bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data driven identification of divergent host immune subgroups in tuberculosis
Authors: Coarfa Cristian , Rajapakshe Kimal , Gandhi Tanmay , Grimm Sandra L , Heyckendorf Jan , Lange Christoph , van Crevel Reinout , Netea Mihai , Cirillo Jeffrey , Kaufmann Stefan H.E. , Mandalakas Anna Maria , DiNardo Andrew 
Published: January 2023

Abstract

BACKGROUND
Immunity is a critical factor of clinical outcomes after Mycobacterial tuberculosis (Mtb) infection, however, the lack of identification of immune correlates of protection has prevented development of host directed therapeutics. TB studies have identified incongruous immune responses that can lead to a similar TB disease phenotype. Therefore, instead of envisioning susceptibility to TB to follow a unique path, we sough evidence by which divergent host immunity could result in TB.

RESULTS
Inspired by multiomics identification of cancer subtypes improving clinical care, we implemented unbiased, RUV clustering from 12 publicly available datasets consisting of data from 717 TB patients and 527 controls, including 12,468 common genes, and identified 4 distinct immune responses among TB patients. The two largest sub-groups displayed divergent metabolic, epigenetic and immune pathways. Cluster A, consisting of 333 TB patients was characterized by increased glycolysis; up-regulation of epigenetic-modifying genes and increased IFN-γ and TNF signaling. In contrast, Cluster B, consisting of 313 TB patients enriched for gene expression signatures similar to patients with sepsis and immune exhaustion and was characterized by up-regulated NFAT and hormone metabolism and decreased glycolysis, IFN-γ and TNF signaling. In silico evaluation suggests that drugs beneficial for TB patients in Cluster A are detrimental in Cluster B type disease, and vice versa. Multiplex ELISA using a validation cohort of TB patients confirmed divergent immune sub-types in TB.

CONCLUSION
Host immunity to TB is heterogenous and applying precision medicine may enabled sub-stratification guided host directed therapies for management of TB.
The role of the ER stress response during C. rodentium infection
Authors: Sweet Lydia , Duerkop Sharon , Keestra-Gounder Marijke 
Published: January 2023

Abstract
C. rodentium is a mucosal pathogen of mice that shares several pathogenic mechanisms with enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC), which are two clinically important human gastrointestinal pathogens. The C. rodentium model of infection is used to study host pathogen interactions in the gastrointestinal tract and to study ulcerative colitis (UC). Mutations in unfolded protein response (UPR) pathways have been linked to a higher risk of UC development. The ER is an important organelle for protein synthesis and protein folding. Dysregulation of ER stress results in the activation of the UPR to restore homeostasis. Chop is activated downstream of the PERK arm of the UPR and is a transcription factor for multiple targets including cell death and inflammatory pathways. We hypothesized that Chop activation increases cell death and inflammation during C. rodentium infection which then promotes infection and tissue damage. We found that when a mouse epithelial cell line was treated with an ER stress inducing drug or C. rodentium there was an upregulation of Il6 and Il23 but when we inhibited Chop expression the upregulation was lost. We next infected Chop knockout mice with C. rodentium and these mice showed less colon pathology and colon colonization at Day 10. These data suggest that Chop has a role in the ability of C. rodentium to trigger inflammation and in tissue pathology.
Sytemic and Cellular Metabolic Phenotype of Infection and Immune Response to Listeria monocytogenes
Authors: Schwartz Elizabeth Hiltbold , Johnson Robert , Olatunde Adesola , Woodie Lauren , Greene Michael 
Published: January 2023

