bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intake of low dietary fiber changes microbiota composition and reduces IL-10 production from small intestinal T cells
Authors: Rivera-Rodriguez Dormarie E , Rodriguez-Marino Naomi C , Royer Charlotte J , Yaceczko Madelyn , Cervantes-Barragan Luisa C R 
Published: August 2023

Abstract
Regulatory immune responses are crucial for intestinal homeostasis against stimuli like diet and microbiota. The microbiota influences the regulatory immune response by inducing colonic Foxp3+ regulatory T cells and other lymphocytes by metabolizing diet-derived products. For example, fiber-fermenting microbiota process fermentable fiber into metabolites like short-chain-fatty-acids (SCFA) and help activate IL-10-producing T cells. However, studies showed that high-fat (low-fiber) diet alters the abundance of Treg-inducing commensal bacteria promoting intestinal inflammation. Previous studies in our lab showed that low fermentable fiber affects the generation of many intestinal T cells, especially intraepithelial CD4+CD8aa+ T cells (DP IELs) and CD8aa IELs. However, it is still uncertain how dietary fiber affects small intestinal T cell function, including IL-10 production. To address this, we fed IL-10-GFP reporter mice with a regular chow diet or an isocaloric isonitrogenous diet that replaced fiber with non-fermentable fiber (LFF). After four weeks, the lymphocytes and microbiota from the small intestine were analyzed. Our preliminary findings show that IL-10 mRNA expression and IL-10-GFP production from intestinal lymphocytes was lower in mice fed LFF diet when compared to the control. Moreover, 16S RNA sequencing of intestinal contents showed changes in relative frequencies of several OTUs between diets. These results suggests that certain bacterial species affected by the diet could be significant in promoting IL-10 production by small intestinal T cells. Further studies will seek to understand how fiber plays a role in orchestrating the host-microbiota interactions to maintain intestinal tolerance.
These studies were conducted at Emory University and funded by the following NIH grants: 1R01DK129950-01 (NIDDK-NIH from LCB); 5T32AI106699-08 (NIDDK-NIH from Antimicrobial Resistance and Therapeutic Discovery Training Program)
Diversity of gut commensal flagellins results in distinct intestinal epithelial cell immune responses
Authors: Jennings Melissa S , Duck Wayne , Zhao Qing , Alexander Katie , Muir Rachel Q , Hsu Jung-Shan , Klocke Barbara J , Lee Goo , Elson Charles O , Maynard Craig L 
Published: August 2023

Abstract
Flagellins from bacteria in the Lachnospiraceae family are immunodominant antigens in inflammatory bowel disease. Flagellin is the basic unit of flagella which is used for bacterial motility and is recognized by toll-like receptor 5 (TLR5). Due to the diversity in flagellated organisms that reside in proximity to the intestinal epithelium, we asked whether this resulted in distinct interactions between commensal flagellins and the immune system. Analysis of over 200 flagellins, primarily from Lachnospiraceae organisms, revealed a divergence in peptide sequences in specific non-conserved regions of the D0 domain that broadly separate the flagellins examined into 2 clusters which we refer to as Group 1 and Group 2 flagellins. We stimulated HEK-Blue mTLR5 cells and murine intestinal epithelial cells (IECs) with selected Group 1 or Group 2 flagellins to assess TLR5 activity and IEC production of lipocalin-2 (Lcn-2) - a biomarker of inflammation - respectively. Group 2 flagellin strongly activated TLR5 signaling in the mTLR5 HEK cell line, even more so than Salmonella typhimurium (S. typhi) flagellin. Conversely, cells stimulated with the Group 1 flagellin exhibited significantly reduced TLR5 signaling relative to both Group 2 and S. typhi flagellins. While IEC stimulation with Group 1 flagellin resulted in undetectable Lcn-2, stimulation with Group 2 flagellin led to robust Lcn-2 production; more so than stimulation with S. typhi flagellin. These findings demonstrate that flagellins of commensal bacteria elicit differential IEC response via selective activation of TLR5. These functional differences are dependent on specific motifs in non-conserved regions of their D0 domains.
Supported by R01 AI162736, R21 DK118386, T32 AI007051.
Commensal bacteria regulate host TGF-β and retinoic acid metabolism to promote intestinal homeostasis
Authors: Puente Armando Andres , Nagler Cathryn 
Published: August 2023

