bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of a protective, transmissible, and type 2 inflammation-skewing intestinal microbiome
Authors: Grifka-Walk Heather M , Pinkham Nicholas V , Balasubramanian Narayanaganesh , Jenkins Brittany R , Looby Nicholas , Deuling Benjamin , Swain Steve D , Liss Hailey , Walk Seth T , Kominsky Douglas J 
Published: January 2023

Abstract
We recently discovered a transmissible, dominant, and remarkably protective intestinal microbiome (a “Magical Microbiome,” MM) in the setting of a murine model of colitis. The objective of this project is to fill current knowledge gaps regarding the molecular mechanisms underlying protection in this novel model of microbiome-mediated protection. Protection can be transmitted to unmanipulated conventional or germ-free C57Bl/6 mice via cohousing or oral gavage of MM+ stool. During DSS-induced colitis, MM+ mice develop less weight loss, intestinal pathology, and production of proinflammatory molecules relative to genetically identical C57Bl/6 MM-controls. Preliminary results suggest that the eukaryotic and bacterial microbiome under investigation re-programs the host inflammation to prevent disease or promote repair. MM-mediated protection is IL-13-dependent and associated with enhanced type 2 inflammation, as transcript levels of type 2-associated genes including IL-4, IL-13, and Fizz1 were significantly higher in colons of MM+ mice. 16s rRNA gene sequencing and eukaryote screening demonstrated that MM+ mice have a bacterial microbiome distinct from controls and host a novel Tritrichomonas species. Transfer of Tritrichomonas to wild-type mice correlated with protection, but vancomycin treatment ameliorates the protection while maintaining Tritrichomonas, suggesting a possible interaction between bacteria and protist. Stool metabolites are also distinct between MM+ and MM− hosts, further supporting a distinct microbiome function. Overall, we possess a unique microbiome that can be used to understand protective host-microbe interactions and identify novel therapeutic targets for inflammatory diseases.
Contribution of the Microbiome to Maintenance of the CD4:CD8 Ratio in Inbred and Congenic Mouse Strains
Authors: Sarafova Sophia D , Soden Kaitlin , Dankwa Sedem , Watt Aren , Thurtle-Schmidt Debbie 
Published: January 2023

Abstract
The gut microbiome is known to play an integral role in the regulation of the immune system. Previous studies indicate that species diversity and overall abundance of commensal bacteria in the gut influences immune system function by altering total T cell counts and the ratio of CD4+ to CD8+ T cells in peripheral lymphoid organs and blood. In normal individuals, the CD4:CD8 ratio is greater than one. However, the congenic B10.A mouse strain in our conventional facility consistently demonstrates an inverted CD4:CD8 ratio in a sex- and age-dependent manner, in contrast to both the parental C57Bl/10 strain and B10.A kept under SPF conditions. To determine whether this phenomenon is due to the composition and diversity of the gut microbiome affecting the homeostasis of the CD4:CD8 ratio, we altered the microbiome by supplementing the diet with the prebiotic inulin and looked for changes in the number of Peyer’s patches and changes in the CD4:CD8 ratio in gut lymphoid organs and blood in both B10.A and C57Bl/10 strains. In addition, we followed the changes in the microbiome upon treatment. We find that the mice in our facility have lower microbiome diversity and very different composition from mice kept at SPF conditions. The inulin treatment significantly increased the CD4:CD8 ratio in the blood of the C57Bl/10 mice, but not the B10.A mice. In addition, males of both strains had a significant increase in Peyer’s patch number, while the females had a significant increase in the CD4:CD8 ratio in the Peyer’s patches.
Novel decidual innate lymphoid cells display lineage plasticity
Authors: Vazquez Jessica , Fisher Rachel Catherine , Stanic Aleksandar K 
Published: January 2023

