bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cold-induced stress modulates the maturation of immune cells of mice during Chlamydia muridarum genital infection
Authors: Belay Tesfaye 
Published: January 2023

Abstract
Chlamydia genital infection caused by Chlamydia trachomatis is the most common bacterial sexually transmitted disease (STD) in the United States. Results in a cold-induced stress mouse model established in our laboratory show that cold-induced stress increases the intensity of chlamydia genital infection. This study was to survey the production of T helper cell type 1 (Th1) and (Th2) cytokines in the stress mouse model. Cells harvested from bone marrow or T cells from spleens of stressed and non-stressed mice during Chlamydia muridarum genital infection were allowed to proliferate in vitro. Cytokine production in culture supernatants was tested by ELISA. Gene expression of GATA 3, T-bet and INF-γ in splenic T cells were determined by QPCR. Production of IL-12 by dendritic cells of stressed mice was 0μg compared to 41.06 μg in non stressed mice. However, C. muridarum infection induced increased IL-12 production (97.27 μg and 123 μg) in stressed and non-stressed mice, respectively. Stress induced a 2-fold decrease in T-bet gene expression in T-cells compared to non-stressed group. In contrast, gene expression of GATA 3 in T cells of stressed mice was significantly increased compared to all other groups tested. INF-γ gene expression in T cells of stressed mice showed a 4-fold decrease compared to T cells of non stressed mice. Stress resulted in decreased IL-12 production in dendritic cells and macrophages, INF-γ production and gene expression of T-bet by Th1 cells. Furthermore, the increased gene expression of GATA 3 only in stressed chlamydia infected T cell suggests that cold-induced stress leads to a skewed immune response toward marked increase in production of Th2 cytokines that favor immunosuppression during chlamydia genital infection.
An alternative mechanism for durable protective immunity to Staphylococcus aureus skin infection
Authors: Dillen Carly A , Farber Orly N , Pinsker Bret L , Liu Haiyun , Archer Nathan K , Lee Da B , Wang Yu , Ortines Roger V , Lee Steven K , Cai Shuting , Ashbaugh Alyssa G , Holland Steven M , Freeman Alexandra F , Milner Joshua D , Miller Lloyd S 
Published: January 2023

Abstract
The immune mechanisms for durable immunity against S. aureus skin infections are unclear as reinfections are common despite specific antibodies and Th1/Th17 cells. Using a CA-MRSA skin reinfection model in mice involving a primary infection (1°) in the lower back (cleared by 14 days) followed by a secondary infection (2°) in the upper back on day 28, we found that 1° and 2° wt mice had similar responses. In contrast, 1° IL-1β−/− mice had increased lesions and bacterial burden with impaired neutrophil recruitment whereas 2° IL-1β−/− mice were protected and resembled wt mice. Transfer of serum containing CA-MRSA specific antibodies did not confer protection to 1° IL-1β−/− mice and depletion of CD4+ T cells did not alter the protection of 2° IL-1β−/− mice, indicating a lack of a role of antibodies or CD4+ T cells. However, 2° IL-1β−/− mice were no longer protected if the egress of lymphocytes from lymph nodes was blocked in 2° IL-1β−/− mice (FTY720 treatment) and the immune impairment in naïve IL-1β−/− mice could be rescued by adoptive transfer of total lymph nodes cells from d28 IL-1β−/− mice. Moreover, transfer of only 50,000 γδ T cells from lymph nodes of day 28 IL-1β−/− mice conferred protection to 1° IL-1β−/− mice. These γδ T cells produced IFNγ/TNF-α, but not IL-17/IL-22, and neutralizing IFNγ/TNF-α activity resulted in loss of protection in 2° IL-1β−/− mice. In humans, similar IFNγ/TNF-α-producing γδ T cells were found in individuals with IRAK4 deficiency whose susceptibility to S. aureus skin infections improves with age but not from individuals with chronic granulomatous disease whose susceptibility is lifelong. These findings define an alternative mechanism to therapeutically target for long-term protection against CA-MRSA skin infections.
CD4+ T cell control of Salmonella infection and persistence is dependent on different macrophage subsets
Authors: Goldberg Michael F , Jenkins Marc K 
Published: January 2023