Abstract
It is generally accepted that immune response and pathogen clearance are metabolically demanding. Additionally, shifts in cellular metabolism are known to occur during immune responses. However, we lack a grasp of how the numerous components of protective immunity contribute to the metabolic demand of illness. Previous studies using model antigens or purified PAMPs have been unable to represent the dynamics of live pathogen infection and immune response. Therefore, we sought to measure the systemic and cellular metabolism of infection and immune response to a well-characterized bacterial pathogen, Listeria monocytogenes. Mice infected with Listeria were monitored over the course of 12 days in multi-parameter metabolic cages. The metabolic phenotype data collected included body weight, activity, sleep, respiratory exchange rate, and energy expenditure. In a parallel study, mice infected with Listeria were utilized to measure bacterial burden, Listeria-specific T cell response, and cellular metabolism of the immune system. We found the early stages of infection (day 1–5), corresponding to the kinetics of the innate immune response, had the greatest metabolic impact on the organism as indicated by weight loss, reduced activity, increased sleep, and decreased energy expenditure. At later timepoints, corresponding to the timing of the adaptive response, there was little evidence of metabolic impact over uninfected controls. We also observed changes in myeloid cell metabolism over the course of the infection. Overall, our results indicate that the innate immune response is more metabolically demanding, compared to the adaptive immune response, linking “sickness behavior” to the timing of the innate immune response.
The Function of Phosphatidylinositol 3-Kinase delta (

PI3Kδ

) Enzyme in Protective Immunity to Trypanosoma congolense Infection in Mice: The Role of Regulatory B cells
Authors: Olayinka-Adefemi Folayemi , Onyilagha Chukwunonso , Jayachandran Nipun , Hou Sen , Jia Ping , Uzonna Jude E , Marshall Aaron J 
Published: January 2023

Abstract
The delta isoform of PI 3-kinase (PI3Kδ) has important functions in B cell activation. Trypanosoma parasites utilize several mechanisms to exploit and evade host B cell and antibody responses critical for immunity.
We sought to determine the impact of PI3Kδ in immunity to Trypanosoma congolense infection. We found that PI3KδD910A mutant mice show a surprisingly enhanced control of parasitemia in early infection (7–9 days) when compared to wild-type (WT) C57BL/6 mice. Drug treatment with Idelalisib to acutely inhibit PI3Kδ during infection in WT mice led to improved early control of parasitemia, consistent with results from genetically deficient mice. Both mutant mice and Idelalisib-treated mice showed a delay in polyclonal B cell activation and CD80/86 expression.
Analysis of cytokine levels in the blood and peritoneal cavity showed higher IFNg and lower IL-10 levels in the drug-treated group at early time points, indicating a more pro-inflammatory environment. B1 cells were identified as the major IL-10 producing cells in the peritoneal cavity in early infection, and B1 cell production of IL-10 was significantly impaired by PI3Kδ-inhibitor treatment. We further observed increased Nitric oxide production in drug-treated mice, which correlated with increased parasite killing in early infection. Despite the improved early parasite control, there was a 100% mortality in PI3KδD910A mutants and 25% mortality in Idelalisib treated mice, presumably due to compromised generation of parasite-specific antibodies required to clear the first wave of blood infection.
Our findings suggest that PI3Kδ inhibition impacts both regulatory B cell functions, affecting the early innate response, and generation of critical protective antibodies.
Myeloid and lymphoid cell immune exhaustion profiles during murine visceral leishmaniasis
Authors: Valadares Diogo Garcia , Scorza Breanna , Davis Richard , Petersen Christine , Wilson Mary E 
Published: January 2023

Abstract
Leishmaniasis is a chronic disease of reticuloendothelial organs that is usually controlled by TH1-type CD4 T cells. Anti-microbicidal responses are ineffective during disease progression, and it is reported that T cells in humans and dogs with visceral leishmaniasis (VL) express markers of cell exhaustion. We hypothesized that myeloid cells provide counter-receptors for inhibitory receptors on T cells at the local sites of Leishmania infantum infection, inhibiting T cell effector functions. We examined inhibitory receptors PD1, LAG3, CTLA4 and TIM3 on lymphoid cells, and ligands PDL1, MHCII, CD80 and Galectin 9 on myeloid cells using flow cytometry, throughout 10 weeks of infection. In livers of infected mice, an increased population of neutrophils with DC features (CD11c+MHCII+) expressing PD-L1 and IL-10 was also observed. In all infected samples an increased DC subset with reduced expression of MHCII, CD80 and CCR7 and higher expression of Galectin 9, PD-L1 and IL-10, was also detected suggesting a pro-exhaustion profile of those cells in infected mice. Furthermore, CD4 and CD8 T cells in infected mice expressed higher levels of the exhaustion markers LAG3, CTLA4 and PD-1 than uninfected mice, with greater proportions of exhausted CD8 than CD4 T cells in livers and spleens. Majority of Ag-experienced CD8 T PD-1+ cells in liver and spleens produced IL-10, whereas most Ag-experienced CD4 T PD-1+ cells produced IFN-γ at the time points studied, suggesting that CD8 T cells assume an exhausted phenotype earlier than CD4 T cells. Data also suggest that both DC and neutrophil subsets could represent a pro-exhaustion myeloid population that may influence the unresponsiveness of lymphocytes in infected tissues during visceral leishmaniasis.
The herbal medicine ‘Indigo naturalis’ altered gut microbiota to accumulate IL-22+ ILC3s
Authors: Yoshimatsu Yusuke , Teratani Toshiaki , Sujino Tomohisa , Mikami Yohei , Ichikawa Masataka , Hagihara Yuya , Takada Yoshiaki , Tanemoto Shun , Umeda Satoko , Nomura Ena , Ono Keiko , Sugimoto Shinya , Nanki Kosaku , Naganuma Makoto , Kanai Takanori 
Published: January 2023