Abstract
Immune cells at the maternal-fetal interface play a complex role in regulation of vascular remodeling, fetal tolerance and protection from infection. We have previously reported the identification of two novel CD56high innate lymphoid cells (ILCs) based on Eomes (lo/hi) expression in the decidua. Preliminary experiments suggest that cytokines can modify the expression of canonical transcription factors (TF) by decidual ILCs.
Decidual specimens were dissected from term placentas and mononuclear cells (MCs) were isolated by mechanical/enzymatic disruption, then cultured in the presence of IL7/IL15, IL1β/IL23, or IL2/TGFβ for 7 days, with matched samples processed without culturing for ex vivo assessment. MCs were labeled with fluorochrome-conjugated antibodies against CD3, 14, 16, 19, 34, 45, 49a, 56, 94, 117, 127, GATA3, Eomes, RORγt, and Tbet. Data was acquired using the BD Fortessa flow cytometer and analyzed using FlowJo 10.2.
Our assessment of TF expression revealed significant differences between cytokine-stimulated cultured cells and direct ex vivo samples. GATA3 expression was highest in EomesLo (C2) and EomesHi (C10) cells cultured with IL7/IL15, compared to ex vivo cells. Interestingly, Eomes expression did not change across treatments, while Tbet expression was highest in C2/C10 cells cultured with IL7/IL15. Contrary to our expectations, culturing with IL1β/IL23 did not lead to higher RORγt expression, which was instead upregulated by IL7/IL15.
Preliminary results suggest that both C10 and C2 decidual ILCs demonstrate a level of lineage plasticity. Further analysis will reveal if these novel subsets have the capacity of transdifferentiating fully or if they maintain a limited phenotypic and functional capacity.
MAIT cells are imprinted by the microbiota in early life and promote tissue repair
Authors: Constantinides Michael G , Link Verena M. , Tamoutounour Samira , Wong Andrea C. , Perez-Chaparro P. Juliana , Han Seong-Ji , Chen Y. Erin , Li Kelin , Farhat Sepideh , Weckel Antonin , Krishnamurthy Siddharth R. , Vujkovic-Cvijin Ivan , Linehan Jonathan L. , Bouladoux Nicolas , Merrill E. Dean , Roy Sobhan , Cua Daniel J. , Adams Erin J. , Bhandoola Avinash , Scharschmidt Tiffany C. , Aubé Jeffrey , Fischbach Michael A. , Belkaid Yasmine 
Published: January 2023

Abstract
Early-life microbial colonization has been shown to impart long-lasting effects on host fitness. Because mucosal-associated invariant T (MAIT) cells are predominantly located in tissues colonized by the microbiota and characterized by their recognition of microbial-derived riboflavin intermediates, they are thought to be particularly dependent on the microbiota. However, little is known about their development and how they contribute to tissue physiology. MAIT cells accumulated in barrier tissues between 2 and 3 weeks of age, suggesting that MAIT cells develop during a very specific temporal window and in response to defined microbial exposure. The isolation of early-life intestinal commensals and subsequent colonization of neonatal germ-free mice with defined bacteria induced MAIT cell development. Conversely, colonization later in life failed to promote their development within tissues, indicating that microbial exposure must occur during an early-life window. Following their development, MAIT cells represented a dominant type-17 subset in the skin and cutaneous MAIT cells uniquely expressed a transcriptional program associated with tissue repair. Cutaneous MAIT cells responded locally to skin commensals in a manner that required IL-1 and IL-18, as well as MR1-mediated presentation of riboflavin metabolites. Topical application of a riboflavin derivative selectively increased MAIT cells in the skin and was sufficient to promote cutaneous wound healing. Our work demonstrates that MAIT cells are induced during a specific early-life window in response to riboflavin-synthesizing commensals, which permanently imprints the abundance of this subset in tissues, thereby controlling tissue repair and homeostasis.
The Contribution of Pulmonary Dendritic Cells to the Induction and Regulation of T Cell Responses During Respiratory Infection
Authors: Lopez Christopher , Zacharias Zeb Raplh , Waldstein Kody , Legge Kevin L 
Published: January 2023

Abstract
The respiratory tract represents a major portal of entry for pathogens, including Group A Streptococci (GAS). GAS represents a significant burden in cases of primary infection as well as cases of secondary bacterial pneumonia following influenza virus infection. Control of infection and eventual resolution is dependent on the local adaptive immune response. This is facilitated by the uptake and subsequent presentation of antigen by dendritic cells (DC) to T cells. Furthermore, after GAS infection, DC drive T cell development towards a Th17 immune response that is associated with pathogen control. Our hypothesis is that pulmonary DC, both resident and recruited, contribute locally to the maintenance and regulation of an effector CD4 T cell response in the context of a GAS infection. Toward this end, our studies are defining the contribution of local DC: T cell interactions in shaping the phenotype and magnitude of Th17 and Tfh responses within the lungs during GAS infection. An improved understanding of the contribution of these DC to the development and regulation of these CD4 T cells responses during GAS infection should elaborate strategies to the development of better therapies.
A new therapeutic influenza virus vaccine that uses host cell-restricted attenuation by artificial microRNAs
Authors: Guo Hua , Wen Ke , Wang Haiyan , Chen Yanping , Yang Xing , Yang Huixiao , Pena Adilene Realivazquez , Zeng Mingtao 
Published: January 2023

