bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ranked abundance of 115 proteins following simultaneous measurement by multiplex immunoassay in serum, plasma, and cell culture supernatant samples.
Authors: Droll Deborah , Saporita Anthony , Gilliam Brooke , Grana Paula , Qiang Xiao 
Published: November 2024

Abstract
MILLIPLEX™ PLEXpedition, a customizable multiplex immunoassay kit, was developed to simultaneously screen up to 115 targets including cytokines, chemokines, growth factors, matrix metalloproteinases, and biomarkers of bone health, metabolism, and cardiovascular disease. Two Luminex™ instruments, the xMAP™ INTELLIFLEX™ and the FLEXMAP 3D™, can accommodate all 115 bead regions with comparable sensitivity and sample correlation observed between them. The analyte selection incorporates many biomarkers critical to the field of immunology, using assays developed for two MILLIPLEX™ 48-plex human cytokine, chemokine, and growth factor kits (Cat. No. HCYTA-60K and Cat. No. HCYTB-60K). Sample correlation in serum, plasma, and cell culture supernatants demonstrated that this discovery biomarker panel with a matrix-free format can be used to transition seamlessly to our highly qualified panels, MILLIPLEX™ Human Cytokine Panel A and B, which have optimized serum matrix and lot-to-lot verification for absolute quantification of protein concentration. To probe the relative abundance of each analyte in typical sample matrices, the 115-plex assay was run with a set of 8 cell culture supernatants and 24 healthy and disease serum and plasma samples. Additionally, analytes were ranked by their response to stimulation by LPS or ConA in PBMCs. Our results highlight the utility of the novel PLEXpedition screening kit for evaluating relative abundance in biological samples.
Deciphering the metabolic regulation of immunosuppressive CD11b+Gr1+ myeloid cells in epithelial ovarian cancer.
Authors: Udumula Mary Priyanka , Singh Harshit , Rashid Faraz , Hijaz Miriana , Gogoi Radhika , Philip Philip , Munkarah Adnan , Giri Shailendra , Rattan Ramandeep 
Published: November 2024

Abstract
Immunosuppressive CD11b+Gr1+ myeloid cells are key drivers of immunosuppression and decrease immunotherapy efficacy in epithelial ovarian cancer (EOC). We showed that EOC enhances CD11b+Gr1+ myeloid cell immunosuppression capacity by upregulating αKGDC (ketoglutarate dehydrogenase complex) expression, resulting in increased TCA cycle- glutamine anaplerosis causing enhanced oxidative phosphorylation (OXPHOS), increased immunosuppression markers and T cell suppression. Inhibition of TCA-glutamine anaplerosis by CPI-613 decreased OXPHOS and CD11b+Gr1+ immunosuppressive ability resulting in restored anti-tumor T cell response and inhibition of EOC. Targeted metabolomics of CPI-613 treated CD11b+Gr1+ cells showed a profound decrease in TCA metabolite α-ketoglutarate (αKG). Among all TCA metabolites, only αKG supplementation reversed the OXPHOS inhibition, T cell immunosuppression by CPI-613 and increased immunosuppressive markers in ex-vivo conditions. In vivo treatment of αKG alone replicated the ex-vivo effect and enhanced CD11b+Gr1+ myeloid cell OXPHOS and immunosuppressive ability but did not affect survival. In combination with CPI-613, αKG was able to reverse the inhibitory effect of CPI-613 on immunosuppression, OXPHOS and decreased survival. Our study shows that αKG generated by TCA- glutamine anaplerosis is crucial for supporting an immunosuppressive phenotype of CD11b+Gr1+ myeloid cells in EOC, and targeting αKG may enhance anti-tumor immune responses.
Single-cell transcriptomics of colorectal cancer metastases identifies enrichment for a therapeutically targetable population of TREM2+ macrophages in peritoneal metastases.
Authors: Cottam Matthew , Mirza Muhammad , Arner Emily , Hatem Zaid , Shameer Muhammad , Beckermann Kathryn , Idrees Kamran 
Published: November 2024

