bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering the crosstalk between skin commensals and the immune system
Authors: Bouladoux Nicolas , Chen Y Erin , Fischbach Michael A , Belkaid Yasmine 
Published: August 2023

Abstract
The mechanisms underlying the crosstalk between the microbiota and the immune system remains largely unknown. We previously established that skin colonization with Staphylococcus epidermidis results in the induction of T cell responses that control tissue function in a way that both enhances cutaneous immunity and promotes tissue repair. To uncover the molecular determinants of S. epidermidis that stimulate T cells, we engineered a library of S. epidermidis mutants with defined cell envelope alterations. Under physiological cutaneous colonization, we found that S. epidermidis cell envelope mutants elicit marked changes in the composition and function of the T cell populations in the skin. The removal of cell envelope lipoproteins and D-alanylation of teichoic acids almost completely abolished CD8+ T cell induction without significant effect on CD4+ T cell stimulation. Deletion of Tlr2 gene also strongly reduced the CD8+ T cell response after S. epidermidis colonization, while the CD4+ T cell response remained unchanged, a phenotype similar to the elimination of cell envelope lipoproteins and D-alanylation of teichoic acid in S. epidermidis. Furthermore, suprabasal keratinocytes express the highest level of TLR2 among keratinocyte subsets. Together, these results support the notion that the ability of S. epidermidis to induce CD8+ T cells is partially dependent on the host sensing of S. epidermidis wall teichoic acids and lipoprotein through TLR2. Using complementary strategies including novel mice models and imaging, current studies are focusing on deciphering on which cell population(s) TLR2 sensing of S. epidermidis molecular determinants is required for the induction of CD8+ T cell responses.
The differential influence of commensal and pathogenic flagella on intestinal barrier function
Authors: Patry Robert T , Kemter Andrea , Mimee Mark , Arnold Jack , Hesser Lauren A , Ionescu Edward , Nagler Cathryn 
Published: August 2023

Abstract
It is well known that accumulated changes in microbiota composition over several decades have contributed to an increase in non-communicable chronic diseases. While much effort has been devoted toward achieving a consensus on the microbes, and their products, driving this increase, inconsistent results suggest more research is required to understand the disparity in observed outcomes. Previous work from our lab identified a consortium of commensal Clostridia that alone was sufficient to preserve intestinal barrier integrity and prevent sensitization to food allergens in mice by inducing IL-22. Further investigation determined that members of this consortium display flagella. When isolated, these commensal flagella (Fla-C) exhibited TLR5-dependent IL-22 induction at a magnitude comparable to flagellin from SalmonellaTyphimurium (Fla-ST). However, mice treated with Fla-C maintained intestinal barrier function significantly more effectively than Fla-ST or negative control PBS-treated mice as measured by a serum FITC-dextran permeability assay. This was accompanied by a striking difference in the expression of Reg3 antimicrobial peptides and IL-17; all of which were significantly increased by treatment with Fla-ST when compared to Fla-C. Sequencing of Clostridia consortium-derived flagellated isolates revealed flagellin genes with unique hypervariable regions when compared to fliC from S. Typhimurium. These results highlight the distinct impacts of commensal and pathogenic flagella and suggest an important role for flagellated commensal bacteria in the maintenance of intestinal epithelial barrier function.
Supported by a grant from National Institutes of Health (RO1 AI06302)
Microbial regulation of anti-tumor immunity in colorectal cancer
Authors: Chung Charlie , Habel Jill , Shen Zeli , Rubino Rachel , Westcott Peter , Fox James G , Beyaz Semir 
Published: August 2023

