or chronic MNV. At days 3, 4, 5 and 8 post-infection, the phenotype and quantity of adoptively transferred MNV specific CD8 T cells in the spleen, mesenteric lymph node (MLN), and intestines are analyzed by flow cytometry. Concurrently, fluorescent microscopy is used to determine the biogeographical distribution of antiviral CD8 T cells throughout the intestine. Flow cytometry shows activated MNV-specific CD8 T cells first accumulate in the MLN following oral infection with either virus suggesting this is the site of immune activation though CR6 infection results in a delayed, reduced CD8 T cell response as shown by CFSE dilution. Supporting the MLN as a primary initiation site of the antiviral CD8 T cell response, prevention of T cell egress from activation sites by FTY720 treatment enriches activated CD8 T cells in the MLN in CW3 infections with a concurrent decrease in the spleen. Furthermore, by day 8 post-infection CD8 T cell populations are skewed to memory precursors or short-lived effectors in CW3 and CR6, respectively. These data suggest these highly related viral strains may induce activation of distinct populations of, or pathways in, APC populations with long-lasting effects on CD8 T cell function and the outcome of infection.
The Wnt-β-catenin-IL-10 signaling axis in intestinal antigen-presenting cells protects mice from colitis-associated colon cancer in response to gut microbiota
Authors: Hussein Mohamed Ahmed Shawky , Swafford Daniel , Shanmugam Arulkumaran , Ranganathan Punithavathi , Manicassamy Santhakumar 
Published: January 2023

Abstract
Loss of immune tolerance to gut microflora is inextricably linked to inflammatory bowel disease (IBD) and colitis-associated colon cancer (CAC). Intestinal antigen presenting cells (APCs) play a pivotal role in regulating intestinal inflammation and CAC, but underlying signaling pathways and molecular mechanisms remain largely unknown. In the present study, using a mouse model of CAC, we show that the low-density lipoprotein receptor-related proteins 5 and 6 (LRP5/6)-β-catenin-IL-10 signaling axis in CD11c+ APCs suppresses CAC by regulating the expression of tumor-promoting inflammatory factors in response to commensal flora. Genetic deletion of Wnt co-receptors LRP5/6 in CD11c+ APCs in mice (LRP5/6ΔCD11c) resulted in enhanced susceptibility to CAC. This is due to a microbiota-dependent increased expression of tumor-promoting pro-inflammatory factors and decreased expression of the immunosuppressive cytokine, IL-10. This condition could be improved in LRP5/6ΔCD11c mice by depleting the gut flora, indicating the importance of LRP5/6 in mediating immune tolerance to the gut flora. Moreover, mechanistic studies show that LRP5/6 suppresses the expression of tumor promoting inflammatory factors in CD11c+ APCs via the β-catenin-IL-10 axis. Accordingly, conditional activation of β-catenin in CD11c+ APCs or in vivo administration of IL-10 in LRP5/6ΔCD11c mice markedly reduced intestinal inflammation and CAC by suppressing the expression of inflammatory factors. In summary, here we identify a key role for the LRP5/6-β-catenin-IL-10 signaling pathway in intestinal APCs in regulating CAC in response to the commensal flora and suggest potential means for therapeutic intervention in inflammatory intestinal diseases.
Glucose promotes Treg differentiation and suppresses intestinal inflammation
Authors: Yu Yu , Yang Wenjing , Yu Yanbo , Zhao Xiaojing , Zhou Zheng , Bilotta Anthony J , Yao Suxia , Cong Yingzi 
Published: January 2023

Abstract
Glucose, the most abundant monosaccharide, has been characterized as the most important source of energy in human body, which is also considered as a potential risk factor in varies of diseases. However, the roles of glucose in regulation of intestinal T cell responses and inflammation are still controversial. In this report, we investigated whether and how glucose regulates the CD4+ T cell responses in intestinal inflammation. We treated Rag−/− mice which were transferred with CBir1 CD4+ T cells, which are specific for immunodominant microbiota antigen CBir1 flagellin, with drinking water with or without 0.6% or 6% (w/v) glucose for two weeks. We found that 6%, but not 0.6%, glucose in drinking water promoted regulatory T cells (Treg), but not Th1 and Th17 cells, differentiation in the mesenteric lymph nodes (MLN). In vivo administration of glucose to WT mice at the dose of 6%, but not 0.6%, also increased Treg cells in MLN. Within in vitro assay, glucose promoted Treg differentiation in a dose-dependent manner from 4500ug/ml to 15000ug/ml, but inhibited Treg differentiation with the dose higher than 15000ug/ml. Moreover, glucose-treated T cells cultured under Treg conditions showed enhanced suppressive activity toward naïve T cell proliferation. Mechanistically, glucose upregulated the expression of EGFR, Areg and Gzmb, the genes associated with regulation of Treg suppressive function. Furthermore, glucose at the dose of 6% alleviated the colitis in RAG−/− mice induced by CBir1 T cells, and increased Treg, but not Th1 and Th17, cells in MLN. Collectively, our study indicates that glucose promotes Treg differentiation and function under certain conditions, which plays an important role in intestinal homeostasis.
Indole-3-carbinol prevents colitis and regulates microbial dysbiosis by induction of anti-microbial peptides and mucins in an IL-22 dependent manner
Authors: Busbee Philip Brandon , Wilson Kiesha , Nagarkatti Mitzi , Nagarkatti Prakash S. 
Published: January 2023