Abstract
New strategies are urgently needed for developing vaccines and/or anti-viral drugs against influenza viruses, because antigenic shift and drift inevitably occurs in circulating strains each year, and new strains resistant to anti-viral drugs have recently emerged. In our study, we designed and incorporated artificial microRNAs (amiRNAs) into the NA segment of rescued influenza viruses to separately target two host genes, CLK1 and SON, which were found to play an essential role in virus replication. Mouse epithelial fibroblast (MEF) or A549 cells infected with engineered influenza PR8 based viruses containing amiR-30CLK1 (PR8-amiR-30CLK1) or amiR-93SON (PR8-amiR-93SON) had reduced expression of host proteins CLK1 and SON, respectively. All engineered influenza viruses functioned as attenuated vaccines, induced significantly higher antibody responses, and provided significantly greater protective efficacy. In addition, they were found to be safe, based on the mouse weight changes and clinical signs observed. In contrast to the engineered viruses targeting SON, mice treated with engineered viruses targeting CLK1 by 6 hours after lethal-dose PR8 infection, recovered from weight loss and survived lethal infection, suggesting that our PR8-amiR-30CLK1-engineered influenza virus could be used as a new post exposure therapeutic influenza vaccine.
ClinicoPathological Correlation (CPC) ImmunoTechnologies for Monitoring Lymphotoxin Alpha
Authors: Harbi Shaghayegh , Wang Rong , Harbi Vahid Dean , Kerbawy John , Park Hannah Lui , Gonzales John 
Published: January 2023

Abstract
Neuroinflammation has been proposed as a target for neuroprotection. Therefore significant opportunities for preventing neurologic decline exist. ClinicoPathological Correlation (CPC) ImmunoTechnologies are critically needed for clinical utility for acute and chronic immunological and inflammatory disorders (including autoimmune neurological disorders such as Parkinson’s disease and Alzheimer’s disease) to determine if an individual has variants associated with a higher risk of disease (Gain of Function [GoF] variants); and elevated levels of analytes (circulating biomarkers).
We hypothesize the neurovascular compartment plays a critical role in neurodegeneration. Using a multipronged approach, we identified specific immune cell subsets and inflammatory factors in the blood, which can potentially play a critical role in the early stages of neurodegeneration by disrupting homeostatic regulation, destabilizing the neurovascular compartment; and elevated levels of analytes (proteomic multiplexed quantification) in the cerebrospinal fluid (CSF) and plasma, which can potentially serve as robust, indicative biomarkers consistent with model of neuroinflammation contributing to neurovascular dysfunction, potentially leading to neurodegeneration. More specifically, we identified analytes (lymphotoxin/TNF-beta/LTA) in the plasma (low levels in CSF); TNF-alpha levels were low in plasma and CSF. Next-generation sequencing enabled the identification of risk variants, pathogen/virus profiles and LTA GoF variant strongly associated with increased protein production. We included distinct LTA inflammatory/autoimmune disease controls (rheumatoid arthritis, multiple sclerosis, uveitis or vasculitis).
Comprehensive profiling of TCR and BCR repertoire of infiltrated lymphocytes in the mouse injured skeletal muscle
Authors: Iwabuchi Kumiko A. , Sasakawa Noriko , Hotta Akitsu 
Published: January 2023