Abstract
Ulcerative colitis (UC) is a chronic inflammation of the large intestine led by the dysregulation of adaptive and innate immune responses. Recently, specific microbiota has been reported to instruct the immune cells and immune response. We have recently proved the clinical efficacy of “indigo naturalis (IN)”, a Chinese herbal medicine, on patients with UC by the multicenter randomized-controlled trial (INDIGO study, Gastroenterology 2018).
4%IN-fed mice ameliorated DSS-colitis (IN-DSS mice) compared to the normal diet-fed mice (ctrl-DSS mice). The number of IL-22+ ILC3s in the colonic lamina propria in IN-DSS mice increased more than the one in ctrl-DSS mice. We also confirmed that IN-fed diet mice significantly altered gut microbiota composition compared to the normal diet-fed mice.
We next inoculated feces obtained from IN-fed mice or normal diet-fed mice to antibiotic treated mice (IN-FMT mice, ctrl-FMT mice respectively). Interestingly, IN-FMT mice significantly restored the pathology of DSS-induced colitis than ctrl-FMT mice with increased number of IL-22+ ILC3s. We showed IN induced specific microbiota which accumulated IL-22+ ILC3s in gut.
Toll-like Receptor 2 is crucial for commensal-specific immune responses on the ocular surface
Authors: Zhu Wenjie , Xu Xiaoyan , St. Leger Anthony J , Almaghrabi Fatimah , Horai Reiko , Caspi Rachel R 
Published: January 2023

Abstract
Conjunctiva of the eye is a mucosal immune tissue and harbors a variety of immune cells. It is exposed to diverse microorganisms that come in contact with the ocular surface. Previously, we demonstrated that colonization of the ocular mucosa with the commensal bacterium, Corynebacterium mastitidis (C. mast), results in increased resistance of the ocular surface to infectious fungal and bacterial pathogens, and that this effect is mediated by IL-17A produced by γδ T cells that respond to C. mast. In this study, we show that Toll-like receptor 2 (TLR2) is important for activation and proliferation of γδ T cells and for their IL-17A production in response to C. mast.
TLR2−/− mice failed to recruit γδ T cells and neutrophils to the conjunctiva upon C. mast inoculation, and IL-17A-producing γδ T cells were reduced in eye-draining lymph nodes of these mice. In vitro experiments revealed that IL-17A production to C. mast by gd T cells was dependent on APC and that TLR2 expression was needed on both γδ T cells and APCs. Exogenous IL-1 could only partly compensate for the deficiency in IL-17A production by TLR2−/− gdT cells, indicating a need for another TLR2-dependent signal. Flow cytometry and RNA-Seq analyses suggested that dependence on TLR2 for IL-17A production and IL-17A related gene expression in response to C. mast is higher in the Vγ6 than in the Vγ4 subset. Notably, the transcriptomic analysis also implicated dysregulation of mitochondrial pathways in TLR2−/− cells, which was functionally confirmed by the Seahorse assay.
We conclude that TLR2 is required for sensing the commensal C. mast in the conjunctiva and eye-draining lymph nodes, to drive the local IL-17 response and maintain immune homeostasis at the ocular surface.
Mucin degrading bacteria accelerates intestinal stem cells-derived epithelial development
Authors: KIM SEUNGIL , Kim Yeji , Kim Tae-Young , Lee Su-Hyun , Kweon Mi-Na 
Published: January 2023