Abstract
The control of the persistent phagosomal pathogen, Salmonella enterica (Se), by the adaptive immune system is dependent on pathogen-specific CD4+ T-helper 1 (Th1) cells. To explore the hypothesis that Se uses a specific cellular niche to evade Th1 cells in order to persist, we generated a strain of Se that expresses a chromosomally-encoded dTomato protein that displays bright and stable fluorescence in vivo. Following oral infection in 129sv/J mice we found dTomato+ cells in macrophage (MΦ), monocyte, and neutrophil populations. Depletion of neutrophils during infection had no effect on bacterial burden or survival. In contrast, depletion of monocytes and MΦ in CCR2 or LysM-Cre CD115 stop-flox diphtheria toxin (DT) receptor transgenic mice increased bacterial counts and death 6–8 days after DT treatment, indicating an important role for these cells in maintaining Se persistence. Depletion of CD4+ T cells led to increases in bacterial counts and an altered infected cell profile compared to control animals. The frequency of infected CD11bHi MerTKInt infiltrating MΦ was increased, while infected CD11bIntMerTKHi tissue resident MΦ remained relatively constant, suggesting that Th1 cells interact preferentially with infiltrating MΦ. Infected tissue resident MΦ expressed less MHCII, CD86 and more PD-L1 and PD-L2 than uninfected counterparts, and a reciprocal expression pattern was observed on infected infiltrating MΦ. These data suggest that Th1 cells promote killing of intracellular Se in infiltrating MΦ and either ignore or are inhibited by infected tissue resident MΦ providing a reservoir where Se can persist for the lifetime of the infected animal.
Exploring the differences in intestinal dysbiosis induced by CNS inflammatory demyelination and diabetes in non-obese diabetic mice
Authors: Kirby Trevor O , Keever Abby , Seagrave Elizabeth , Turkistani Abdulgader , Lopez Susana , Garcia Daniel , Johnson Cory , McClendon Paige , Ramelow Christina , Harding Christopher , Tigranyan Arman , Rogers Jacqueline , Gonzales Marlene , Magori Krisztian , Ochoa-Repáraz Javier 
Published: January 2023

Abstract
Intestinal dysbiosis is being evaluated as an influencing factor in human diseases. Our laboratory works on the general hypothesis that the association is bidirectional and that disease induction affects the composition of the microbiota. Non-obese diabetic (NOD) mice develop spontaneous diabetes unless active experimental autoimmune encephalomyelitis (EAE), a murine model of multiple sclerosis, is induced. It was proposed that the complete Freund’s adjuvant used for active induction of EAE protect against diabetes. Interestingly, although oral antibiotics treatment reduces EAE severity in SJL and C57BL/6 mice, others showed that the same treatment exacerbates diabetes in adult NOD mice. We questioned whether two different diseases affecting one animal strain, the NOD mice, affected the microbiota composition differently. We hypothesized that the gut microbiota differs between the acute inflammatory and chronic progressive stages that characterize the NOD EAE model. Further, we proposed differences in the microbiota/disease axis in EAE and diabetes. We observed significant changes in the microbiota of NOD mice that developed a severe secondary form of EAE when compared with healthy control mice. The genera Coprococcus, Ruminococcus, and Akkermansia were found elevated in EAE mice while undetermined members of the families Lactobacillaceae and Christensenellaceae were significantly reduced. Furthermore, we compared the EAE and diabetes microbiome and evaluated the effects of transplantation stool samples obtained from EAE, diabetes and control mice on diabetes progression. Our findings support the hypothesis that there are reciprocal effects between disease induction and the modification of the microbiome.
Increase in T cell surface thiol levels are linked with activation and diabetogenicity
Authors: Tse Hubert Ming , Padgett Lindsey E. , Heath Katie E. 
Published: January 2023

Abstract
Free radicals contribute to Type 1 diabetes (T1D) autoimmune responses. We recently demonstrated that superoxide-deficient CD4 T cells exhibited increased effector responses and diabetogenicity, but the redox-dependent mechanism(s) mediating T cell activation were unclear. We hypothesized that during T1D progression, CD4 T cells with a reduced cell surface state would exhibit a concomitant increase in pro-inflammatory cytokine and chemokine responses. To test this, alexa fluor 647-conjugated maleimide (ALM)-labeling of cell surface reduced thiols on diabetogenic mouse and human CD4 T cells was performed. We observed an increase in ALM percentage and gMFI from peripheral Non-obese diabetic (NOD) mouse CD4 T cells during progression to overt diabetes. Cognate autoantigen stimulation elicited a 2- and 20-fold increase in CD4 ALM T cell percentage and gMFI, respectively. In addition to serving as a T cell activation marker, ALM gMFI of reduced CD4 T cell surface thiols was enhanced (1.2-fold) with Th1 polarization and blunted (12.2-fold) following Treg polarization in contrast to Th0 conditions. Cell surface reduced thiols from human CD4 T cells with recent-onset T1D exhibited elevated ALM percentage (1.6-fold, p &lt; 0.05) and gMFI (1.7-fold, p = 0.1503) in comparison to age-matched healthy controls following polyclonal stimulation. Mirroring the increase in ALM with T1D individuals, PBMCs (n=12) also synthesized increased IFNγ (1.2-fold, p=0.0031), TNFα (1.3-fold, p=0.0022), and CXCL10 (1.2-fold, p=0.0145) in contrast to healthy controls (n=7). Our studies point to the exciting potential that oxidation of cell surface thiols on diabetogenic CD4 T cells could abrogate effector responses and correlate with CD4 T cell activation.
Antibiotics ameliorate lupus-like symptoms in mice
Authors: Luo Xin M 
Published: January 2023