Abstract
Colorectal cancer (CRC) is one of the most common and deadly types of cancer. Although recent advances in early detection and revolutionary therapies such as checkpoint blockade immunotherapy resulted in improved outcomes in CRC, a large fraction of CRC patients, particularly with metastasis, do not respond well to existing immunotherapy modalities. This necessitates a better mechanistic understanding on tumor – immune cell interactions in the context of CRC. Microbiome influences multiple biological aspects of the host including immune responses against cancers. We recently defined a causal role for microbiome in regulating epithelial stem cell MHC-II expression and tumor initiation in the intestine. Here we expound on the significance of microbiome - MHC-II axis in CRC progression and metastasis. We found that colonization of microbes that correlate epithelial MHC-II expression in the intestine restricts CRC progression and improves overall survival in three different clinically-relevant orthotopic CRC models across mice strains. Notably, microbiome-induced anti-tumor effects are dependent on T cells. Finally, genetic inactivation of MHC-II in cancer cells diminished tumor preventing effects of microbes. These results underscore a causal role for microbe - MHC-II axis in regulating anti-tumor immunity during tumor progression. Microbes that boost MHC-II expression promote anti-tumor immunity in the colon, which may synergize with therapeutic approaches such as immunotherapy.
NIH (P30CA045508-33 to S.B.), the Oliver S. and Jennie R. Donaldson Charitable Trust (S.B.), The Harold and Leila Y. Mathers Charitable Foundation (S.B), The Mark Foundation for Cancer Research (20-028-EDV to S.B.) and STARR Cancer Consortium (I13-0052 to S.B.), Chan Zuckerberg Initiative / Silicon Valley Community Foundation (2021-239862)
Roles of the dynamic gut microbiota and their associated immunoregulatory effects for successful oral immunotherapy treatment
Authors: Goldberg Michael R , Appel Michael Y , Mor Hadar , Neriya Dafna Magid , Mazgal Faiga , Muller Efrat , Nachshon Liat , Borenstein Elchanan , Tamir Snait , Youngster Ilan , Louzon Yoram , Koren Omry , Elizur Arnon 
Published: August 2023

Abstract

Background
We previously demonstrated that patients with IgE-mediated food allergy (FA) have a unique gut microbial signature.

Objectives
To characterize the changes to the gut microbiome populations and putative immunoregulatory effects, associated with successful OIT.

Methods
Stool samples were collected at inception of treatment from 252 patients undergoing OIT, and from 58 non-allergic controls. Additional samples were collected at successful completion of treatment (n=66). Bacterial 16S rRNA gene sequences from extracted sample DNA were amplified by PCR, with microbial communities analyzed by QIIME2. Stool extracts were evaluated for allergen-specific IgA2, and for their induction capability of immunoregulatory genes in a colonic epithelial line (Caco-2).

Results
For all FA types, patients with higher initial allergen eliciting doses (ED) had microbiota populations significantly closer to that of controls, compared to more sensitive patients with lower ED (p&lt;0.0001). The relative abundance of Prevotella and Bacteroides/Firmicutes ratio significantly varied during OIT progression, increasing towards controls. Post-OIT stool eluents induced mRNA expression of APRIL and ZO-1 in Caco-2 cells and allergen-specific IgA2 was significantly increased in post- vs pre-OIT eluents (p&lt;0.01). In Transwell assays, heat killed Bacteroides fragilis decreased FITC-dextran4 leakage across the epithelial layer.

Conclusions
Gut microbiome populations are dynamic during OIT, possibly reflecting a recovery from a FA to a nonallergic state. Immunoregulatory changes and positive effects on epithelial cell integrity suggest causative roles for the gut microbiome in maintaining the desensitized state.

Supported by a grant from the Israeli Science Foundation (1527/21)
A vanishing family of commensal bacteria and its impact on host health and disease
Authors: Pepin Deanna M , Popple Sarah , Ghezzi Hans , Seo Jung Hee , Osborne Lisa , Tropini Carolina 
Published: August 2023

Abstract
The gut microbiome plays a critical role in intestinal structure, immune homeostasis, and inflammatory diseases. The rise of these diseases in industrialized countries has been correlated with the loss of microbial diversity in the gut. One bacterial family, Muribaculaceae (Mb), is becoming a lost member in industrialized human microbiomes and many studies have correlated low Mb abundance with different disease states. Our goal is to determine how Mb depletion may be connected to disease, if introducing Mb back can ameliorate the impact of disease, and uncover immune mechanisms necessary for colonization of Mb. To study this, we developed two mouse models with complex microbiomes; one containing Mb (Mb positive), and one without Mb (Mb naïve). We evaluated intestinal structure with confocal microscopy, measured the production of short-chain fatty acids (SCFAs), and compared these mice in a Citrobacter rodentium (C. rodentium) infection model. Mice without Mb lost colonic mucus striation and had a significant drop in the production of SCFAs. Additionally, Mb positive mice had reduced C. rodentium colonization compared to mice lacking Mb. Lastly, we introduced 8 characterized Mb isolates to the Mb naïve mice to quantify immune responses by flow cytometry. We found that Mb is capable of establishing in Mb naïve mice, resulting in robust germinal centre B cell responses, yet no subsequent plasmablast accumulation in the mLN or lamina propria. Determining the mechanisms involved in disease amelioration by Mb and its impact on host immune responses is a novel research direction that could increase our understanding of colonization dynamics and highlights the potential of this bacteria as a model for microbiota therapies.
Supported by grants from The W. Garfield Weston Foundation
B cells regulate luminal bile acid composition in the small intestine
Authors: Mohammed Ahmed Dawood , Ball Ryan A , Nagarkatti Mitzi , Nagarkatti Prakash S , Kubinak Jason 
Published: August 2023

