bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of Paneth cells alters intestinal innate lymphoid cells and enhances weight gain in mice.
Authors: Joldrichsen Marisa R , Kim Eunsoo , Steiner Haley E , Cormet-Boyaka Estelle , Boyaka Prosper N 
Published: January 2023

Abstract
Paneth cells are a subset of small intestinal epithelial cells specialized in the production of antimicrobial products and cytokines. Gastrointestinal dysbiosis has been linked to many health concerns and is believed to be a contributing factor in obesity. Despite the role of Paneth cells as a major source of antimicrobial products, the contribution of these cells to health or disease conditions has not been fully explored. We examine the impact loss of Paneth cells would have on the gut microbiota and whether the subsequent dysbiosis could affect metabolic functions of the host and fat accumulation in a mouse model of diet induced obesity. For this purpose, were used wild-type and Sox9ΔIEC mice, which lack Paneth cells due to a Sox9 gene deletion within the intestinal epithelium. Compared to control wild-type mice, the small intestine of Sox9ΔIEC exhibited an altered profile of ILCs characterized by increase ILC2 and decrease ILC3 numbers. After exposure to a high-fat diet for 13 weeks, the Sox9ΔIEC mice gained more weight and had higher glucose intolerance. The intestinal homeostasis was also affected, with an increase in intestinal permeability and an increase in ILC1s within the small intestine of Sox9ΔIEC mice. In the abdominal fat Sox9ΔIEC mice showed increased numbers of immune cells including inflammatory macrophages, T cells, and B cells. Finally, fecal material transplantation experiments revealed that fecal material from the Sox9ΔIEC mice transfer the phenotype in recipient germ-free mice as indicated by a trend towards an increase in weight gain and immune cell infiltration of abdominal fat. These results highlight the importance of Paneth cells as regulators of metabolic functions of the host and fat accumulation.
Supported by grants from OSU and NIH.
Expanding the use of clustering and dimensionality reduction in high parameter flow cytometry data through machine learning for novel samples.
Authors: Lownik Joseph Cornelius , Mahov Simeon , Alkan Serhan , Merchant Akil , Kitahara Sumire 
Published: January 2023

Abstract
High parameter flow cytometry is a highly utilized tool for accurate immunophenotyping and diagnostics in immunology, oncology, and many other disciplines. Over the past decade, several methods have been developed for automated clustering and dimensionality reduction of high parameter flow cytometry data which has sped up and simplified the discovery of cell populations not observed by manual gating strategies. However, the input and output of such tools are stochastic in nature, thus making their results difficult to reuse with novel samples. To address this challenge, we present a method utilizing machine learning to predict cluster labels and dimensionality reduction coordinates on novel samples. For proof of principle, we utilized high parameter (22 marker) flow cytometry data which examines myeloid hematopoiesis on bone marrow aspirate samples. Training data for machine learning consisted of pooled, normal, bone marrow. Phenograph was used for initial population clustering and UMAP for dimensionality reduction. A random forest model was found to be most accurate in predicting Phenograph clusters (98%) on novel data while a k-nearest neighbors (knn) model was found most accurate for UMAP coordinate prediction. The utility of this model was observed by examining acute myeloid leukemia with aberrant immunophenotypes, which were not included in the training data set. For these samples, predicted clusters and UMAP coordinates correlated with early progenitor populations from the training set. This approach allows for a de novo sample clustering and dimensionality reduction assignment onto an already established and characterized model, allowing for rapid, automated interpretation of high dimensional flow cytometry data.
Supported by Cedars-Sinai Pathology and Laboratory Medicine Minigrant
Robust Serum- and Feeder-Free Expansion of Mouse B Cells In Vitro
Authors: Arora Hitesh , Babic Sandra , Lee Tracy , Rogers Trevor , Eaves Allen C , Louis Sharon A , Brown Mark A , Kokaji Andy I , Tabatabaei-Zavareh Nooshin 
Published: January 2023

