bluuebunny/crossref_metadata_2025_split huggingface dataset:
B cells drive tertiary lymphoid organ formation in ileal inflammation
Authors: Erlich Emma , Czepielewski Rafael , Kumar Shashi , Field Rachael , Zhang Xinya , Saleh Leila , Guilak Farshid , Brestoff Jonathan , Ellebedy Ali , Randolph Gwendalyn J 
Published: January 2023

Abstract
Crohn’s disease [CD] is one of the two most common forms of inflammatory bowel disease, affecting over half a million Americans. Like many other diseases with chronic inflammation, some patients with CD develop tertiary lymphoid organs [TLO] in areas of the gastrointestinal tract with active disease. TLOs are organized clusters of lymphocytes, similar in structure to secondary lymphoid organs, though they develop after birth and their contribution to pathogenesis in CD, or other diseases, is unclear. We, and others, have also found B cell rich lymphoid aggregates in the mesenteric fat of CD patients along dramatically remodeled lymphatic vessels. TNFΔARE/+ is a murine model of ileal inflammation that recapitulates several key features of ileal CD, including development of mesenteric tertiary lymphoid organs. Use of this model revealed that mesenteric TLOs block cellular and molecular export from the gut, leading us to wonder if mechanisms that interfere with their development might reduce ileitis. TNFΔARE/+ mice that lack B cells revealed that B cells are required for tertiary lymphoid organ formation in this model. Without these TLOs, lymphatic outflow from the intestine was restored. Nonetheless, histological and flow cytometric approaches reveal no difference in local inflammation in the ileum. However, systemic inflammation, as assessed by metabolic cages and changes in body weight over time, increased. This suggests that TLOs may act to trap inflammatory signals locally, preventing systemic dissemination of inflammatory cells or mediators.
Work supported by NIH grants DP1-DK109668-04 and T32-DK077653-27 and the Kenneth Rainin Foundation
Expression of a BTB-ZF transcription factor controls the function of an innate-like Tregs essential for intestinal homeostasis
Authors: Krzyzanowska Agata K , Haynes Rashade A , Kovalovsky Damian , Lin Hsinching , Edelblum Karen L , Corcoran Lynn M , Rabson Arnold B , Denzin Lisa K , Sant’Angelo Derek B 
Published: January 2023

Abstract
The BTB-ZF genes are a family of 49 transcription factors that control the lineage specification and development of key effector functions of different subsets of lymphocytes. Using a single-cell BTB-ZF transcription factor expression analysis, we identified a unique subset of T regulatory cells (Tregs). These Tregs are genetically and phenotypically distinct from the larger conventional Treg population. For instance, analogous to natural killer (NKT) cells they have an activated phenotype (CD62Llo, CD44hi) and constitutively express IL-10. Interestingly, these characteristics are acquired early during T cell development. The defining transcription factor is induced during thymic development, binds the IL-10 promoter, and enables T cells to rapidly produce the cytokine. The subset of Tregs is enriched in the intestine and expands during acute colitis. The deletion of the defining transcription factor in T cells results in intestinal epithelial layer damage causing loss of the barrier function making mice highly vulnerable to severe disease and death from induced colitis. Moreover, in the absence of the transcription factor in T cells, normal intestinal macrophage responses are disrupted most likely due to decreased production of IL-10 by the Tregs. Therefore, by profiling BTB-ZF transcription factor expression, we have identified a distinct subset of T cells with potent immunosuppressive abilities that are essential for the health of the intestine. Numerous aspects of these Tregs are parallel to NKT cells, indicating an existence of “naïve” Tregs that have innate-like effector functions acquired independently from the differentiation in the periphery.
Supported by NIH/NIAID R01 AI122757-01 Careers in Immunology Fellowships – 2021
Regulatory T cell coordination of the mucosal NK cell response during viral infection.
Authors: Vick Sarah C , Lund Jennifer M 
Published: January 2023