Abstract
Colorectal cancer (CRC) is recognized as the third most common cancer and the second leading cause of cancer-related mortality globally. The primary driver behind this mortality is metastatic disease, which significantly worsens the prognosis for CRC patients. Over the past decade, there has been a modest improvement of only 2% in the 5-year survival rate for metastatic CRC (mCRC). To improve our understanding of the cellular composition in mCRC tumors, we performed single-cell RNAseq (scRNAseq) on matched primary colorectal tumors, metastases to the lung, liver, and peritoneum, and malignant ascites from 14 patients. Tumor-associated macrophages (TAMs) were found to be one of the most abundant populations across all samples and TAMs from metastases had increased expression of M2-like alternative activation markers relative to primary tumors, suggesting that TAMs in mCRC are immunosuppressive. Gene co-expression analysis identified a signature of lipid handling containing genes linked to lipid transport, such as APOE, FABP5, PLTP, and CD9, and genes coding for the scavenger receptors CD36, MSR1, MARCO, and TREM2. Consistent with transcriptomics, the majority of CD11b+CD68+ TAMs from resected liver and peritoneal metastases had high TREM2 expression by flow cytometry. In a mouse model of peritoneal mCRC, treatment with anti-TREM2 decreased CD11b+F4/80+ TAMs and increased CD8+ effector T cells, suggesting that TREM2 may be an effective target for immunotherapy in mCRC.
Expanding the split-pool combinatorial barcoding toolkit to characterize the effects of aging in mouse TCR diversity.
Authors: Papalexi Efthymia , Hariadi Bryan , Suyama Alexa , Curca Crina , Roco Charles , Rosenberg Alexander 
Published: November 2024

Abstract
We recently released a flexible and high throughput single-cell sequencing method that leverages split-pool combinatorial barcoding to simultaneously profile the whole transcriptome and T cell receptor (TCR) sequences of up to 1 million human T cells from up to 96 samples. This technology is able to recover reproducibly paired TCR sequences in the majority of assayed T cells across different sample types (CAR-Ts, culture activated T cells, etc).
Here, we report on the extension of our method to be able to recover the immune repertoire and gene expression profiles from mouse T cells. We use our assay to characterize TCR diversity changes during the mouse lifecycle. Specifically, we profile hundreds of thousands of mouse spleen-resident T cells at different stages of life. We perform transcriptome-based clustering and demonstrate that this approach identifies all major T cell populations (CD4+, CD8+, Tregs, etc.) while efficiently detecting paired TCR sequences. Furthermore, consistent with previous findings, we show differences in clonotype diversity that correlate with age.
Overall, we present an extension of our TCR technology that allows for the characterization of mouse TCR sequences and showcases its utility in studying the effects of aging in TCR repertoire diversity. We envision our method will help researchers gain additional insights in mouse models of autoimmune and infectious diseases, as well as cancer.
Blocking of NLRP3 inflammasome activity alleviates iron-induced adverse effects in murine models of colitis
Authors: Saha Piu , Yeoh Beng San , Vijay-Kumar Matam 
Published: November 2024