Abstract
Colitis is an inflammatory bowel disease (IBD) characterized by acute or chronic inflammation within the colon and significant alterations in the microbiome, a term known as microbial dysbiosis. In our previous reports, we showed that a natural indole product and aryl hydrocarbon receptor (AhR) ligand found in cruciferous vegetables (Indole-3-carbinol, or I3C) was able to reduce colitis-induced disease severity and prevent colitis-associated microbial dysbiosis. In the current study, we performed 10× Genomics single cell analysis on colonic epithelial cells (CECs) and lamina propria-derived immune cells from 2,4,6-Trinitrobenzenesulfonic acid solution (TNBS)-induced colitis treated with or without I3C. Single cell analysis showed that treatment with I3C results in alterations in the immune cell profiles, which included increases in both anti-inflammatory regulatory T cells (Tregs), as well as IL-22 producing cells. Additionally, CEC cells in I3C-treated mice showed an increase in host defense responses to microbes, such as mucin (muc2) and anti-microbial peptide (AMP) production. Increased AMP production included mainly beta-defensins (BDs) and regenerating islet-derived protein 3 (Reg3) types. Gene transcriptome array and PCR validation experiments confirmed the results obtained from the single cell analysis. Lastly, as IL-22 is known to play a key role in regulating host defense responses by mucin and AMP production, we neutralized IL-22 in vivo and showed that the ability of I3C to reduce colitis severity and prevent colitis-associated microbial dysbiosis was lost.
Compartmentalized effects of aging on group 2 innate lymphoid cell development and function
Authors: D’Souza Shanti , Shen Xiaofei , Fung Ivan T. H. , Ye Longyun , Kuentzel Marcy , Chittur Sridar V. , Furuya Yoichi , Siebel Christian W. , Maillard Ivan P. , Metzger Dennis W. , Yang Qi 
Published: January 2023

Abstract
The effects of aging on innate immunity and the resulting impacts on immunosenescence remain poorly understood. Here, we report that aging induces compartmentalized changes to the development and function of group 2 innate lymphoid cells (ILC2), an ILC subset implicated in pulmonary homeostasis and tissue repair. Aging enhances bone marrow early ILC2 development through Notch signaling, but the newly generated circulating ILC2 are unable to settle in the lungs to replenish the concomitantly declining mature lung ILC2 pool in aged mice. Aged lung ILC2 are transcriptomically heterogeneous and functionally compromised, failing to produce cytokines at homeostasis and during influenza infection. They have reduced expression of Cyp2e1, a cytochrome P450 oxidase required for optimal ILC2 function. Transfer of lung ILC2 from young mice enhances resistance to influenza infection in old mice. These data highlight compartmentalized effects of aging on ILC and indicate that targeting tissue-resident ILCs might unlock therapies to enhance resistance to infections and diseases in the elderly.
Reduced A20 expression in nasal epithelial cells correlates with disease severity in patients with chronic rhinosinusitis with nasal polyps
Authors: chen cailing , Liu Zheng 
Published: January 2023

Abstract

Objective
Chronic rhinosinusitis with nasal polyps (CRSwNP) is a multifactorial disorder characterized by heightened and sustained inflammation. A20 is a novel multifunctional protein with immunomodulatory effects. We sought to investigate the expression of A20 in sinonasal mucosa, and its association with local inflammation and disease severity in patients with CRSwNP.

Methods
The expression of A20 in sinonasal samples was assessed by quantitative RT-PCR, IHC, and Western blot. The numbers of local inflammatory cells were counted. CT scan findings and symptom severity were scored. Primary nasal epithelial cells were cultured to explore the regulation of A20 expression.