Abstract
In many infections the mucosal barrier is the site of pathogen exposure, yet the regulation of mucosal immunity is not well understood. Herpes simplex virus-2 (HSV-2) is one of the most prevalent mucosal infections, making this disease an ideal model to study mucosal anti-viral immune response. My goal is to define how regulatory T cells (Tregs) shape anti-viral immune responses through modulation of natural killer (NK) cells during mucosal virus infection. To accomplish my goal, I utilized a mouse model of intravaginal HSV-2 infection. NK cell phenotypes were examined using high parameter flow cytometry. To define how transient Treg depletion during HSV-2 infection impacts NK cells, I utilized Foxp3DTR mice. Treg depletion led to increased maturation of NK cells in the vaginal tract (VT). KLRG1 is associated with NK cell maturation and is a marker of terminally mature NK cell subsets. I found a significant increase in the frequency and total number of KLRG1+ NK cells in the VT two days after HSV-2 infection in the absence of Tregs. I further analyzed NK cell maturation using the expression of the two surface markers CD11b and CD27 and found a significant increase in CD11b+CD27+ NK cells after Treg depletion. This subset of NK cells is known to be significant producers of pro-inflammatory cytokines. The cytokine IL-15 is necessary for NK cell development and maturation. I found that in the VT, CD11b+Ly6C+ monocyte-derived DCs display increased IL-15 transpresentation after Treg depletion. My data suggests that Tregs have a modulatory effect on NK cell development in the VT as Treg depletion leads to altered NK cell maturation and development. This demonstrates the role of Tregs in mediating an effective immune response while limiting immune pathology.
Supported by grants from NIH (R01 AI141435-01, T32 AI 7509-21)
Imaging the lung microenvironment during Coccidioidomycosis
Authors: Miranda Nadia Esmeralda , Diep Anh , Tejeda-Garibay Susana , Hoyer Katrina K 
Published: January 2023

Abstract
Valley fever is a respiratory disease caused by the fungal pathogen Coccidioides. Very little is known about how the fungus interacts with the immune system and the lung microenvironment, hampering vaccine and therapy development. There is a critical need to identify which immune cells are interacting with the fungus in the lungs and how these cells control infection. Granulomas form within the lung to control infection, but the formation, maintenance, and molecular and immune players in these processes are largely unexplored. Granuloma cell mass can be identified in X-rays and MRI scans only to be misdiagnosed for tumors, until a lung biopsy is analyzed. To investigate immune cells present in Coccidioides granulomas, we utilized tissue immunohistochemistry via fixed-formalin paraffin-embedded (FFPE) and fresh frozen embedded samples to assess immune cell and Coccidioides interactions. Various labeling methods have been investigated using infected mouse lungs to optimize procedures before switching to patient samples. Hematoxylin and eosin (H&E) staining combined with periodic acid–Schiff (PAS) identifies Coccidioides spread within the lung following fungal inhalation in mice. Lung imaging challenges include the presence of endogenous peroxidases that cause non-specific antibody binding. Antigen retrieval following paraffin embedding, have now been optimized to fit the lung and specific to the antibody that is being used. Here we highlight various troubleshooting methods with successful immunofluorescence FFPE lung imaging.
Supported by University of California Office of the President grant VFR-19-633952 & R21
Lung-resident memory CD4 T cells recognizing antigen in the airway enhance the kinetics of antigen presentation and naive T cell activation in draining lymph nodes
Authors: Finn Caroline M , Prokop Emily , McKinstry Karl Kai 
Published: January 2023

Abstract
CD4+ tissue-resident memory (TRM) T cells act as sentinels at previous sites of infection and rapidly initiate protective inflammatory responses upon antigen re-encounter. Here, we tested if beyond local impacts in the lung, TRM responses lead to faster egress of antigen-loaded dendritic cells (DC) resulting in their more rapid accumulation in draining lymph nodes (DLN). To do so, we used a mouse model originally developed to examine CD4+ TRM-mediated protection against influenza virus infection. We established a TRM population in otherwise naïve mice by intranasal transfer of memory CD4 T cells specific for ovalbumin (OVA). The mice were then challenged with fluorescently-labelled OVA protein intranasally. Faster migration from the lung to the DLN by OVA+ DC was seen within 48 hours of protein administration in mice receiving TRM compared to controls without TRM transfer. We hypothesized that the enhanced kinetics of OVA presentation in DLN mediated by TRM antigen recognition would result in more rapid systemic activation of OVA-specific CD4 T cells. We thus transferred an indicator population of naïve OVA-specific CD4 T cells intravenously to mice receiving TRM transfer or not prior to OVA protein administration. Faster kinetics of naïve T cell activation were seen in recipients of TRM within 3 days as judged by expression of activation markers and proliferation. Most importantly, by day 4, responding naïve cells reached the lung in greater numbers and were more functional in mice receiving TRM. Our results reveal that CD4+ TRM activation can enhance the kinetics of antigen presentation in DLNs and suggest this mechanism can be harnessed by vaccines to fully integrate protective local and systemic CD4 T cell responses.
Supported by grants from NIH (R21 R21AI148882)
Mycobacterium avium via oral route provide enhanced protection against pulmonary tuberculosis: An essential role of B cells and germinal centers
Authors: Dutt Taru S , Karger Burton Richard , Fox Amy , Youssef Nathan , Dadhwal Rhythm , Obregon-Henao Andres , Henao-Tamayo Marcela 
Published: January 2023