Abstract
Recent studies have demonstrated that bile acids (BA) influence immune cell homeostasis in the gut. However, whether and how, the host immune response can influence BA biochemistry is unknown. This is an important question to answer because small shifts in BA composition in the gut can have significant pathophysiological consequences. Previously, we have demonstrated that CD19−/− mice, which have a defect in B cell activation and consequently an aberrant humoral immune response, develop a small intestine (SI) enteropathy that is associated with abnormal luminal BA composition. However, CD19−/− mice are not B-cell-deficient and present with multiple aberrant immune phenotypes. Here, we used B cell-deficient JHminus;/minus; mice to more effectively define this interaction. Results of our experiments provide three key observations. First, JH−/− mice develop altered SI BA pools compared to their WT littermates. Second, adoptive transfer of WT B cells into neonatal JH−/− mice led to the development of normal BA pools and rescued mice from SI enteropathy. Third, adoptive transfer of B cells incapable of secreting IgA into neonatal JH−/− mice failed to restore normal bile acid composition and only moderately protected animals from developing SI enteropathy. Collectively, the results of our experiments clearly demonstrate that B cells regulate bile acid composition in the SI and that the synthesis of mucosal IgA may be particularly important for driving this effect.
Oral mucosa resident CD8+ T cell reactivation exacerbates murine periodontitis
Authors: Saavedra de Paula Flávia M , Herzberg Mark C , Masopust David , Stolley J Michael 
Published: August 2023

Abstract
Periodontitis is the world’s most common chronic inflammatory condition. Progressive forms of periodontitis are initiated by dysbiotic subgingival biofilms yet sustained by unresolved local inflammation. While gingival CD4+ T cells are thought to be major drivers of periodontal inflammation, the role of tissue resident memory (TRM) CD8+ T cells in periodontitis progression and severity remains unknown. We sought to determine whether local reactivation of oral CD8+ TRM of a defined antigen specificity would accelerate ligature-induced periodontitis (LIP), a well-established murine model of experimental periodontitis. Ovalbumin (OVA)-specific OT-I T cells were transferred and expanded though systemic viral infection in naïve hosts. Six-days later, OT-I T cells were ‘pulled’ into the oral mucosa via swabbing of the oral surfaces with OVA peptide in irritants. This approach, collectively referred to as Viral-Prime: Epitope-Pull (VPEP), durably augments oral OT-I TRM in the oral mucosa to manipulate and study. Utilizing ‘VPEP’ memory mice, oral CD8+ TRM were reactivated with OVA peptide concurrent with LIP. Control mice received oral swabbing with an irrelevant peptide. Alveolar bone loss and interstitial immune infiltrates were characterized using microCT imaging and flow cytometry, respectively. We found that oral TRM reactivation accelerated alveolar bone loss and enriched neutrophils, macrophages and CD8+ T cells within ligature-proximal gingiva. Bulk RNAseq analysis revealed several inflammatory and matrix-remodeling genes induced in maxillary and mandibular gingiva upon oral TRM reactivation. Collectively, we provide evidence that oral CD8+ TRM reactivation can exacerbate periodontitis.
This work is supported by NIH/NIDCR grants R90 DE023058 to F.M.S. and T90 DE 022732 & K99DE031014 to J.M.S
Investigating the Distinct Tissue Repair and Immunosuppressive Roles of Regulatory T cells in HSV-2 Infection
Authors: Talavera Irene Cruz , Traxinger Brianna R , Arkatkar Tanvi , Lund Jennifer M 
Published: August 2023