Abstract
One serious extra-intestinal manifestation of Inflammatory Bowel Disease (IBD) is iron deficiency anemia (IDA). The first choice for IDA therapy is oral iron supplementation; yet the rhetoric that IDA can be ‘treated’ with iron is far from accurate, given the high incidence of severe side effects. We herein investigated the extent to which NLRP3 (NOD-like receptor 3) inflammasome could influence iron-induced adverse effects in IBD. Wild-type (WT) and NLRP3-deficient (Nlrp3KO) mice were treated with dextran sodium sulfate (DSS) for 7 days and then oral FeSO4 (Fe2+) was administered for 3 days. Fe2+ augmented colonic inflammation in WT, but not in Nlrp3KO mice. Histological analysis revealed that iron+DSS treated WT colitic mice displayed more inflammation than Nlrp3KO mice. Interestingly, oral administration of β-hydroxybutyrate (BHB, inhibitor of NLRP3) significantly reduced the Fe2+ induced inflammation in WT mice. Next, to evaluate the role of endogenous iron in colitis, we used homeostatic iron regulator protein (HFE)-deficient mice (HfeKO), which were noted to be highly susceptible to IL-10R neutralization-induced colitis. Intriguingly, deficiency of NLRP3 in HfeKO mice (Hfe-Nlrp3-DKO) significantly protected them from IL-10R neutralization-induced colitis. In conclusion, our study demonstrates that excess iron could exacerbate inflammation during IBD and that BHB could be used as a therapeutic to mitigate iron-induced inflammation in IBD.
The Role of Invariant Natural Killer T (iNKT) Cells in Early Responses to Influenza A Virus (IAV)
Authors: Luczak Justyna , Milek Oliwia , Carter Hannah , Alberola-Ila Jose 
Published: November 2024

Abstract
iNKT cells are a CD1d-restricted innate-like lineage of ⍺ßT cells that are prevalent in mucosal tissues, where they influence early immune responses. iNKT cells differentiate in the thymus into—iNKT1, iNKT2, and iNKT17 analogous to Th1, Th2, and Th17 cells. We have shown in ET-2;CD4cre mice, that sustained E protein activity results in changes in iNKT subset composition, with a shift from iNKT1s towards iNKT2/NKT17 cells and other subsets. To understand the physiological relevance of these changes, we tested the response of ET2 mice to IAV. ET2 mice showed less weight loss, reduction in lung-infected areas, decreased neutrophil infiltration, lower activation markers in inflammatory monocytes, reduced levels of CCL2 and interferon-responsive genes in ET2. We observed increased levels of IFNλ in infected ET2 mice vs. elevated IFNα in WT mice 24 hours post-infection. scRNA-seq analysis of sorted iNKT from WT and ET2 mice showed that ET2 profiles are closer to conventional naïve T cells, and that, after infection, their response is marked by overexpression of Ccr7, -Lselectin, IL1R1. WT response is predominantly type 1. Gene Ontology pathway analysis of infected WT show enrichment of cytokine production and immune cell activation pathways, while pathways enriched in infected ET-2 are associated with adhesion and repair. These experiments suggest that early type 1 responses driven by NKT cells during IAV infection can be deleterious, intensifying inflammation, and neutrophilia.
A clonally restricted subset of exhausted CD8+ T cells maintains the capacity to form memory
Authors: Raposo Colin , Hiam-Gálvez Kamir , Satpathy Ansu 
Published: November 2024

Abstract
Chronic stimulation of CD8+ T cells leads them to enter a state of restrained functionality known as exhaustion. Removal of chronic stimulation leads exhausted T cells to take on a memory phenotype that retains an epigenetic imprint of previous chronic stimulation. However, the fate of individual exhausted T cell clones upon antigen removal remains unclear. Our group has recently shown that CD8+ T cell responses to chronic infection are comprised of many T cell clones with unique T cell receptors that each take on unique distributions of fates. To study the impact of antigen clearance on individual exhausted T cell clones, we analyzed T cell repertoires of mice infected with chronic lymphocytic choriomeningitis virus (LCMV) during infection and after peripheral viral clearance. We show that individual LCMV-specific clones have differential capacity to persist past viral clearance and take on clonally and phenotypically distinct cell states. These states include exhausted phenotypes and central memory-like cells that are characterized by minimal epigenetic imprinting of chronic stimulation. Furthermore, chronic memory cells have altered ability to differentiate upon rechallenge, which enables their preferential survival compared to acute memory cells when rechallenged with chronic LCMV. Together, these data illustrate that a subset of clones within the exhausted T cell pool is primed to form memory and protect the host from a secondary infection.
The role of dendritic cell subsets in Invasive Pulmonary Aspergillosis
Authors: Dhruva Pari 
Published: November 2024