Abstract
TGF-β signaling and retinoic acid (RA) metabolism are essential to intestinal homeostasis, but the mechanisms by which the microbiota influence these host processes are not clear. We have previously reported a mouse model of cow’s milk allergy (CMA) in which germ-free mice were colonized with the fecal microbiota of healthy infants or infants with CMA. That study revealed that Tgfbr3 was part of an ileal transcriptomic signature that distinguished healthy from CMA-colonized mice. Follow-up experiments using RT-qPCR confirmed that Tgfbr3 expression was significantly higher in the ileum of healthy-colonized than CMA-colonized mice. Tgfbr3 encodes a TGF-β co-receptor, and its expression is reported to be induced by RA; genes in the CMA transcriptomic signature encode enzymes with RA catabolic activity (Cyp2c29, Cyp2b10, Cyp3a59, and Akr1c19). The expression of RA-catabolic enzymes and concurrent downregulation of Tgfbr3 led us to hypothesize that these distinct microbiotas differentially modulate host RA metabolism, and consequently influence TGF-β signaling through the induction of Tgfbr3. In support of this hypothesis, we found lower ileal expression of Aldh1a1 in CMA-colonized mice, suggesting a lower capacity to produce RA. Furthermore, Tgfbr3 expression correlated with the transcript levels of TGF-β pathway mediators, Smad3 and Smad7, both of which are increased in the ileum of healthy-colonized mice. Ongoing experiments will use single cell RNA-sequencing to identify the cell populations responsible for the differential expression of Tgfbr3 in the ileum and to characterize the microbial mechanisms responsible for modulating host RA metabolism.
Supported by NIH R01 AI146099
Supported by NIH R01 AI146099
Microbiota engage a HDAC3 rheostat to shape ILC3 metabolism and function in the gut
Authors: Jensen Samantha N , Teng Fei , Alenghat Theresa , Lazar Mitchell A , Sonnenberg Gregory F 
Published: August 2023

Abstract
Group 3 innate lymphoid cells (ILC3s) respond to microbial colonization of the intestine to coordinate tissue health. This process involves interpretation of host- or microbial-derived signals that must be tightly regulated to preserve immunologic homeostasis. Here we examine a key epigenomic regulator that is responsive to microbial-derived factors, histone deacetylase 3 (HDAC3), and find that lineage-specific deletion results in reduced ILC3s and increased susceptibility to intestinal damage. In contrast, the lineage-specific deletion of an essential corepressor, NCOR1, results in elevated ILC3s and enhanced protection from intestinal damage. This indicates that HDAC3 mediates both a supportive deacetylase-independent role and a repressive deacetylase-dependent role in ILC3s. To explore genes promoted by HDAC3, we performed RNA sequencing and found that HDAC3 deficient ILC3s exhibit impaired transcription of genes involved in polyamine synthesis including the polyamine rate limiting enzyme ornithine decarboxylase 1 (ODC1) and spermine oxidase (SMOX). At steady state, ILC3s uniquely express high levels of ODC1 and SMOX compared to other lymphocytes, and transcription of these genes is influenced by IL-23 and the presence of the microbiota. Overall, this indicates that HDAC3 is a rheostat of ILC3 functionality in the intestine, with the hypothesis that HDAC3/NCOR1 limit tissue protective ILC3 responses, and NCOR1 independent HDAC3-mediated transcription of polyamine synthesis genes promotes ILC3 tissue protective responses.
Supported by NIDDK National Research Service Award (NRSA) T32 Diversity Administrative Supplement (NOT-DK-21-016), R01AI143842, R01AI123368, R01AI145989, U01AI095608, R21CA249274, R01AI162936, R01CA274534 and the NIAID Mucosal Immunology Studies Team (MIST), an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund, Linda and Glenn Greenberg, the Dalton Family Foundation, and the Roberts Institute for Research in IBD. G.F.S. is a CRI Lloyd J. Old STAR.
Group-3 innate lymphoid cells protect from intestinal inflammation via syndecan-4
Authors: Fiedler Brooke Elizabeth , Zhou Wenqing , Joseph Ann , Sonnenberg Gregory F 
Published: August 2023