Abstract
Gut microbiota and the immune system interact to maintain tissue homeostasis, but whether this interaction is involved in the pathogenesis of systemic lupus erythematosus (SLE) is unclear. Rheumatologists and patients have observed that antibiotics can control lupus flares, suggesting a role for pathogenic microflora in SLE. Here we report that oral antibiotics given during active disease removed harmful bacteria from the gut microbiota and attenuated lupus. Using MRL/lpr mice, we showed that antibiotics ameliorated systemic autoimmunity and kidney histopathology. They also decreased IL-17-producing cells and increased the level of circulating IL-10. In addition, antibiotics removed Lachnospiraceae and increased the relative abundance of Lactobacillus spp., two groups of bacteria previously shown to be associated with deteriorated or improved symptoms in MRL/lpr mice, respectively. Furthermore, we showed that the attenuated disease phenotype could be recapitulated with a single antibiotic vancomycin, suggesting the use of vancomycin as a potential treatment in SLE.
Correlation of alpha- and beta-specific tryptase gene expression with TPSAB1 and TPSB2 genotypes in humans
Authors: Chovanec Jack F , Liu Yihui , Bai Yun , Yin Yuzhi , Metcalfe Dean D. , Milner Joshua D. , Lyons Jonathan J. 
Published: January 2023

Abstract
Germline duplications or triplications of alpha-tryptase encoding sequence at TPSAB1 have been linked to elevated basal serum tryptase and are estimated to effect approximately 5% of the general population. However, no assay currently exists to quantify specific alpha- or beta-tryptase gene expression. Using a similar bioinformatic approach to what we used when designing the alpha- and beta-tryptase sequence-specific TPSAB1 genotyping assay, we developed a novel ddPCR assay able to specifically quantify alpha- and beta-tryptase gene expression. Using this assay, we then interrogated cultured primary human mast cells and isolated basophils from individuals with hereditary alpha tryptasemia syndrome – caused by increased TPSAB1 copy number – and from healthy controls. By correlating these results with individual germline TPSAB1 and TPSB2 genotypes we found that, as would be predicted, increasing alpha-tryptase encoding copy number at the TPSAB1 locus correlated with higher alpha-tryptase gene expression in healthy volunteers. Similarly volunteers lacking alpha-trytpase sequence at TPSAB1 were not detected to have alpha-tryptase gene expression, confirming the specificity of the assay. However, among individuals harboring extra TPSAB1 copies, alpha-tryptase gene expression levels were several orders of magnitude higher than beta tryptases, even when they were present in allelic balance (e.g. 3,3). These data suggest that elevated basal serum tryptase levels seen in hereditary alpha tryptasemia result predominantly from deregulated alpha-trypase gene expression, likely due to co-inheritance of as yet unidentified enhancer or promoter elements.
RELA/p65 Haploinsufficiency as a Novel Cause of Primary Immune Disorder
Authors: Faruqi Aiman J , Comrie William A , Lenardo Michael , Su Helen , Zhang Yu 
Published: January 2023