Abstract
Mucin degrading bacteria are closely located in intestinal epithelium; however, how they associate differentiation and development of intestinal stem cells (ISCs) is not elucidated. To address an exact role of mucin degrading bacteria on the gut homeostasis, mice were fed with Akkermansia muciniphila, which is specialized to mucin degradation, for one month. We found that oral feeding with A. muciniphila accelerated self-renewal of Lgr5+ ISCs and promoted differentiation of lysozyme+ Paneth cells and Muc2+ goblet cells in the small intestine. Co-cultured with Lgr5+ ISCs and Paneth cells from A. muciniphila-fed mice resulted in augmented organoid forming capacity in comparison to those from PBS-fed control mice in a Wnt3-dependant manner. Of note, levels of acetate and propionate were higher in cecum contents of A. muciniphila-fed mice than those of control mice. Organoids treated with cecum contents obtained from A. muciniphila-fed mice exhibited larger size and these effects were diminished by Gpr41/43 antagonists. In addition, oral feeding with A. muciniphila induced change of gut microbiota composition and a positive correlation between several genus including Akkermansia. Most importantly, pre-treatment with A. muciniphila prevented intestinal epithelial cells damage caused by radiation and chemotherapy. These findings suggest that mucin degrading bacteria (i.e., A. muciniphila) play a crucial role in promoting ISCs-mediated epithelial development and contributed to maintain intestinal homeostasis.
Dietary cellulose prevents gut inflammation by modulating lipid metabolism and gut microbiota
Authors: Kim Yeji , Hwang Sung Wook , Kim Seungil , Lee Yong-Soo , Kim Tae-Young , Lee Su-Hyun , Kim Eun Na , Kweon Mi-Na 
Published: January 2023

Abstract
A Western diet comprising high fat, high carbohydrate, and low fiber content has been suggested to contribute to an increased prevalence of colitis. To clarify the effect of dietary cellulose (an insoluble fiber) on gut homeostasis, for 3 months mice were fed a high-cellulose diet (HCD) or a low-cellulose diet (LCD) based on the AIN-93G formulation. Histologic evaluation showed crypt atrophy and goblet cell depletion in the colons of LCD-fed mice. RNA-sequencing analysis showed a higher expression of genes associated with immune system processes, especially those of chemokines and their receptors, in the colon tissues of LCD-fed mice than in those of HCD-fed mice. The HCD was protective against dextran sodium sulfate-induced colitis in mice, while LCD exacerbated gut inflammation; however, the depletion of gut microbiota by antibiotic treatment diminished both beneficial and non-beneficial effects of the HCD and LCD on colitis, respectively. A comparative analysis of the cecal contents of mice fed the HCD or the LCD showed that the LCD did not influence the diversity of gut microbiota, but it resulted in a higher and lower abundance of Oscillibacter and Akkermansia organisms, respectively. Additionally, linoleic acid, nicotinate, and nicotinamide pathways were most affected by cellulose intake, while the levels of short-chain fatty acids were comparable in HCD- and LCD-fed mice. Finally, oral administration of Akkermansia muciniphila to LCD-fed mice elevated crypt length, increased goblet cells, and ameliorated colitis. These results suggest that dietary cellulose plays a beneficial role in maintaining gut homeostasis through the alteration of gut microbiota and metabolites.
High-fat diet causes rapid microbiota-dependent intestinal ILC3 loss and impairs tolerance and immunity
Authors: Boulenouar Selma 
Published: January 2023