Abstract
Group-3 innate lymphoid cells (ILC3s) are a recently described set of tissue resident immune cells which are enriched in the intestine, express RORγt, and secrete a variety of effector cytokines to orchestrate homeostasis, inflammation, and immunity. Crucially, intestinal ILC3 function and frequency is dysregulated during inflammatory bowel disease (IBD). However, it remains unclear how ILC3s sense and respond to the heterogeneity of signals present in the intestinal microenvironment or how this cell type becomes disrupted during intestinal inflammation.
Recently, a single-cell RNA-sequencing analysis in our laboratory identified that syndecan-4 is highly expressed within ILC3s. Syndecans are a class of heparan sulfate proteoglycans which can become dysregulated in the intestinal epithelium and the lamina propria of IBD patients. Further, mice lacking global expression of syndecan-4 show a heightened susceptibility to models of intestinal inflammation. However, cell-specific and molecular mechanisms for this protection have yet to be elucidated. Here, we unexpectedly identify that syndecan-4 is significantly enriched among ILC3s relative to other intestinal immune cells. IL-1 selectively upregulates ILC3-specific syndecan-4, but during acute and chronic mouse modeling of intestinal inflammation, ILC3 expression of syndecan-4 is reduced. Mice lacking ILC3-specific syndecan-4 exhibit exacerbated susceptibility to intestinal inflammation resulting in greater loss of intestinal epithelial architecture compared to controls. Collectively, our data indicate that syndecan-4 represents a novel pathway by which ILC3s orchestrate intestinal health and limit tissue damage during inflammation.
Research in the Sonnenberg Laboratory is supported by the National Institutes of Health (R01AI143842, R01AI123368, R01AI145989, U01AI095608, R21CA249274, R01AI162936 and R01CA274534), the NIAID Mucosal Immunology Studies Team (MIST), an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund, Linda and Glenn Greenberg, the Dalton Family Foundation, and the Roberts Institute for Research in IBD. B.F. is supported by the NIAID of the National Institutes of Health training grant T32 (5 T32 AI 134632-5). G.F.S. is a CRI Lloyd J. Old STAR.
Lactobacillus johnsonii supplementation modulates functional response of bone-marrow derived dendritic cells in respiratory allergy and viral infection
Authors: Martinez Llilian Arzola , Ethridge Alexander D , Rasky Andrew J , Morris Susan , Fonseca Wendy , Lukacs Nicholas W 
Published: August 2023

Abstract
The immunomodulatory properties of probiotics are particularly important at the establishment of Th1-Th2 immune balance early in life. A skewing to Th2 immune response driven by dendritic cell regulation can lead to airway alteration during respiratory allergy and respiratory virus infection. Previous work from our lab have determined that oral supplementation of mice with Lactobacillus johnsonii (Lj) resulted to be protective against viral and allergen airway exposure. In order to further analyze whether Lj supplementation of moms could alter offspring responses to allergic disease, female mice were supplemented daily with Lj for a week before mating. Allergen-sensitized offspring from Lj supplemented-mothers were protected from airway hyperreactivity, had a diminished mucus production and shown a reduced allergen-restimulated Th2 cytokine response upon later life allergen-induced responses. Maternal Lj supplementation changed the functional response of bone-marrow derived dendritic cells (BMDC) activated in vitro with respiratory syncytial virus (RSV), decreased expression of pathological cytokines and chemokines in non-sensitized pups, but increased protective innate cytokines expression in allergic offspring. Neonates supplemented directly with Lj before early life RSV infection altered long term inflammatory activity of BMDC by reducing expression of proinflammatory innate cytokines. These results have shown the immunomodulatory potential of Lj supplementation during pre- and post-natal periods to protect from allergic and viral immune responses in distal mucosal surfaces by altering systemic immune cell responses.
RO1HL144858
ILC3s restrict intestinal inflammation via IL-10 production
Authors: Li Jing , Jacobse Justin , Goettel Jeremy Allen , Washington Mary Kay 
Published: August 2023