Abstract
Mouse B cells are used in workflows to discover novel therapeutic antibodies or develop preclinical applications using genetically engineered B cells. In vitro expansion of B cells offers the opportunity to improve the recovery of antibody sequences and aids in the potential increase in the diversity of the B cell repertoire. Achieving robust expansion of B cells in culture can be challenging, as it typically requires the addition of serum, feeder cells, or specialized culture plates. The addition of serum can introduce unknown factors and result in lot-to-lot variability. Therefore, we have developed a first-to-market culture system that does not require the use of serum, feeder cells, or specialized culture plates to achieve robust in vitro expansion of mouse pan-B cells. Pan-B cells isolated from mouse splenocytes by immunomagnetic enrichment were cultured in serum-free ImmunoCultTM-XF B Cell Base Medium supplemented with ImmunoCultTM-ACF Mouse B Cell Expansion Supplement for &gt; 9 days, starting with seeding densities of 100,000 cells/well and passaging every 3 days. Although pronounced donor variability was observed in the rate of expansion of viable cells, mean ~13-fold, ~150-fold, and ~200-fold rates were observed after 3, 6, and 9 days in culture, respectively (n=6 donors; range 94- to 328-fold at day 9). The expanded B cells also upregulated expression of activation and differentiation markers such as CD86 (mean 74%; n=6 donors; range 34 – 90%), CD138 (mean 68%; n=6 donors; range 57 – 73%), and CD267 (mean 79%; n=6 donors; range 49 – 91%) at day 9. The expansion supplement should facilitate mouse B cell studies for antibody discovery and diverse basic and translational applications.
The Minimal Information about MHC Multimers (MIAMM)
Authors: Vita Randi J , Mody Apurva , Overton James A , Buus Soren , Haley Stephen T , Willis Richard A , Sette Alessandro , Mallajosyula Vamsee , Peters Bjoern , Altman John D 
Published: January 2023

Abstract
The Minimal Information about MHC Multimers (MIAMM, miamm.lji.org) is a recently established data standard to be applied to publications utilizing these reagents. Available at miamm.lji.org, we explain how to easily represent multimer reagents in a standardized format using ontology terminology. Additionally, we provide a free, publicly available Multimer Validation Tool. This tool helps users adopt this new data standard and was proven to be generally applicable to real life use cases by its validation of the data present in the NIH Tetramer Core Facility and the nearly 18,500 multimer assays in the Immune Epitope Database (IEDB). As the scientific public adopts MIAMM, the quality, reproducibility, and annotatability of MHC multimer reagent data in the scientific literature will be improved.
Funding: JDA, RAW, and DLL acknowledge support from the contract for the NIH Tetramer Facility (75N93020D00005) from the Yerkes National Primate Research Center (P51OD011132), and the Emory Center for AIDS Research (P30AI050409). RV, JAO, AM, and BP acknowledge support from National Institutes of Health grant R24 HG010032. RV, JAO, AM, BP, and AS acknowledge support from National Institutes of Health contract 75N93019C00001
A combination of genetic factors and dietary tryptophan shapes gut microbial dysbiosis in a lupus-prone mouse model
Authors: Ma Longhuan , Brown Josephine , Kanda Nathalie , Terrell Morgan , Ge Yong , Mohamadzadeh Mansour , Morel Laurence 
Published: January 2023

Abstract
Gut microbial dysbiosis, impaired intestinal barrier and altered tryptophan metabolism have been reported in lupus patients. Dietary tryptophan modulated disease activity and modified the composition of microbiota in triple congenic (TC), B6.Sle1.Sle2.Sle3, lupus-prone mice. However, whether this modification is facilitated by tryptophan acting directly on the microbiota, or indirectly through lupus genetic susceptibility remains unknown. To address this question, we transplanted fecal samples from TC and B6 control mice into germ-free or antibiotic-treated B6 mice that were fed with high or low tryptophan. Tryptophan enriched different species of bacteria from transferred TC and B6 microbiota. A bloom of Ruminococcus gnavus, a bacterium associated with human lupus nephritis, only emerged in the recipients of TC microbiota fed with high tryptophan. Further, recipient mice showed distinct fecal metabolite profiles based on dietary tryptophan and the TC or B6 origin of the microbiota. Interestingly, both genetics and tryptophan impaired gut barrier integrity in recipient mice. These results suggest that the dysbiotic lupus microbiota is shaped by a combination of dietary tryptophan and genetic background, the latter most likely through autoimmune inflammation. In particular, the exclusive expansion of the pathobiont Ruminococcus gnavus by high tryptophan from the microbiota of lupus-prone mouse demonstrate that the interplay of genetic and environmental factors can influence the pathogenesis of lupus through modifying gut microbiota and gut permeability.
This work was supported by a grant from the NIH R01 AI43313 to Laurence Morel.
Synergistic effect of CXCR5+CD8+ TAb-supp cell therapy and mTOR inhibition (but not calcineurin inhibition) in suppressing alloantibody following kidney transplant in mice
Authors: Han Jing Light , Zimmerer Jason , Zeng Qiang , Chaudhari Sachi , Breuer Christopher , Bumgardner Ginny L 
Published: January 2023