Abstract
Aspergillus fumigatus is a ubiquitous mold that causes many lung diseases, the most severe of which is invasive pulmonary aspergillosis (IPA). Innate immunity is paramount for controlling IPA. Here, we examined the role of dendritic cells (DCs). Global depletion of DCs using CD11c-DTR mice results in impaired lung clearance of A. fumigatus, suggesting that one or more of these DC subsets plays a protective role. Unexpectedly however, we found that mice deficient in BATF3 (Batf3-/-), which lack type 1 conventional DCs (cDC1s), cleared A. fumigatus more efficiently than WT control mice at early time points (12 h and 24 h), suggesting that cDC1s play an inhibitory or non-protective role during A. fumigatus lung defense. Mechanistically, Batf3-/- displayed a hyper-type 17 response, which we have previously shown to be critical for elimination of A. fumigatus from the lung. This correlated with differential IL-33 (negative for type 17, lower in Batf3-/-) vs. PGE2 (positive for type 17, higher in Batf3-/-) production, an axis we have reported that regulates type 17 responses. Overall, our data indicates that both protective and non-protective DC subsets are present in the lung during IPA.
M2-polarized macrophages prevent preterm birth and improve neonatal survival and immunity
Authors: Garcia-Flores Valeria , Liu Zhenjie , Romero Roberto , Xu Yi , Miller Derek , Galaz Jose , Winters Andrew , Farias-Jofre Marcelo , Theis Kevin , Gomez-Lopez Nardhy 
Published: November 2024

Abstract
Preterm birth (PTB), commonly preceded by preterm labor, is the leading cause of neonatal morbidity and mortality worldwide. Most cases of preterm labor are associated with sterile intra-amniotic inflammation (SIAI), an inflammatory condition without detectable microorganisms. To date, no successful strategies to treat SIAI have been developed. Herein, we present mechanistic proof that treatment with M2-polarized macrophages (M2 MΦ) can effectively prevent PTB [(HMGB1, n = 28 vs. HMGB1+M2 MΦ, n = 29) (p&lt;0.05)] and neonatal mortality [(HMGB1, n = 20 litters vs. HMGB1+M2 MΦ, n = 14 litters) (p&lt;0.001)] induced by the ultrasound-guided intra-amniotic injection of the alarmin HMGB1 in mice. M2 MΦ halt the premature pathway of labor by infiltrating maternal and fetal compartments, where they inhibit NLRP3 inflammasome activation triggered by HMGB1. Furthermore, M2 MΦ dampen the HMGB1-induced inflammatory response in the amniotic cavity and fetal lung. Notably, neonates exposed to HMGB1 in utero display a reduced capacity to clear bacterial infection and gut microbiome dysbiosis, which are restored by M2 MΦ treatment [(HMGB1, n = 10 vs. HMGB1+ M2 MΦ, n = 10) (p&lt;0.001 and p&lt;0.01, respectively)]. Our findings provide cogent evidence that M2 MΦ can serve as a cellular strategy to mitigate PTB and decrease neonatal mortality.
T cell-specific P2RX7 favors lung parenchymal CD4+ T cell accumulation in response to severe lung infections
Authors: Santiago-Carvalho Igor , Almeida-Santos Gislane , De Gois Macedo Bruna , Barbosa-Bomfim Caio Cesar , Moreira Almeida Fabricio , Cione Marcos Vinicius , Lassounskaia Elena , D'Imperio-Lima Maria Regina , Borges da Silva Henrique 
Published: November 2024