Abstract
In this study, we investigated the role of IL-10 production by group 3 innate lymphoid cells (ILC3s) in regulating intestinal immunity. Prior work has established the importance of IL-10 as well as ILC3s in promoting immune homeostasis in the gut. However, the requirement of IL-10 in ILC3s for homeostasis remains unknown.
We examined an ILC3 focused cluster in a publicly available single-cell RNA sequencing dataset from patients with ileal Crohn’s disease and detected ILC3s expressing IL10. We then developed Rag1−/−; Il10GFP; Rosa26lsltdTomato; RorcCre mice and injected them with PBS or anti-CD40 to induce intestinal inflammation and determine if putative ILC3s expressed IL-10. IL-10 was significantly upregulated following treatment with anti-CD40 7 days following disease initiation. To assess whether ILC3 production of IL-10 played a functional role, we targeted IL-10 specifically in ILC3s by generating Rag1−/−; Il10flox/flox; Rosa26lsl−tdTomato; RorcCre (Il10ΔILC3) mice. Il10ΔILC3 mice displayed significantly worse colitis induced by anti-CD40 that was attributed to an increase in Ly6ChiMHCIIhi intestinal macrophages (Mϕ) at baseline. Given the alterations in the phenotype of intestinal Mϕ, we examined whether unfractionated wild-type CD4+ T cells would be sufficient to cause colitis when transferred to Il10ΔILC3 mice despite the presence of regulatory T cells. Mice were monitored weekly for weight loss and colons harvested for histology at 8 weeks. While IL-10-sufficient littermate controls did not develop inflammation as expected, Il10ΔILC3 mice developed severe colitis.
Collectively, our findings identify an essential role for IL-10 production by ILC3s to maintain intestinal immune homeostasis.
Vanderbilt Digestive Disease Research Center Grant (P30DK058404) The National Institute of Diabetes and Digestive and Kidney Diseases R03DK123489
ILC3s select microbiota-specific Treg cells to establish tolerance in the gut
Authors: Lyu Mengze , Suzuki Hiroaki , Kang Lan , Gaspal Fabrina , Zhou Wenqing , Goc Jeremy , Zhou Lei , Zhou Jordan , Zhang Wen ,   JRI Live Cell Bank, Shen Zeli , Fox James G , Sockolow Robbyn E , Laufer Terri M , Fan Yong , Eberl Gerard , Withers David R , Sonnenberg Gregory F 
Published: August 2023

Abstract
Microbial colonization of the mammalian intestine elicits inflammatory or tolerogenic T cell responses, but the mechanisms controlling these distinct outcomes remain poorly understood, and accumulating evidence indicates that aberrant immunity to intestinal microbiota is causally associated with infectious, inflammatory and malignant diseases. Here we define a critical pathway controlling the fate of inflammatory versus tolerogenic T cells that respond to the microbiota and express the transcription factor RORγt. We profiled all RORγt+ immune cells at single-cell resolution from the intestine-draining lymph nodes of mice and reveal a dominant presence of T regulatory (Treg) cells and lymphoid tissue inducer-like group 3 innate lymphoid cells (ILC3s), which co-localize at interfollicular regions. These ILC3s are distinct from but having interconverting potential with extrathymic AIRE-expressing cells, abundantly express major histocompatibility complex class II (MHCII), and are necessary and sufficient to promote microbiota-specific RORγt+ Treg cells and prevent their expansion as inflammatory T helper 17 (TH17) cells. This occurs through ILC3-mediated antigen presentation, αV integrin and competition for interleukin-2. Finally, single-cell analyses suggest that interactions between ILC3s and RORγt+ Treg cells are impaired in inflammatory bowel disease. Our results define a paradigm whereby ILC3s select for antigen-specific RORγt+ Treg cells, and against TH17 cells, to establish immune tolerance to the microbiota and intestinal health.
Crohn’s and Colitis Foundation Research Fellowship Award, 935259
Investigating T cell populations for immune cell exhaustion in myalgic encephalomyelitis/chronic fatigue syndrome
Authors: Maya Jessica , Hanson Maureen R 
Published: August 2023

Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a devastating disease that confines ~65 million people worldwide to a life of pain, severe exhaustion, cognitive deficits, flu-like symptoms, and postexertional malaise. We previously discovered decreased glycolysis, decreased mitochondrial membrane potential, and increased fatty acid oxidation in ME/CFS T cells. These features are commonly found in exhausted T cells, a reversible state seen in chronic viral infections that decreases cell proliferation, survival, and cytotoxicity. Our study evaluated whether exhausted T cell subsets circulate in people with ME/CFS by analyzing CD4+ and CD8+ T cells for associated inhibitory receptors and transcription factors. CD4+ and CD8+ T cells were isolated from 20 patients and 20 sedentary control blood samples and measured for ~15–17 markers at rest and after stimulation using a FACSymphony analyzer. Markers included cell population identifiers for naïve, effector, memory, regulatory, and helper T cells. We found significantly higher abundances and frequencies of transcription factors related to exhaustion in general and within PD-1+ CD8+ T cells in ME/CFS samples. Half of the ME/CFS cohort showed higher PD-1 memory CD8+ T cell frequencies than the control group. Moreover, ME/CFS CD4+ T cells exhibited higher levels of Lag3, CTLA4, and T-bet in various subsets. This research detects a novel state of immune cell dysfunction in ME/CFS that may suggest new treatment options.
Supported by the Alfred P. Sloan Foundation and the National Institute of Neurological Disorders and Stroke (NINDS), NIH (U54NS105541).
Amplified STAT3 signaling alters expression of CD39 in STAT3 gain-of-function (STAT3 GOF) and in healthy donor CD8+T cells
Authors: Campos Duran Jose S , Sayed Samir , Conrey Peyton E , Hay Ceire A , Dalalo Megan C , Schmitt Erica G , Mauracher Andrea A , Romberg Neil D , Holland Steven M , Freeman Alexandra F , Bergerson Jenna R E , Su Helen C , Leiding Jennifer W , Forbes Lisa R , Cooper Megan A , Vogel Tiphanie P , Henrickson Sarah E 
Published: August 2023