Abstract
Herpes Simplex Virus 2 (HSV-2) is the primary cause of genital herpes, affecting 500 million people worldwide of which approximately 64% are women. Despite this disproportionately high burden, the female reproductive tract and its unique mucosal immune environment is surprisingly understudied. Tregs are necessary for CD4+ T cell priming in the draining lymph node (dLN), though their role in shaping tissue-resident memory T cell (Trm) responses during HSV-2 reactivation is unclear. Our preliminary data indicate that activated Tregs accumulate and persist in mouse vaginal tissue (VT) after above baseline out to at least 90 days post-infection (p.i.), thus implicating Tregs in memory recall responses to reinfection. We hypothesize that Tregs restrain robust Trm recall responses to HSV-2 challenge. Additionally, we hypothesize that vaginal Tregs promote tissue healing in the VT in response to inflammatory alarmins through the expression of the epidermal growth factor ligand, amphiregulin (Areg). Female FoxP3DTR mice were infected intravaginally with attenuated HSV-2, then systemically depleted of Tregs via intraperitoneal injection of diphtheria toxin and challenged with WT HSV-2 on day 30 p.i. Systemically Treg-depleted mice show increased activation and proliferation of T cells, and increased frequency of cytotoxic HSV-2-specific CD8+ T cells in the VT by day 3 post-challenge. Treg-depleted mice also have significantly higher pathology scores in H&E-stained VT. We also report that VT Tregs from infected mice express more Areg than dLN Tregs via flow cytometry and single cell RNAseq. Ongoing work includes characterization of Areg expressing VT Tregs and further dissection of the Trm recall responses in Treg-depleted mice.
NIH (T32 AI07140, R01 AI141435)
Plasticity of atypical B cell composition and function in response to malaria
Authors: Reyes Raphael , Batugedara Gayani , Dutta Paramita , Reers Ashley , Greenhouse Bryan , Bol Sebastiaan , Ay Ferhat , Bunnik Evelien 
Published: August 2023

Abstract
Atypical B cells are generated during a normal adaptive immune response, yet the role of these cells in protective immunity is still largely unknown. Here, we used chronic Plasmodium falciparum exposure as a model to gain insight into the function and potential heterogeneity of atypical B cells in the immune response to infection. To this end, we performed single-cell sequencing on circulating B cells from malaria-experienced individuals. Based on distinct gene expression signatures, we identified three novel atypical B cell subsets. Each subset had an effector profile that translated to one of previously proposed roles for atypical B cells: i) quiescent cells ii) antigen-presenting cells or iii) antibody-secreting cell precursors. We identified differentially expressed cell surface markers that allowed us to track each atypical B cell subset by flow cytometry. We observed that the relative abundance of each subset was influenced by the timing of sample collection in relation to infection. Additionally, our analysis revealed an enrichment of CXCR3+ atypical B cells in adults as compared to children, suggesting further heterogeneity in the context of age or chronic antigen stimulation. To explore the contribution of atypical B cells in response to malaria, we used antigen-tetramers to identify parasite-specific cells. All three atypical B cell subsets harbored antigen-specific B cells that decreased in frequency in the absence of exposure, confirming their active and transient role in malaria immunity. Finally, preliminary results suggest that the three subsets differ in their ability to secrete antibodies after stimulation, highlighting the cellular heterogeneity and distinct effector functions of atypical B cells.
National Institutes of Health predoctoral fellowship F31AI169993 (RR) National Institutes of Health grant R35GM128938 (FA) National Institutes of Health grant R01AI153425 (EB)
Strong adaptive immunity in humans with inherited CD4 deficiency
Authors: Guerin Antoine M , Ma Cindy 
Published: August 2023