Abstract
CXCR5+ CD8+ TAb-supp cells inhibit alloantibody (alloAb) production, AMR, and prolong graft survival in mouse models. To determine if this cell therapy is compatible with standard immunosuppression (IS) strategies, we investigate the interaction of CD8+ TAb-supp adoptive cell therapy (ACT) and IS [mTOR inhibitors (mTORi) or CNi] in a mouse model of kidney transplant (KTx). CXCR5+ CD8+ T cell ACT to CCR5 KO recipients on day 1 after KTx (D1) significantly suppresses D14 alloAb titer (1259±114) versus untreated controls (5951±630; p=0.0001). Administration of mTORi significantly inhibits alloAb titer (495±77; p&lt;0.0001), while CNi does not (6473±434; p=ns). ACT combined with mTORi significantly reduces alloAb titer compared to ACT alone (387±63 vs 1259±114; p=0.0007). Conversely, CNi treatment partially negates the beneficial effects of ACT on alloAb titer (2385±114; p=0.03). Similarly, ACT reduced the quantity of D14 splenic germinal center (GC; GL-7+ Fas+ B220+) B cells compared to untreated KO recipients (4037±515 vs 5815±655 cells/mm3; p=0.03). Addition of mTORi to ACT preserves ACT-mediated suppression of GC B cells (4498±940 cells/mm3) while CNi negates ACT-mediated GC B cell suppression (6130±834 cells/mm3; p=0.04). Analysis of persisting GFP+ CXCR5+ CD8+ T cells D14 after ACT shows that concurrent mTORi treatment is associated with comparable quantity (1671±139 cells/mm3; p=ns), while CNi is associated with reduced quantity (900±83 cells/mm3; p=0.01)of transferred GFP+ CXCR5+ CD8+ T cells detected in the spleen compared to ACT alone (1601±116 cells/mm3). ACT with CXCR5+ CD8+ TAb-supp cells is optimal when combined with mTORi, not CNi, to significantly inhibit alloAb production and reduce quantity of splenic GC B cells.
Supported by NIH R01 AI083456 (to GLB), T32 AI106704-07 and F32 AI161844 (to JLH), CA016058, UL1TR002733, the OSU Division of Transplant Surgery, and the OSU College of Medicine.
DNA-PK inhibition plus immune adjuvants promotes CD8 TIL infiltration, neoantigen presentation, and diversifies the tumor-reactive TCRβ repertoire in B16 melanoma
Authors: Christians Allison , Sanchez Amelia , Albert Gabriella , Bradeen Xander GordonRay , Geng Degui , Chen Jiangli , Gonzalez-Rivera Daniela , Davila Eduardo 
Published: January 2023

Abstract
Despite significant improvements in cancer immunotherapies, enhancing immunogenicity of non-responsive tumors warrants further investigation. A prior drug screen of ~3,000 compounds identified NU7441, a DNA PK inhibitor, as an effective compound that promotes immunogenicity of various melanoma lines in vitro. In this study, we hypothesized that in vivo combination therapy NU7441, STING-L, and CD40 agonist will enhance tumor immunogenicity resulting in both expansion and increased cytotoxic activity of CD8+TCRβ tumor-reactive TILs in B16 melanoma models. Results obtained by flow cytometry demonstrated that combination treatment 1) significantly increased the ratio of CD8/CD4 TILs, 2) expanded several tumor-reactive TCRβ clones, 3) increased granzyme B production and expression of 4-1BB and PD-1, 4) increased ratio of DC/MDSC infiltration, and 5) potentially identified a novel cytotoxic CD8+CD11c+GR-1+ population. Additionally, the expansion of tumor-reactive TCRs was attributed to DNA-PKi’s ability to both expand and diversify the number of neoantigen transcripts resulting in a broader neoantigen expression profile. RNA-seq identified 27 unique neoantigens as potential novel targets in melanoma immunotherapy. TILs isolated from B16 tumors were co-cultured with dendritic cells transfected with tandem-mini genes, each encoding ~10 neoantigens, and T cells were analyzed by flow cytometry to quantify the TCRβ repertoire and functional response to neoantigens. We demonstrate combination treatment with NU7441, STING-L and CD40 agonist enhance antitumor responses through increased myeloid cell infiltration and sensitization of tumor cells to T cell-mediated killing from an expanded CD8+TCRβ repertoire.
Supported by R01CA207913 NCI BX004935-01, VA, Merit Award P30CA046934, NCI Leukemia and Lymphoma Society Department of Defense Gates Grubstake University of Colorado Anschutz Medical Campus Cancer League of Colorado
Monocyte-directed targeting of VEGFA in the melanoma microenvironment
Authors: Bu Melissa Tian , Chandrasekhar Pallavi , Ding Lizhong , Hugo Willy 
Published: January 2023