Abstract
It is still unknown whether primary immune regulatory disorders (PIRD) due to genetic variants that amplify T cell receptor and/or inflammatory cytokine signaling yield T cell exhaustion. Here, we investigate the impact of dysregulated cytokine signaling on CD8+ T cells in STAT3 gain-of-function (STAT3 GOF) patients. Immune profiling via 43-parameter CyTOF reveals altered CD8+ T cell differentiation, including loss of naïve cells, increased frequency of effector memory and TEMRA cells, and downregulation of markers of stemness (i.e., TCF-1 and CD127) in STAT3 GOF. Additionally, STAT3 GOF CD8+ T cells demonstrate decreased IL-2 production and proliferation. We identify increased expression of the ecto-enzyme, CD39, which has been reported on exhausted cells and hydrolyzes extracellular ATP, on CD8+ T cells from STAT3 GOF patients and in a mouse model of STAT3 GOF. To identify the signals regulating CD39, healthy donor CD8+ T cells were cultured with STAT3-activating cytokines alone but did not upregulate CD39. However, TCR engagement led to robust CD39 expression which was further augmented with STAT3-activating cytokines. Specifically, CD39 upregulation occurs in pSTAT3Y705+ cells. Finally, sorted CD39+CD8+ T cells hydrolyzed ATP and suppressed effector CD8+ T cell proliferation compared to CD39−CD8+ T cells. These data suggest that STAT3 signaling may play a role in regulating CD39 levels and thus contribute to CD8+ T cell exhaustion, which will be explored in future work. Understanding how dysregulated STAT3 signaling impacts T cell function in these rare patients can improve our understanding of this complex disease and may yield insights into shared aspects of T cell dysfunction found in more common inflammatory diseases.
HHMI Gilliam Fellowship for Advanced Studies (GT15736) Penn Presidential Fellowship PIDTC (Henrickson Lab) IDF (Henrickson Lab) NIH NIAD K08AI135091 (Henrickson Lab) Burroughs Wellcome Fund CAMS (Henrickson Lab)
Dysregulated autophagy in Lymphocytes hints at contribution to immune-mediated thrombotic thrombocytopenic purpura (iTTP)
Authors: Schaller Monica , Milyaev Saveliy , Tschan Mario Paul 
Published: August 2023

Abstract
Immune-mediated TTP is a life-threatening autoimmune disorder characterized by abundant occlusion of the microcirculation. iTTP is caused by a severe autoantibody-mediated deficiency of the von Willebrand factor cleaving protease, ADAMTS-13. Previously, we demonstrated dendritic cells from iTTP patients to have a distinct expression profile of autophagy (ATG)-related genes in 1 relapsing iTTP patient. Contribution of autophagy to the maintenance of autoimmune lymphocytes is crucial to understand the disease pathogenesis of this rare disease.
The autophagy expression profile of purified B- and T-cells isolated from whole blood of iTTP patients or splenocytes using magnetic negative isolation, in the acute or remission phase will be compared to lymphocytes from healthy controls. We choose a panel of nine essential ATG genes (Beclin-1, Atg5, Atg7, Atg14, WIPI1, ULK1, MTOR, NRB1, and WDR45) implicated in other autoimmune diseases to assess a basal level of autophagy by qPCR, autophagic flux (LC3 and p62 expression) will be measured by immunofluorescense. Additionally to discriminate autophagy levels during the acute and relapse phase in relapsing or single episode iTTP patients we will use ImageStream technique.
Preliminary immunofluorescence data from healthy donors indicate that B-lymphocytes show elevated autophagy thanT lymphocytes. These findings are in line with a fact that autophagy participates in antigen presentation and hence may be increased in cells which have antigen presenting function.
Our study will help to shed light on the development and maintenance of iTTP and paves the road to design new treatment strategies based on aberrantly expressed ATG genes by blocking/activating respective autophagy pathways.