Abstract
Human tuberculosis (TB) is caused mainly by Mycobacterium tuberculosis (Mtb) and represents an enormous challenge to global health because of the inadequacy of currently available drugs and vaccines. The most common clinical manifestation is pulmonary TB, and the Bacille Calmette Guerin (BCG) is the only licensed vaccine for protection against TB; however, its efficacy is highly variable. Today at least 52 countries have reported MDR-TB and XDR-TB cases which cannot be cured or contained by current TB therapy. Thus, there is an urgent need to develop new therapies/vaccines that effectively prevent or cure TB. In the last decade, lymphoid follicles (LFs) having ectopic GCs (eGC) have been identified in the lungs of Mtb infected animals and humans; however, a mechanism of its formation and role has not been adequately characterized. Our studies found that mice vaccinated with BCG and exposed to Mycobacterium avium [a non-tuberculous mycobacterium (NTM)] via drinking water provide long-term protection from pulmonary TB than BCG alone as determined by reduced Mtb bacterial burden and inflammatory progression of infection. Interestingly, these mice also developed eGC in the lungs and have increased B cells, anti-Mtb cell lysate specific IgA, and IgG antibodies. These findings suggest that NTM and B cells play a critical role in generating protective immunity against pulmonary Mtb infection, and the formation of eGC in these mice is a crucial factor in this improved immunity. Investigating the mechanism of eGC formation and the role of NTM and B cells in its stimulation is an important question to understand TB pathogenesis and to develop effective vaccines and therapies.
Supported by NIH/NIAID - 1R01AI127475-01AI, Colorado State University’s MIP research team grant
Low and transient salivary neutralizing antibodies after COVID vaccination
Authors: Nahass Georgie , Salomon-Shulman Rachel , Sheikh-Mohamed Salma , Blacker Grace , Haider Kazim , Blish Catherine A , Sanders Erin , Gommerman Jennifer L , Weissman Irving L , Tal Michal Caspi 
Published: January 2023

Abstract
Neutralizing activity found in the blood following intramuscular vaccination protects against systemic disease from SARS-CoV-2 infection. Mild breakthrough mucosal infections in vaccinated individuals can contribute to transmission chains of infection, and as such the contribution of intramuscular vaccination to mucosal immunity is important to understand. We assessed vesicular stomatitis virus (VSV) SARS-CoV-2 SPIKE protein neutralization activities as well as anti-viral spike and RBD IgG and IgA isotype antibody binding, in saliva from individuals who had recovered from SARS-CoV-2 infection and people who received immunization. The various vaccination strategies deployed globally showed key differences in the extent of neutralizing activity that could be measured. Even in subjects with significant peak activity 2–4 weeks following a second dose of mRNA vaccination, this neutralizing activity was transient and significantly reduced within 3–6 months. Among adenoviral vectors, ChAdOx1 elicited significantly more salivary neutralizing activity and antibody levels compared to Ad26.S. A large range of salivary neutralizing activity is induced following different intramuscular SARS-COV-2 vaccination strategies. All were orders of magnitude lower than neutralization levels observed in blood, and it remains to be determined if any of the observed neutralizing activity in the saliva can neutralize virus in the upper respiratory tract upon exposure. Based on studies where high levels of mucosal IgA antibodies were induced in response to stimulation with aerosol intranasal vaccines, such vaccines could be important in lowering transmission of SARS-COV-2.
Supported by The Fairbairn Foundation and SPARK
RAMP3 unexplored relevance for innate-T cell immunity
Authors: Ascui-Gac Gabriel Antonio , Mendis Alba , Phung Eleni , Chandra Shilpi , Han Jihye , Caron Kathleen , Kronenberg Mitchell 
Published: January 2023