Abstract
In the lung there is a fine line between effective or harmful immune responses. A dysregulated lung inflammatory response can cause severe tissue damage and compromise respiratory physiology. CD4 T cells are key components of the immune response during lung infections and can mediate protection against tuberculosis (TB) or influenza. However, CD4 T cells can also promote lung pathology during these infections, making it unclear how these cells control such discrepant effects. Using mouse models of hypervirulent TB and influenza, we observe that exaggerated accumulation of parenchymal CD4 T cells promotes lung damage. Through adoptive transfer models for CD4-KO mice and antibody-mediated CD4 T cell depletion, we reported that low numbers of lung CD4+ T cells, in contrast, are sufficient to protect against hypervirulent TB. The lung damage caused by TB and influenza leads to increased levels of extracellular ATP (eATP). In both situations, lung CD4 T cell accumulation is mediated by CD4 T cell-specific expression of the eATP receptor P2RX7. P2RX7 upregulation in lung CD4 T cells promotes expression of the chemokine receptor CXCR3, favoring parenchymal CD4 T cell accumulation. Our data were validated using CD4 T cells from mycobacterial-infected patients who have or not polymorphism that confers P2RX7 loss of function. Our findings suggest that direct sensing of lung eATP by CD4 T cells is critical to induce tissue CD4 T cell accumulation and pathology during lung infections.
PD-1 endocytosis unleashes the cytolytic potential of check-point blockade in tumor immunity
Authors: Oroya Andres , Ben Saad Elham , Bachais Meriem , Rudd Christopher 
Published: November 2024

Abstract
PD-1 immune checkpoint blockade (ICB) has revolutionized cancer treatment. Present models indicate that anti-PD-1 operates by preventing PD-1 from binding to its ligand PD-L1. Surprisingly, ICB-mediated internalization of PD-1 and its importance have not been fully explored. Here, we demonstrate that PD-1 internalization is associated with increased cytolytic activity during cancer immunotherapy. Anti-hPD-1 and -mPD-1 antibodies induced internalization of PD-1 generating a PD-1int subset, resistant to further internalization. Moreover, anti-PD-1 downregulation was more effective in CD8+ T cells than CD4+ T cells. ICB also induced PD-1 degradation in a proteosome-dependent manner. Interestingly, Nivolumab outperformed Pembrolizumab with both antibodies exhibiting distinct effects on CD8+ effector and effector memory T-cells. Importantly, PD-1 downregulation was dependent on receptor crosslinking by bivalent but not monovalent antibodies. Consistent with this, B16-PD-L1+ tumor-bearing mice treated with bivalent antibodies showed better anti-tumor response relative to monovalent antibodies. While mono and bivalent blockade increased granzyme B expression, only bivalent antibody induced perforin in CD8+ T-cells. Our findings unveil a mechanism beyond steric blockade and underscore the significance of PD-1 endocytosis in optimizing checkpoint blockade. Targeting PD-1 internalization holds promise for enhancing anti-tumor immunity and improving the efficacy of PD-1 ICB.
Protective effect of recombinant thrombomodulin on chemotherapy-induced intestinal mucosal injury in mice
Authors: Gaowa Arong , Yamaguchi Takanori , Shimaoka Motomu 
Published: November 2024

Abstract
Intestinal mucositis is a common side effect of chemotherapy. Cisplatin is an effective chemotherapeutic agent for various types of cancers. However, cisplatin-induced intestinal mucositis limits the dose of cisplatin and reduces its therapeutic efficacy. In this study, we investigated the protective effects of recombinant thrombomodulin (rTM), which is a potent anti-inflammatory agent, against cisplatin-induced intestinal mucositis and its possible molecular mechanisms. We first evaluated the effects of rTM on intestinal mucositis caused by cisplatin in mice. Disease progression was monitored by analyzing loss of body weight and histological changes in intestinal tissue. We then investigated the effects of rTM on mouse intestinal organoid formation and growth. Gene expression levels were analyzed by quantitative real-time polymerase chain reaction, Western blotting, and flow cytometry analysis. We found that rTM treatment significantly attenuated the loss of body weight, histological damage, and gene expression levels of pro-inflammatory cytokines such as interleukin-6, tumor necrosis factor-a and high-mobility group box-1 in a cisplatin-treated mouse model in vivo. Furthermore, rTM alleviated the inflammatory cytokine production and apoptosis in a cisplatin-treated intestinal epithelial organoid model in vitro. Taken together, rTM suppresses cisplatin-induced intestinal epithelial cell-derived cytokine production and alleviates intestinal mucositis.
Medium-chain inulin enhances systemic immunity and intestinal health by modulating the gut microbiota and metabolome in C57BL/6 mice
Authors: Zhang Guiguo , Lee Yunkyoung , Kim Eunnyoung , Wang Yunpeng , Cui Jiamei , Wang Xiagojun 
Published: November 2024