Results
Compared with control tissues and non-eosinophilic polyps, the mRNA and protein expression of A20 was significantly down-regulated in eosinophilic polyps. A20 was mainly expressed by epithelial cells. The expression of A20 in nasal epithelial cells was significantly reduced in eosinophilic polyps in comparison with those in non-eosinophilic polyps and control tissues. There was a further decrease in A20 expression in nasal epithelial cells in patients with eosinophilic polyps with asthma compared to those without asthma. A20 mRNA was induced by TNF-α, LPS, dsRNA, and dexamethasone, whereas was inhibited by IL-4 and IL-13 in human primary nasal epithelial cells. A20 mRNA levels in nasal epithelial cells negatively correlated with IL-4 and IL-13 levels and eosinophil numbers in sinonasal mucosa. Importantly, mRNA levels of A20 in nasal epithelial cells negatively correlated with disease duration and so on.

Conclusions
The decreased expression of A20 might contribute to eosinophilic inflammation and disease progression in patients with CRSwNP.
Early dynamic accumulation of tissue resident memory T cells in the human lung during infancy
Authors: Matsumoto Rei , Connors Thomas , Ural Basak Burcu , Guyer Rebecca , Idzikowski Emma , Poon Maya M.L. , Thapa Puspa , Farber Donna L 
Published: January 2023

Abstract
Infants exhibit increased susceptibility to viral and bacterial pathogens with pulmonary infections representing one of the top causes of infant mortality worldwide. Optimal protection from pathogens is mediated by coordinated functions of different T cell subsets, with tissue resident populations maintaining site-specific immunity in the respiratory tract. Currently, little is known of how tissue localized T cells populate and mediate mucosal immune responses in early life in humans. Here we analyzed T cell populations in the lungs obtained from infant and pediatric organ donors aged 8 days postnatal (PN) to 8 years by imaging and flow cytometry. In the earliest stage of life at 8 days PN, few αβ T cells were present in the lung, while innate-type γδ T cells were present around the airways. During the first two years of life, αβ T cells exhibiting memory phenotypes preferentially accumulated around the central airways and expressed canonical markers of tissue residency (CD69 and CD103), consistent with flow cytometry data. By contrast, the total number of γδ T cells in the lung did not change significantly with age for up to 8 years of life; for example, the ratio of αβ:γδ T cells in neonatal donors was 1.5:1, which increased to 16:1 in lungs of a 3 year old donor. Consistent with the imaging data, the frequency of γδ T cells by flow cytometry was significantly reduced after the early neonatal period. These results show that γδ T cells populate the lung during the early neonatal period and are maintained in relatively constant numbers over childhood, while tissue resident αβ T cells accumulate over first 2 years of life and predominate thereafter. Our results demonstrate the dynamic nature of lung-localized T cell immune responses in a mucosal site.
Deletion of Dnase1L3 from Macrophages results in reduced serum Dnase activity in mice
Authors: Engavale Minal B. , Keyel Peter A 
Published: January 2023

Abstract
Dnase1L3 deficiency leads to 100% penetrance of pediatric onset Systemic lupus erythematous (SLE) while reduce Dnase1L3 levels is seen in adult-onset. Dnase1L3 is an endonuclease primarily secreted by myeloid cells like macrophages into the serum, where it degrades apoptotic bodies and chromatin, which reduces auto antibody formation and prevents SLE in both humans and mice. Importantly, reduction in the Dnase1L3 protein levels occurs both in adult-onset SLE in humans, and in polygenic murine models. This suggests that different levels of Dnase1L3 contribute to SLE progression. Also, decreasing Dnase1L3 levels leads to progressively worse SLE. However, the amount of serum Dnase1L3 needed, or whether the impact of Dnase1L3 is analog or digital remains unknown. In order to reduce Dnase1L3 protein levels, we generated Dnase1L3fl/fl x LysM-cre+/− conditional knockout (cKO) mice on B6 background. We determined the contribution of macrophage Dnase1L3 by measuring the Dnase1L3 protein levels and enzymatic activity by Dnase activity assay. We found that cKO mice showed ~2-log reduction in the serum Dnase activity. These cKO mice represent a cell-specific model to study the impact of Dnase1L3 protein levels on SLE pathogenesis. Together these findings suggest that macrophage specific Dnase1L3 may be a key player in lupus, however there could be other nucleases involved which we plan to inhibit using certain specific inhibitors. Overall, our findings suggest that macrophage specific Dnase1L3 is critical to prevent autoantibody formation in protecting lupus onset