Abstract
RAMP3 is a chaperon protein that aids in the transport, activity modulation and pharmacological switch of G-protein coupled receptors (GPCR). Chemokine receptors involved in immune cell recruitment and activation are GPCRs, but the role of RAMP3 in the function of the immune system has not been explored. Our lab found that Ramp3 gene is highly expressed in innate-like T cells in the lungs of mice, particularly for Mucosal-associated invariant T (MAIT) cells. Ramp3 KO mice have an increased absolute number of MAIT cells, while other innate T cells are not affected. These differences are even higher after vaccinations with a live attenuated Salmonella strain containing MAIT-cell antigens. Both at steady-state and after vaccination, Ramp3 KO mice MAIT cells have increased levels of CXCR6, a chemokine receptor that has been associated to lung homing and T cell maintenance in the periphery. Ramp3 KO mice also have a decreased proportion of IL17A-producing MAIT cells in the lung; IL-17-producing innate cells have been shown to be protective, for example following Streptococcus pneumoniae infection. Consistent with the MAIT17 decrease, there was increased bacterial burden after lung infections. While Ramp3 has been reported in several gene signatures related to T cell regulation, its role for T cell immunity has not been explored. This is the first evidence of the relevance of Ramp3 for immune cell function and host protection, influencing innate-like T cell mediated immune function and protection against lung bacterial infections.
Supported by grants from NIH 5R01AI137230-04
Leveraging Resident Memory T Cells to Fortify Oral Immunity
Authors: Stolley Michael , Masopust David 
Published: January 2023

Abstract
Resident memory T cells (TRM) durably survey barrier tissues for reinfection and orchestrate collaborative immune responses upon activation. Importantly, peptides derived from previously encountered viral infections can locally reactivate TRM. This biology may have convenient therapeutic ramifications for augmenting tissue-specific immunity. Yet, while TRM have been well-characterized in the gut, skin, and urogenital mucosa, the mouth remains a barrier tissue largely overlooked by T cell biologists. We asked whether TRM in the oral mucosa could be reactivated using virus-mimicking peptides, and if so, how that might impact oral immunity. This question was addressed using a novel prime-pull model for generating preternaturally abundant TRM in the mouths of SPF mice to manipulate and study. Oral TRM reactivation perpetuated a robust oral anti-pathogen state, including induction of key antiviral and interferon-stimulated genes, and recruitment of innate and adaptive cells into the oral mucosa. Oral peptide pre-exposure thwarted infection with an antigenically unrelated virus. Thus, mouth-resident T cells are amenable to local peptide reactivation, and their proinflammatory potential can be intentionally deployed to bolster oral immunity.
Supported by T90 DE 022732 K99DE031014 OMIC Pilot Grant
Goblet cells regulate expansion of colonic iNKT cells in CD1d-dependent manner
Authors: John Vini , Barrios Bibiana , Udayan Sreeram , Floyd Alexandria , Schill Ellen M , McDonald Keely G , Blumberg Richard S , Newberry Rodney D 
Published: January 2023