Abstract
VEGFA plays a critical role in the immunosuppressive cancer response and related immunotherapy resistance. Combined with immune checkpoint inhibitors (ICI) such as those against CTLA-4 and PD-L1, anti-VEGFA agents have demonstrated early clinical success in metastatic melanoma and renal cell carcinomas. To overcome toxicity limitations, thereby opening a wider therapeutic window, VEGFA should be targeted near its production source. Recently, localized co-targeting of TGFβ, an immunosuppressive factor, near CD4+ T cells through bispecific “trap” antibodies have demonstrated robust pre-clinical success. Thus, we assert the superiority of a bispecific antibody guiding a “trap” for VEGFA to its cellular source over global anti-VEGFA agents combined with ICIs. We set out to identify the cell population responsible for secreting VEGFA in the melanoma microenvironment. Upon re-analysis of two existing, independent single cell RNA Sequencing datasets of patient-derived melanoma treated with ICIs, we identified myeloid populations as the main producers of VEGFA. We specifically found a classical monocyte population (CD14+ FCN1+ S100A8+) to express high levels of VEGFA. Of note, we discovered significantly higher VEGFA expression in monocytes from non-responders versus responders to ICIs. VEGFA-expressing monocytes are localized to the intratumoral environment, as our analysis of PBMC-derived monocytes lacked high VEGFA expression in comparison to those that were tumor-derived. Based on our findings, we propose the design of a bispecific antibody that simultaneously targets VEGFA and CD14 to leverage the synergistic pro-immune effects and toxicity diminishment that result from localized inhibition.
Supported by the NIH (R01 CA236910) and Melanoma Research Alliance Young Investigator Award to Willy Hugo.
T-cell phenotype varies in distinct tumor microenvironments and CD57+ TFH cells are associated with disease progression and inferior survival in follicular lymphoma
Authors: Yang Zhi-Zhang , Kim Hyo Jin , Wu Hongyan , Tang Xinyi , Krull Jordan , Mondello Patrizia , Villasboas Jose , Novak Anne , Ansell Stephen 
Published: January 2023

Abstract
The tumor microenvironment (TME) plays a crucial role in mediating the tumor immune response, thereby affecting patient outcomes in follicular lymphoma (FL). Using CyTOF, we analyzed a cohort of 82 FL patients with biopsy specimens collected before the first treatment regimen was administered. Our results showed that there was a difference in the T-cell phenotype in patients with various TMEs. Patients with TMEs rich in monocyte/macrophages/NK cells had more CD8+ cells and tended to have fewer TN, but more TEMRA and TEXH cells. Patients enriched with T cells exhibited a T-cell phenotype skewed toward to TCM and patients with B cell dominance tended to have significant higher number of TFH cells. T-cell phenotypes with more terminally differentiated, senescent and exhausted cells were highly represented in patients with less T cells when compared to patients with more T cells. We observed that CD57+ TFH cells was significantly more abundant in patients who had disease progression than patients who had complete response to therapy, suggesting a role for CD57+ TFH cells in promoting malignant cell growth in FL. Consistent with this finding, we observed that increased numbers of CD57+ TFH cells correlated with an inferior survival in FL. Using CITE-seq technology, we found that CD57+ TFH cells exhibited a substantially different transcriptome from CD57− TFH cells. Genes that were differentially upregulated in CD57+ TFH cells when compared to CD57− TFH cells included genes involved in cell survival, compromised inflammatory response, and metabolic activation. Taken together, our results indicate different tumor microenvironments among patient groups that is associated with variable T-cell phenotypes.
Androgen deprivation therapy allows for effective anti-TIGIT immunotherapy in murine model of castration resistant prostate cancer.
Authors: Polesso Fanny , Guan Xiangnan , Xia Zheng , Moran Amy E 
Published: January 2023