Abstract
This study investigated the impact of medium-chain inulin on systemic immunity and its mechanisms. Sixty healthy male C57BL/6 mice, three weeks old, were divided into five groups of twelve, housed in three cages each. They were fed a normal diet, with variations including 0%, 1%, 3%, 5%, or 7% medium-chain inulin. The study found that inulin supplementation at 3% or higher reduced serum cholesterol, triglycerides, and LDL levels, while increasing IgG and IgA levels. Inulin also enhanced intestinal health, as indicated by a reduction in crypt depth, and increases in villus height and villus-to-crypt ratio. Moreover, inulin, particularly at 3% or higher, boosted populations of specific gut bacteria like Candidatus_Saccharimonas, Prevotellaceae_UCG-001, Bifidobacterium, Bacteroides, and Dubosiella. It also raised levels of certain metabolites such as stearamide, fatty acid-hydroxy fatty acids (4:0/18:0), L-malate, orotic acid, and bilirubin. Notably, these inulin-induced changes in microbes and metabolites were positively associated with improved immune and intestinal health. Overall, the study concluded that dietary inulin supplementation above 3% enhances systemic immunity and intestinal health, primarily by promoting beneficial gut bacteria and metabolites.
Unveiling the immune dynamics of Neisseria persistent oral colonization: a roadmap for innovative vaccine strategies
Authors: Alles Mario , Gunasena Manuja , Zia Tauqir , D'Mello Adonis , Bhattarai Saroj , Mulhern Will , Terry Luke , Scherger Trenton , Wijeratne Saranga , Singh Sachleen , Wijeratne Asela , Kasturiratna Dhanuja , Tettelin Hervé , Weyand Nathan , Liyanage Namal 
Published: November 2024

Abstract
Commensals shape host physiology and immunity. Neisseria gonorrhoeae (NG), a human pathogen, causes asymptomatic colonization and animal studies on NG for vaccine-design have been unsuccessful. N. musculi (NM), a mouse commensal, shares host-interaction genes with NG and is a surrogate to study NG colonization.
Eight A/J mice were orally inoculated with NM; uninoculated mice served as controls (n=8). Four from each group were euthanized at day 5 and the rest at day 33. Immune signatures and palate transcriptome were compared between inoculated and control mice using Wilcoxon rank-sum test.
Transcriptomics revealed enriched mucosal immunity and inflammation in colonized tissue. Day 5 data suggested reduced colonization resistance (reduced monocytes), while data at day 33 showed enriched adaptive (memory B cells) and immunoregulatory cells (Tregs) in colonized tissue.
At day 5 of colonization, systemic immune response was pro-inflammatory. Splenic NK cells showed higher IL22, suggesting reinforcement of mucosal immunity during colonization. Systemic immune response displayed reduced enrichment of immune signatures at day 33 of colonization suggesting homeostasis. Positive correlations between NM palate colony counts and enriched immune subsets suggest impact of mucosal colonization on immunophenotypes (p&lt;0.05 for all).
This data is crucial for defining transcriptional and immunological endpoints of NM mucosal colonization, aiding in developing vaccine candidates against NG.