Abstract
Autoimmune lymphoproliferative syndrome (ALPS) is a primary immune disorder most commonly characterized by defective lymphocyte apoptosis. ALPS patients classically present with chronic non-malignant lymphadenopathy and/or splenomegaly and typically exhibit defects in FAS signaling. We identified an ALPS-like patient with normal FAS-mediated apoptosis. Whole exome sequencing identified a de novo nonsense mutation in one allele of the NF-κB subunit RELA/p65. NF-κB is a ubiquitous and rapid-acting family of transcription factors whose signaling has been implicated in numerous physiological processes including inflammatory responses, innate immunity, lymphocyte homeostasis, lymphoid organogenesis, and immune tolerance. We found the patient mutation resulted in reduced expression of p65; enhanced T cell effector responses; reduced FOXP3 expression and iTreg formation; and an over-representation of p65:p50 heterodimers in CD4+ T cells compared to normal controls. These observations, coupled with the previously demonstrated importance of NF-κB in establishing and maintaining lymphocyte homeostasis and immune tolerance, lead us to posit RELA/p65 haploinsufficiency as a novel cause of ALPS-like disease.
Germline hypomorphic, dominant interfering CARD11 mutations drive severe atopic disease
Authors: Snow Andrew L , Ma Chi , Stinson Jeffrey R , Zhang Yuan , Abbott Jordan K , Weinrich Michael A , Hauk Pia J , Reynolds Paul R , Lyons Jonathan J , Nelson Celeste G , Ruffo Elisa , Dorjbal Batsukh , Glauzy Salome , Stoddard Jennifer , Niemela Julie , Rosenzweig Sergio D , McElwee Joshua J , DiMaggio Thomas , Stone Kelly D , Palma Alejandro , Oleastro Matias , Prieto Emma , Bernasconi Andrea R , Dubra Geronimo , Danielian Silvia , Zaiat Jonathan , Marti Marcello A , Kim Brian S , Cooper Megan A , Romberg Neil , Meffre Eric , Gelfand Erwin W , Milner Joshua D. 
Published: January 2023

Abstract
Monogenic causes for serious manifestations of common allergic disease inform our mechanistic understanding of the pathogenesis of atopy. However, infections and other syndromic phenotypes often accompany such disorders. We performed next-generation sequencing on a cohort of patients with severe atopic dermatitis with evidence of familial inheritance, regardless of comorbidities. We discovered 9 individuals from 5 families harboring distinct, novel heterozygous mutations in CARD11, a lymphocyte scaffolding protein that facilitates NF-κB and mTOR signaling following antigen receptor (AgR) engagement. Significant infections beyond the skin, and non-immunologic comorbidities, were documented in some but not all patients. Improvement of skin and infectious history were noted in the majority of the patients. Each CARD11 mutant exhibited attenuated AgR-driven signaling to NF-κB and mTORC1, and dominantly interfered with the ability of WT CARD11 to activate these pathways in transfected T cell lines. Primary patient T cells also showed defects in AgR-induced activation of NF-κB and mTORC1, which is critical for promoting Th1 and preventing Th2 responses. Impaired proliferation, mTORC1 signaling and IFN-γ production were partially rescued by supplementing with excess glutamine, which requires CARD11 for import into T cells. In contrast to B cell lymphoproliferative disease associated with gain-of-function CARD11 mutations, and severe combined immunodeficiency associated with null CARD11 mutations, our new findings indicate single hypomorphic mutations in CARD11 can cause potentially correctable cellular defects that lead to severe atopy.
Expression and splicing of Ikaros family members in murine and human thymocytes
Authors: Seng Amara , Mitchell Julie L. , Yankee Thomas M. 
Published: January 2023

Abstract
The Ikaros family of transcription factors consists of five highly homologous zinc-finger proteins: Ikaros, Helios, Eos, Aiolos and Pegasus. These family members can homodimerize or heterodimerize in any combination which can alter transcriptional activity. Ikaros family member function can further vary with alternative splicing that affects DNA-binding. Previous studies have demonstrated that abolishing the function of the entire Ikaros family blocks lymphocyte development. Whereas eliminating the function of one Ikaros family member results in relatively minor defects. These data indicate that multiple Ikaros family members play a role in lymphocyte development. The goal of this study was to fully characterize expression and splicing of Ikaros family members in murine and human T cell development from the CD4−CD8− double negative (DN) developmental stage to the CD4+CD8+ double positive (DP) stage. In both mice and humans, Aiolos and Ikaros mRNA levels increase during the progression of T cell development from the DN to DP stages. However, the corresponding increase in Aiolos and Ikaros protein levels was only observed in mice. Additionally, extensive alternative splicing of Ikaros and Aiolos was observed in mice, but only Ikaros was extensively spliced in humans. Helios mRNA and protein levels decreased during murine T cell development, but increased in human T cell development. These data indicate that differences in human and murine T cell development may be regulated by differences in Ikaros family member expression and splicing.
Analysis of lymphoid tissue markers in angiomatoid fibrous histiocytoma
Authors: Nomura Takashi , Kogame Toshiaki , Kabashima Kenji 
Published: January 2023