Abstract
Innate lymphoid cells (ILCs) are increasingly appreciated to play a critical role in tissue homeostasis, immunity, and tolerance. At steady state, intestinal ILC3 are the main source of IL-22, ensuring epithelial barrier integrity and defense against pathogenic bacteria. In addition, ILC3 support intestinal tolerance to commensal bacteria and dietary antigens. ILC3 can also sense changes in dietary nutrients, such as vitamin A and aryl hydrocarbon receptor ligands that affect their development, function and ultimately intestinal health. Here we show that ILC3 are severely depleted from the small and large intestine of obese mice fed high-fat diet (HFD) but not in leptin or leptin receptor-deficient obese mice. Notably, consumption of HFD for only 24 hours is sufficient to trigger ILC3 cell death. Total loss of ILC3 is reached after one week of HFD without significant weight gain. We found that this short-term consumption of HFD increases host susceptibility to Citrobacter rodentium infection and impairs tolerance to dietary antigens. Unexpectedly, we found that ILC3 were maintained in germ-free mice fed HFD. However, ILC3 were depleted when HFD-fed GF mice were inoculated with either living, heat-killed bacteria or with LPS. Furthermore, HFD-fed TLR4 deficient mice are protected from intestinal ILC3 loss. TNFα blockade is sufficient to prevent HFD-induced ILC3 loss. Collectively, our findings show that short term consumption of HFD, rather than obesity potentiates rapid loss of ILC3 in presence of microbiota that leads to early impairment of gut integrity, tolerance, and protection against pathogens.
Assessment of Antibody Functional Affinity using FluoroSpot
Authors: Kirchenbaum Greg A , Sautto Giuseppe A , Abreu Rodrigo B , Lehmann Paul V , Ross Ted M 
Published: January 2023

Abstract
Studies of B cell immunity often rely upon serologic methodologies that primarily assess antibody specificity. However, functional affinity of the antigen-specific antibody repertoire is a key determinant of protective efficacy. Presently, detailed assessment of single B cell/antibody functional affinity is labor-intensive and low-throughput. Therefore, we sought to evaluate whether B cell FluoroSpot assays would enable distinction between B cells with differential functional affinity since fluorescent intensity is directly proportional to antibody abundance in this assay. To test our prediction, murine B cell hybridomas (P65C6-2, 36–65 and 36–71) secreting monoclonal antibodies (mAb) with differential affinity for the p-azophenylarsonate (Ars) hapten were utilized as model antibody-secreting cells (ASC). Additionally, usage of an anti-idiotypic mAb (17–63) specific for the high-affinity anti-Ars mAb (36–71) confirmed unambiguous segregation of Ars-specific ASC. Moreover, we also evaluated the capacity of a multiplexed FluoroSpot assay to simultaneously distinguish antibody functional affinity among influenza hemagglutinin-reactive murine B cell hybridomas, or in vivo differentiated ASC from immunized mice, secreting various IgG subclasses (IgG1/IgG2a/IgG2b) in parallel. Collectively, our data support the notion that FluoroSpot assays can be used to assess the functional affinity of antigen-specific B cells, and that this approach is well-suited for detailed assessment of humoral immunity.
A new interpretable machine learning approach for single-cell data discovers correlates of clinical outcome in cancer immunotherapy
Authors: Greg Finak , Greene Evan , D’Amico Leonard , Bhardwaj Nina , Church Candice , Morishima Chihiro , Ramchurren Nirasha , Taube Janis , Nghiem Paul , Cheever Martin , Fling Steven , Gottardo Raphael 
Published: January 2023

Abstract
High-dimensional cytometry is routinely used to characterize patient responses to cancer immunotherapy and other treatments, producing a wealth of datasets ripe for exploration but whose biological and technical heterogeneity make them difficult to analyze with current tools. We introduce a new interpretable machine learning method for single-cell mass and flow cytometry studies, FAUST, that robustly performs unbiased cell population discovery and annotation and enables data integration across studies and platforms. FAUST returns biologically interpretable cell phenotypes that can be compared across studies, making it well-suited for the analysis and integration of complex datasets. We use FAUST to perform candidate biomarker discovery and validation by applying it to flow and mass cytometry datasets from melanoma anti-PD-1 trials in order to discover and validate new CD4+ and CD8+ effector-memory T cell correlates of outcome co-expressing PD-1, HLA-DR, and CD28. Existing state-of-the-art computational discovery approaches as well as prior manual analyses did not detect any statistically significant T cell correlates associated with anti-PD-1 treatment these data. We use FAUST to replicate the discovery of published myeloid cell correlates and validate these by identifying them de novo in independent trials. FAUST’s phenotypic annotations are used to perform cross-study integration diverse data sets, allowing hypothesis-driven inference about cell sub-populations through a Phenotypic and Functional Differential Abundance (PFDA) framework. We showcase this approach on data across multiple trials. These results establish FAUST as a powerful new approach for unbiased discovery in single-cell cytometry.