Abstract
Lymphocytes infiltrating to the injured skeletal muscle have been shown to play an important role in muscle regeneration. Site-specific infiltrating/expanding lymphocytes and its molecular features are potential resources for bioengineering such as a drug delivery system. Although some previous studies showed the accumulation of lymphocytes to the injured skeletal muscle, the actual frequency of distinct lymphocyte clones in situ is still unclear. Hence, a comprehensive picture of the lymphocyte repertoire has yet to be described in detail. To this end, we conducted a comprehensive profiling of TCR and BCR repertoire of infiltrating lymphocytes in the mouse injured skeletal muscle model by next-generation sequencing. In the TCR repertoire profiling, we found that the expression level of TCR transcripts contains unique CDR3 α and distinct population of CDR3 β were increased (7.6–17% and 6.7–15%) in infiltrating T cells in both of cardiotoxin- or cryo-injured skeletal muscle, whereas no clonal expansion of specific TCR α/β transcripts observed in control splenic T cells (&lt;1% respectively). While in the BCR repertoire profiling, various transcripts of immunoglobulin kappa chains showed expansion in infiltrated fraction, despite the proportion of immunoglobulin heavy and lambda chain were remained similar to control splenic B cells. Together these data have allowed us to identify TCR/BCR candidates targeting injured skeletal muscles. Furthermore, we aim to utilize the T cells/B cells expressing high-affinity TCR/BCR for the drug delivery system, especially for large protein complexes.
Antibody-suppressor CD8+ T cells ameliorate antibody-mediated rejection following kidney transplant in mice
Authors: Han Jing Light , Zimmerer Jason M , Zeng Qiang , Ringwald Bryce A , Cassol Clarissa , Warren Robert T , Abdel-Rasoul Mahmoud , Breuer Christopher K , Bumgardner Ginny L 
Published: January 2023

Abstract

Purpose
CCR5 KO kidney transplant (KT) mice produce high titer alloantibody (alloAb) associated with severe antibody-mediated rejection (AMR) that reproduces AMR histology observed in human KT recipients. We previously reported the novel alloAb suppressor activity of alloprimed CXCR5+IFNγ+CD8+ T (Tab-supp) cells following hepatocellular transplant in mice. Here, we investigated the biologic impact of alloprimed CD8+ Tab-supp cells and their capacity to suppress alloAb following adoptive cell transfer (ACT) into CCR5 KO KT mice.

Methods
CCR5 KO (H-2b) mice were transplanted with allogeneic A/J (H-2a) kidneys, and on postoperative day (POD) 5 underwent ACT of alloprimed CD8+ Tab-supp cells (retrieved from C57BL/6 mice alloprimed with A/J alloantigen). A second cohort received concomitant bilateral native nephrectomy, and allograft survival was monitored with serial serum creatinine (&gt;100 μmol/L defines KT graft loss). Untreated CCR5 KO KT mice served as controls.

Results
CCR5 KO KT mice developed high alloAb titer compared to wild-type (WT) recipients (5,800±700 vs 1,200±100; p=0.0003). ACT significantly inhibited alloAb production by 5-fold (1,200±200; p&lt;0.0001) and POD14 AMR pathology (peritubular capillary margination and C4d deposition, arteritis) in CCR5 KO KT mice (composite histologic score 3.6±1.5 vs 8.4±0.2 in untreated controls; p=0.006). Following ACT, alloAb remained suppressed beyond POD 30, correlating with enhanced allograft survival (MST 52 vs 14 days; p=0.006).

Conclusion
ACT of CD8+ Tab-supp cells effectively inhibits alloAb production and AMR not only after allogeneic hepatocellular transplant, but also after vascularized solid organ transplant such as in CCR5 KO KT recipients.
Posttransplant cyclophosphamide as a platform for immunotherapy after allogeneic stem cell transplantation for multiple myeloma
Authors: Minnie Simone A , Kuns Rachel D , Ensbey Kathleen S , Samson Luke D , Chesi Marta , Gartlan Kate H , Smyth Mark J , Vuckovic Slavica , Hill Geoffrey R 
Published: January 2023