Abstract
Prostate cancer is the second leading cause of cancer associated mortality in men, and for reasons that remain unclear, immunotherapy treatments have largely failed in patients with advanced prostate cancer. Standard of care therapy for these patients relies on androgen deprivation therapies (ADT) to block testosterone production combined with small molecules that inhibit androgen synthesis and/or the function of the androgen receptor (AR). Importantly, androgens are reported to be immunosuppressive; therefore, we postulated that androgen axis blockade might promote response to immunotherapy. In the recent years, the co-inhibitory receptor TIGIT has emerged as a promising immunotherapy target, and we observed that TIGIT is highly expressed on tumor infiltrating T cells and NK cells in metastatic castration resistant prostate cancer (CRPC) patients treated with the AR antagonist enzalutamide. Likewise, in a mouse model of CRPC, we show that tumor infiltrating T cells express TIGIT and that treatment with enzalutamide increases its expression. In this model, neither treatment with anti-TIGIT alone nor with chemical castration and enzalutamide affects tumor growth. Remarkably, the combination of anti-TIGIT with chemical castration and enzalutamide leads to delayed tumor growth and long-term cures in about 60% of the animals. Taken together, our data suggest that androgen receptor blockade sensitizes immune cells in the tumor to respond to anti-TIGIT immunotherapy.
This work was largely supported by an OHSU Foundation grant and a sponsored research agreement with AstraZeneca to A.E.M. Additional funding was provided by Collins Medical Trust and Prostate Cancer Foundation.
Opposite effects of CXCR1 and CXCR2 overexpression in prostate tumorigenesis
Authors: Richardson Micheler , Adekoya Timothy , Smith Nikia , Kothari Parag 
Published: January 2023

Abstract
Chemokines and their receptors play important role in tumor progression and metastasis. In prostate cancer (PCa), some members of the CXC chemokine receptor have been shown to enhance angiogenesis, proliferation and metastasis. In this study we assess the roles of the interleukin-8 (IL-8/CXCL8) receptors CXCR1 and CXCR2 in prostate tumorigenesis, using MDA PCa 2b and LNCaP cell lines. Our results show that overexpression of CXCR2 enhanced in-vitro cell proliferation, soft agar growth and in-vivo tumor xenograft in nude mice, whereas overexpression of CXCR1 inhibited cell proliferation and tumor growth, relative to control cells. CXCR1 cells showed decrease prostate specific antigen (PSA) expression whereas CXCR2 exhibited decrease androgen receptor (AR) expression. Interestingly, tumor lysates from CXCR1 cells displayed significant increase in ERK and AKT activation as well as chemokines production relative to control and CXCR2 tumors. CXCR1 tumors also exhibited a more mesenchymal phenotype, characterized by reduced E-Cadherin but increased N-Cadherin and Vimentin expression relative to CXCR2 or control tumors. Altogether, these results indicate that CXCR1 and CXCR2 may couple to distinct pathways to modulate prostate tumorigenesis.
Supported by CA156735, MD012392
Single-cell myeloid diversity in human fallopian tube and its implications for early high grade serous ovarian cancer
Authors: Brand Joshua , Haro Marcela , Abbasi Forough , Lin Xianzhi , Siedhoff Matthew , Li Andrew , Rimel Bobbie , Medeiros Fabiola , Lawrenson Kate , Dinh Huy 
Published: January 2023

Abstract
The 5-year survival rate of high grade serous ovarian cancer (HGSOC) has remained below 40% for decades. This rises significantly to 90% when detected early. Increasing evidence suggests that HGSOC tumors originate in the fallopian tube (FT). However, little is known about FT’s immune cell heterogeneity and how it contributes to HGSOC development. Here we show a single-cell transcriptome analysis of non-malignant FT samples, revealing high monocyte diversity that is lost in HGSOC. FT monocyte subsets display distinct inflammatory gene signatures such as IL1A, CCL3/4 and others. Trajectory inference showed potential monocyte maturation steps that started with early cytokine/chemokine secreting monocytes that gain MHCII expression and develop into macrophages or dendritic cells. We found the macrophage-to-monocyte ratio is remarkably elevated in tumors compared to adjacent normal ovary and non-cancerous FT tissues in ours and publicly available scRNA-Seq. Intriguingly, analysis of FT of patients with BRCA1/2 germline mutations revealed half of these high-risk individuals are more like those found in HGSOC tumors than in normal FT. They also showed distinct T cell phenotypes in their FTs. Our data suggested that myeloid diversity, and their interactions with T cells in the FT, might contribute to early HGSOC development. Understanding tissue-of-origins immune microenvironment has a potential contribution to early cancer detection. We anticipate this work provides evidence of how myeloid cell plasticity induces tumorigenesis and can shape different tumor microenvironments.
Supported by startup grants from UW-Madison School of Medicine and Public Health and UW-Madison Cellular and Molecular Pathology Graduate Training Program travel awards