Abstract
Since the early 1970s when the T cell receptor was first characterized, the role of human CD4 in adaptative immunity has been extensively studied, especially in the context of HIV infection and inborn error of immunity (e.g. HLA class II deficiency). Nonetheless, it was only recently (2019, 2021) that patients with inactivating germline mutations in CD4 has been described. Herein, we present five novel patients from three unrelated kindred with bi-allelic rare variants in CD4. Consistent with previous studies, patients showed a broad spectrum of clinical infectious susceptibility which was rather mild given their lack of detectable CD4+ T cells in peripheral blood mononuclear cells (PBMCs). Despite an almost unremarkable immunophenotype, patient’s PBMCs were characterized by the expansion of an enigmatic CD4−CD8 − (DN) TCRαβ+ T cells population which retained some functional characteristic of typical CD4+ T cells. We observed that the patient’s DN cells transcriptionally (Sc-RNAseq) and functionally (cytokine production/secretion) were comparable to that of healthy donor CD8− T cells. Interestingly, using cutting-edge long-read sc-RNAseq technology we revealed that patient’s DN cells expressed normal TCR repertoires, and paired TCRαβ sequences comparable to healthy donor CD4+ T cells. Furthermore, via biochemical studies we identified a CD4 alternative transcript expressed in patient’s PBMCs (also detected in healthy donor cells) leading to the surface expression of an unreported CD4 shorter isoform which is not detectable with conventional CD4 antibodies. To conclude, our study not only characterizes novel CD4-deficient patients, but also reveals alternative CD4 isoform expression and its compensatory role in immunity.
AAI Careers in Immunology Fellowship 2022 (RG222573)
MR1-restricted T cell clonotypes are associated with resistance to Mycobacterium tuberculosis infection
Authors: Cross Deborah L , Layton Erik D , Yu Krystle K Q , Smith Malisa T , Aguilar Melissa S , Li Shamin , Mayanja-Kizza Harriet , Stein Catherine M , Boom Willem Henry , Hawn Thomas R , Bradley Philip , Newell Evan , Seshadri Chetan 
Published: August 2023

Abstract
T-cells are a critical facet of the adaptive immune system and have been shown in both human and animal studies to be essential for control of Mycobacterium tuberculosis (Mtb) infection. T-cells recognize foreign antigens presented by infected cells via a unique T-cell receptor (TCR). Understanding the specific TCRs that mediate recognition and clearance of Mtb-infected cells is essential to inform vaccine design. We recently described a cohort of Ugandan household contacts of tuberculosis cases that appear to ‘resist’ Mtb infection (RSTRs) and showed that these individuals harbor IFN-γ independent T-cell responses to Mtb peptide antigens. The role of unconventional T-cells that recognize non-peptide antigens, such as gd T-cells, CD1-restricted and MR1-restricted T-cells (MR1T), in “resistance” is unknown. In this study, we aimed to characterize the frequencies, functional programs, and repertoire of unconventional T-cells in RSTRs in comparison with latently infected (LTBI) controls. We used multi-parameter flow cytometry, single cell RNA and TCR sequencing and immunosequencing to address these gaps. We observed a 1.65-fold increase in frequency of circulating MR1T cells among RSTRs in comparison with LTBI (p=0.03). Single-cell RNA-sequencing of 18,251 sorted MR1T cells revealed 5,150 clonotypes expressing a common transcriptional program, the majority of which were private. Immunosequencing of the TCR-α/d repertoire revealed several TCRα clonotypes that were expanded in RSTRs (p &lt;0.01), including at least two MR1T clonotypes. Overall, our data reveal unexpected donor-specific diversity in the TCR repertoire of human MR1T cells as well as associations between MR1 clonotypes and ‘resistance’ to Mtb infection.
This work was supported by grants from the NIH (R01-AI124348 to Boom, Stein, and Hawn; R01-AI125189 and R01-AI146072 to Seshadri) and the Bill & Melinda Gates Foundation (OPP1151836 and OPP1109001 to Hawn and GH-VAP-IS-ID5 to Seshadri).
Single Cell Immune Atlas of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Identifies Substantial Transcriptional Dysregulation
Authors: Iu David S , Grimson Andrew 
Published: August 2023

Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a severe, debilitating disease with striking similarities to long-COVID/PASC, but its etiology remains unclear. Patients typically experience overwhleming fatigue, inflammatory symptoms and cognitive impairment, exacerbated by physical or mental exertion, also known as Post-Exertional Malaise (PEM). Mounting evidence points to immune system dysfunction being a key contributor to ME/CFS pathology, but our current understanding of gene regulation in ME/CFS leukocytes is hampered by a lack of quantitative and temporal resolution.
To comprehensively characterize the gene regulatory state and precisely define the cell types underlying transcriptional dysregulation, we have generated single cell transcriptomes and chromatin profiles of peripheral blood mononuclear cells (PBMCs) using single cell RNA-seq and single cell ATAC-seq in matched patients and controls, at baseline and after exercise challenge. At baseline, ME/CFS patients displayed dysregulation of classical monocytes pointing to increased migration to tissues as well as inappropriate chemokine signaling, as well as dysregulation of certain subsets of effector CD8+ T cells, leading to a more inflammatory transcriptional program. Taken together, these data identify substantial immunological defects and serves as an important resource for understanding ME/CFS pathology.