Abstract
Angiomatoid fibrous histiocytoma (AFH) is a rare soft tissue neoplasm of uncertain differentiation. AFH is characterized by nodular distribution of ovoid and spindle cells with blood-filled cystic cavities. It is circumscribed by thick fibrous pseudo-capsule and a surrounding dense lympho-plasmacytic infiltration encompassing germinal centers. In this study, we analyzed the structure of AFH with immunohistochemistry using markers for lymphoid organogenesis.
The tumor was a circumscribed pyriform mass, composed of histiocytoid and spindle cells. The top part of the mass encompassed cribriform vasculature, which was positive for CD31, a marker for blood endothelial cells (BECs). This BEC-dominant area contained numerous lymphoid, histiocytoid, or fibroblastoid cells, which expressed CD4 (but not CD3), CD31, CXCL13, SDF-1 (CXCL12), and receptor for LTβ (LTβR). The peripheral lymph node address in (PNAd), a marker for high endothelial venules (HEVs), was positive in some vessels, where T and B cells were clustered. The bottom part of the mass was occupied with polygonal cells expressing podolanin, a marker for lymphatic epithelial cells (LECs). The whole mass was encapsulated with CD10+ fibroblast-like cells and surrounded by organized lymphoid infiltration containing T cell areas and B cell follicles with germinal centers.
Our analysis illustrates a case of AFH composed of BEC- and LEC-dominant compartments. The well-organized peritumoral lymphoid infiltration indicated that AFH may produce an environment suitable for inducing inducible skin associated lymphoid tissue (iSALT).
Influence of AIRE-dependent versus -independent tissue restricted antigen expression by medullary thymic epithelial cells on T cell tolerance
Authors: Lebel Marie-Eve , Fournier Marilaine , Melichar Heather J 
Published: January 2023

Abstract
Thymocytes with high reactivity to self-antigens are, in large part, rendered tolerant through a number of mechanisms including clonal deletion and diversion toward regulatory T cell fates. Medullary thymic epithelial cells (mTECs) contribute to self-tolerance via the expression of tissue restricted antigens (TRAs). AIRE is responsible for the expression of approximately one third of TRAs, whereas AIRE-independent expression of TRAs by mTECs is less well characterized. To identify differences in AIRE-dependent and -independent tolerance, we generated new transgenic mouse models expressing a modified OVA-GFP fusion protein that contains several additional, well-characterized epitopes (2W, LCMV gp33 and LCMV gp66) in an AIRE-dependant or -independent manner. These models have enabled us to characterize distinct modes of tolerance for both MHC class I and II-restricted T cells in response to model peptides directed by AIRE-dependent and -independent TRA expression. Using organotypic culture of thymic slices overlaid with antigen-specific TCR transgenic thymocytes as well as tetramer analysis of the endogenous polyclonal T cell populations, we observed both antigen expression and peptide-specific differences in thymic selection. In addition, these difference lead to distinct levels of response to pathogen challenge and we are currently investigating the cellular interactions in the thymus associated with AIRE-dependent and -independent TRA induced tolerance by two-photon microscopy. These studies will lead to a better understanding of T cell tolerance mechanisms, and, in the longer term, inform the design of improved treatments for autoimmune diseases and cancer immunotherapies.
Distinct T cell clones are deleted during the two waves of thymic negative selection
Authors: Lee S Thera , Ruscher Roland , Hogquist Kristin Ann 
Published: January 2023

Abstract
T cells are the central mediators of adaptive immunity and provide diverse receptors to recognize pathogens. While this diversity protects the host from a wide variety of pathogens, it comes with the potential for harmful autoreactivity. To circumvent autoimmune disease, thymocytes bearing T cell receptors (TCRs) that bind with high affinity to self-peptide/MHC are removed in a process called negative selection, while cells with a low degree of affinity mature into conventional T cells. Recently, it has been shown that the process of negative selection occurs in two stages during thymocyte development, corresponding to medullary or cortical localization in the thymus. Little is known about the self-antigens that are presented and selected against in these locations, and thereby the corresponding T cell repertoires. We examined the T cell repertoires of these two deletion stages by sequencing thymocyte TCRs from mice with impaired negative selection (Bim−/−). These mice were crossed with transgenic Nur77GFP mice, in which GFP expression correlates with TCR signaling strength. Therefore, the rescued autoreactive clones can be identified in Bim deficient mice based on high GFP expression. The two pools of autoreactive clones – CD4+CD8+ double positive thymocytes (largely cortical and CCR7−) and CD4+ single positive thymocytes (predominantly medullary and CCR7+) – had only partially overlapping TCR sequences. As deletion selectively pruned clones, these observations indicate that thymocytes encounter different self-peptide/MHC molecules in the thymic cortex and thymic medulla. To further test if negative selection is TCR intrinsic, we are creating ‘retrogenic’ mice with auto-reactive TCRs identified from each wave.