Abstract
Invariant natural killer T (iNKT) cells are innate-like T cells that secrete a wide array of cytokines and immune mediators. These cells recognize self or microbial ligands presented by cells expressing CD1d, and can contribute to host protection or/and pathogenesis during intestinal inflammation. The colonic iNKT cell population is established in early life under the influence of the microbiota and current understanding is that this iNKT cells are not manipulable in later life. Previous studies have identified that goblet cell associated passages (GAPs) play a role in luminal antigen delivery and the induction and maintenance of peripherally induced T regulatory cells in the steady state. Colonic GAPs are largely absent in adult mice due to goblet cell (GC) microbial sensing, which inhibits GAP formation. We hypothesized, that when present, colonic GAPs may deliver glycolipids to stimulate colonic iNKT cells. We found that the glycolipids can be delivered through GAPs and that inducing colonic GAPs in adult mice using pharmacological inhibitors or transgenic mouse models resulted in significant iNKT cell expansion. Further deletion of CD1d on GCs inhibited iNKT cell expansion suggesting a role for colonic GCs in presenting glycolipids to iNKT cells. Single cell RNA sequencing of sorted colonic iNKT cells showed significantly expanded iNKT2 and iNKT1 subsets after colonic GAP induction. Furthermore, the iNKT cells expanding after opening colonic GAPs were protective in DSS-induced colitis. Our findings suggest that the GAP function and CD1d expression by GCs plays a role in modulating colonic iNKT cell subsets in adulthood and can be protective in some colitis models.
The Novel Roles of Dusp6 in Gut Barrier Modulation and Microbiome Shaping in a Mouse Colitis Model
Authors: Kao Cheng-Yuan , Chang Cherng-Shyang , Liao Yi-Chu , Huang Chih-Ting , Lin Chiao-Mei , Tsai Yi-Ting , Lin I-Jung , Ruan Jhen-Wei , Liao Yu-Chieh 
Published: January 2023

Abstract
Gut microbiota dysbiosis and barrier integrity are important contributors to overall health and many diseases. Our study demonstrated that dual-specificity phosphatase 6 (Dusp6)-depletion is a novel modulator that enhances baseline gut barrier integrity. We found that Dusp6-knockout mice were more resistant to dextran sulfate sodium (DSS)-induced colitis and had enhanced intrinsic colonic tight-junctions and elongated microvilli before exposure to DSS. Our FMT in germ-free mice and co-housing experiments found that the Dusp6-knockout-derived gut microbiota contribute substantially to colitis resistance in mice. Further gut microbiome analysis showed that Dusp6-knockout mice harbored fewer pathobiont facultative anaerobes and more obligate anaerobes than wild-type mice after DSS treatment. Through multi-omics analysis, we found that epithelial barrier integrity and hypoxic and oxygen homeostasis regulation related pathways were more enriched in DUSP6-depleted Caco-2 cells and with a cultivation-based approach, we reported 11 new mouse gut microbiome members. Finally using microbe-phenotype triangulation and mono-colonization of germ-free mice, we found that the newly discovered Duncaniella species contributed to the colitis protection. In sum, identifying functioning gut microbiota members that shape host physiology and disease susceptibility will be vital to the advance of microbiota-based therapeutics.
This work was supported by the following grants: IM-108-PP-04 from NHRI and 106-2628-B-400-001-MY3, 106-2923-B-400-001-MY3, 108-2321-B-400-011-, 109-2327-B-400-001-, 109-2320-B-400-008-MY3, 110-2327-B-400-005- from MOST.
Th17-driven immunity to oral candidiasis is dependent on the microbiome and can be triggered by mono-colonization with segmented filamentous bacteria.
Authors: Aggor Felix E Y , Zhou Chunsheng , Abbott Darryl , Musgrove Javonn , Bruno Vincent , Hand Timothy W , Gaffen Sarah L 
Published: January 2023

Abstract
The opportunistic infection oropharyngeal candidiasis (OPC; oral thrush) is a common oral infection among the immunocompromised. The oral cavity is a major entry portal to the body and oral health impacts several aspects of host immunity. While much is now known about microbiome dependent Th17 induction and protection against intestinal candidiasis and other Th17 driven responses, our understanding of the role of the microbiome in oral Th17 induction and oral antifungal immunity is rather rudimentary. We demonstrate a direct role for the microbiome in triggering protection against OPC. While wildtype (WT) mice raised under specific pathogen free (SPF) conditions are resistant to OPC, WT germ free (GF) mice succumbed to infection. Reconstitution of WT-GF mice with segmented filamentous bacteria (SFB) was sufficient to restore protection against OPC with associated increase in Th17 cells, neutrophils, and antimicrobial responses in the oral mucosa. Thus, SFB mono-colonization in WT-GF mice triggers oral mucosal Th17 induction to protect against oral thrush and reveals a role of the microbiome in promoting oral mucosal immunity.
Supported by R37-DE022550