Abstract
Allogeneic stem cell transplantation (alloSCT) is a highly effective, curative therapy for leukemia yet does not provide a survival benefit above autologous SCT in patients with multiple myeloma (MM). To explore this, we developed preclinical models of SCT using C57Bl/6 recipient mice and either C57Bl/6 (ASCT) or C3H.SW (alloSCT) donor grafts. Importantly, these models recapitulated the clinical setting whereby alloSCT provided superior outcomes, compared to ASCT, in recipients bearing MLL-AF9-driven acute myeloid leukemia (AML) but not in those bearing Vk*MYC-MM. Interestingly, we found that MM-specific, T cell-mediated immunity was generated after ASCT, which failed due to MM-induced T cell exhaustion. MM relapse after ASCT could be prevented by TIGIT or PD-1 targeted immune checkpoint inhibition or via depletion of suppressive CSF1-R+ myeloid cells. Conversely, after alloSCT, T cell exhaustion was driven principally by alloantigen and CD8 T cells expressed high levels of PD-1, TIGIT and TIM-3. Furthermore, Vk*MYC myeloma exploited this alloantigen-driven T cell exhaustion via expression of high levels of PD-L1 and CD155 (the cognate ligands for PD-1 and TIGIT), which were expressed minimally on MLL-AF9 AML. To exploit alloSCT in MM, we used post-transplant cyclophosphamide (PT-Cy) to delete high affinity alloreactive T cells that generate the exhausted donor T cell pool. Subsequent administration of CD137 agonists enhanced T cell activation and cytolytic activity within bone marrow, without exacerbating GVHD. Thus, PT-Cy provides a platform for optimizing immunotherapy after alloSCT.
Exopolysaccharide from a commensal bacterium ameliorates aGVHD by decreasing alloreactive donor T cell activation
Authors: Kalinina Olga , Talley Sarah , Zamora-Pineda Jesus Bernabe , Paik Won , Campbell Edward , Knight Katherine L 
Published: January 2023

Abstract
Acute graft versus host disease (aGVHD) is a severe and often lethal complication of allogeneic bone marrow transplantation (BMT). We found that mice injected with exopolysaccharide (EPS) secreted by a commensal bacterium, Bacillus subtilis, significantly improved survival, reduced weight loss and decreased production of systemic pro-inflammatory cytokines in GVHD mice. We utilized a novel biosensor mouse model to assess the activation of donor T cells in live mice during aGVHD and found that EPS inhibited the activation of alloreactive donor T cells. EPS also inhibited alloreactive T cell activation in mixed lymphocyte reactions (MLR) in vitro and this inhibition required DCs. Treating DCs with EPS led to upregulation of the inhibitory molecule PD-L1 and secretion of the anti-inflammatory cytokine IL-10, characteristic of inhibitory DCs. We determined that EPS induces inhibitory DCs through TLR4, signaling through both MyD88 and TRIF signaling pathways. The inhibition of alloreactive T cells by these inhibitory DCs is mediated by indoleamine 2,3-dioxygenase (IDO). We hypothesized that inhibition of alloreactive donor T cell activation in GVHD mice by EPS is also mediated by DCs and that EPS induces inhibitory DCs in vivo as well as in vitro. The data demonstrate the potential of EPS or EPS-treated DCs as novel reagents for preventing GVHD.
Circulating tumor cell clusters exhibit enhanced immune evasion from natural killer cells
Authors: Lo Hin Ching , Xu Zhan , Kim Ik Sun , Muscarella Aaron , Liu Jun , Hein Sarah , Wang Hai , Krupnick Alexander , Neilson Joel , Paust Silke , Rosen Jeffrey , Zhang Xiang 
Published: January 2023

Abstract
During cancer metastasis, the ability to evade immunosurveillance is key to the survival of circulating tumor cells (CTCs). Recent studies have found that in addition to single CTCs, multicellular clusters of CTCs can be detected in patient blood. Strikingly, CTC clusters show higher metastatic potential than single CTCs, but the molecular mechanism is unclear. We hypothesize that CTC clusters adopt immune evasive strategies, which enhance their metastatic ability. In mouse models of breast cancer, CTC clusters show enhanced metastatic growth over single cells in immunocompetent mice, but this difference is abrogated in immunodeficient mice lacking NK cells or mice treated with NK cell-depleting antibodies. Adoptive transfer of NK cells into NK cell-deficient hosts selectively suppresses metastatic growth by single CTCs, suggesting that single CTCs are more sensitive to NK cells than clusters. Analysis of cell line and patient RNA-seq data reveal that CTC clusters have elevated expression of cell-cell adhesion and epithelial genes as compared to single cells, which is in turn associated with decreased expression of NK cell-activating NKG2D ligands. Furthermore, modulation of tumor cell epithelial status alters NK ligand expression and sensitivity to NK cell killing, but this effect is attenuated by the addition of an NKG2D-blocking antibody. Taken together, we propose a model in which the epithelial characteristics of CTC clusters promotes their resistance to NK cell attack and thus their overall metastatic success. These findings reveal that NK cells play an important role in determining the fate of CTCs of different epithelial/mesenchymal states, and illuminate our understanding of immune evasion mechanisms by CTCs.