bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic analysis of Paired Nasal and Bronchial brushes in Cystic Fibrosis Patients
Authors: Erb Carla J , Chen Kong 
Published: January 2023

Abstract
Cystic Fibrosis is a genetic disorder affecting approximately 30,000 people in the United States. CF mainly affects the lungs and digestive track, leaving individuals with CF more susceptible to lung infections. Transcriptomic analysis of bronchial brushing can be used to identify gene signatures of inflammatory lung diseases such as asthma and CF. However, due to the invasiveness of this technique, the application is limited in pediatric patients. We sought to determine whether nasal brushes could be used as an alternative for transcriptomic analysis of the airway by determination of the similarities and differences in nasal and bronchial gene expression, and whether there is a correlation between nasal transcriptomes and their bronchial counterparts. To address this, we compared five pairs of Nasal and Bronchial Brushes obtained from pediatric CF patients.
The initial principal component analysis (PCA) analysis showed distinct clustering of the bronchial and nasal data. A Pearson correlation test was run on each pair of nasal and bronchial data sets for all genes and revealed both weak and strong correlations with correlation coefficient value ranging from 0.244 to 0.872. To visualize the correlation of CF specific genes, we generatedheatmaps of a few subsets of genes chosen from published literature including top differentially expressed genes in CF vs non-CF. Our finding suggested that patients with overall higher correlation coefficient tend to have better correlations in top genes down-regulated in CF versus non-CF bronchial epithelium. However, further analysis and data set collection might be necessary due to the heterogeneous nature of these samples.
Human G-CSF knockin NOG mice support the differentiation of human neutrophils and recapitulate an emergency granulopoiesis after bacterial infection
Authors: Ito Ryoji , Katano Ikumi , Takahashi Takeshi , Goto Motohito , Takahashi Riichi , Ito Mamoru 
Published: January 2023

Abstract
Humanized mice, in which the human hematopoietic system is reconstituted in immunodeficient mice, are a useful animal model to study human hematology and immunology. Although human T or B lymphocytes significantly differentiated in human hematopoietic stem cells (HSC)-transferred humanized mice, myeloid lineage cells, especially granulocytes, do not fully develop in them. In this study, we generated a novel NOG mouse strain, human G-CSF knockin (KI) mouse, to reconstitute mature human neutrophils in their circulation. We constructed the KI vector that the human G-CSF gene is driven by CMV promoter and targeted murine G-CSF receptor locus to exclude the cross reaction to murine G-CSF receptor. Severe murine neutropenia was observed in hG-CSF KI mice due to the dysfunction of murine G-CSF receptor, and the human G-CSF cytokine was extremely produced in their serum. To analyze human hematopoiesis, we transferred human HSC into x-ray irradiated hG-CSF KI mice. During weeks 4–12 of transplantation, human neutrophils and monocytes were significantly developed in hG-CSF KI mice compared to conventional NOG mice. An emergency granulopoiesis was recapitulated in them, since human neutrophils were highly mobilized into PB after zymosan treatment or E. coli infection. In ex-vivo experiments, neutrophils produced ROS after LPS or PMA stimulation, suggesting these neutrophils are functionally matured. This strain is the first humanized mouse that mature human neutrophils developed in PB and is useful to study innate host defense against bacterial infections.
Simultaneous mRNA, protein, and immune-repertoire profiling of thousands of single cells
Authors: Chang Christina , Nakamoto Margaret , Lai Janice , Siddique Imteaz , Mortimer Stefanie 
Published: January 2023

Abstract
High-throughput single cell RNA-seq (scRNA-seq) has transformed our understanding of heterogenous immune populations. Advances in scRNA-seq, such as oligo-conjugated antibody technologies that enable protein expression profiling alongside mRNA, are expanding the range of molecules that can be profiled at the single cell level. Although sequencing the T-cell and B-cell immune repertoire can provide crucial insights into the complexities of the adaptive immune system, thus advancing discoveries in immunology and immune-oncology, the ability to extract this information from single cells requires new technology to profile regions of the mRNA missed by conventional 3′ scRNA-seq. Here we demonstrate a novel approach using the BD Rhapsody™ system to extract immune-repertoire information in addition to gene-expression information from the same cells. In a single workflow, we profiled a panel of 400 mRNA targets and 40 protein markers as well as the CDR3 region of T- and B-cell receptors in thousands of human PBMCs. After using the mRNA and protein information to robustly annotate different lymphocyte populations, we examined the T- and B-cell repertoires for differences in their clonal diversity. We were able to identify clonally expanded T cells and B cells and examine how their gene-expression profiles differ from that of non-expanded cells. This study demonstrates the power of combining mRNA, protein, and immune repertoire analysis at the single cell level to answer complex and important biological and clinical questions.
For Research Use Only. Not for use in diagnostic or therapeutic procedures.
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Disruption of TOX transcription factors enhances CAR T cells function in solid tumors
Authors: Seo Hyungseok , Chen Joyce , Avalos Edahi Gonzalez , Castruita Daniela Samaniego , Moyado Issac Lopez , Wu Cheng-Jang , Das Arundhoti , Lu Li-Fan , Bhandoola Avinash , Rao Anjana 
Published: January 2023

Abstract
T cells expressing chimeric antigen receptors (CARs) have shown impressive therapeutic efficacy against leukemias and lymphomas, but have not been as effective against solid tumors because chronic stimulation with tumor antigens causes them to enter a hyporesponsive (“exhausted” or “dysfunctional”) state. Here we show that the high-mobility group (HMG)-box transcription factors TOX and TOX2 are highly expressed in CAR-expressing exhausted (PD-1highTim3high) CD8+ tumor-infiltrating lymphocytes (TILs). CAR TILs deficient in both TOX and TOX2 (TOX DKO) suppressed tumor growth and prolonged survival of tumor-bearing mice, compared to wildtype (WT), TOX-deficient or TOX2-deficient CAR TILs; they also showed increased effector function with increased TCF1 expression and decreased expression of the inhibitory receptors PD-1, LAG3 and CD160. Like NR4A transcription factors, TOX and TOX2 are critical for the transcriptional program of hyporesponsiveness downstream of NFAT. Disruption of TOX expression or activity could be a promising strategy for cancer immunotherapy.
Inflammasome Signaling Mediates Myeloid Immunosuppression within the Tumor Microenvironment
Authors: Lang Cara N , Kim Young 
Published: January 2023

Abstract
Myeloid Derived Suppressor Cells (MDSCs) are important mediators of immune evasion in cancer and have been associated with worse overall survival and progression free survival in patients with multiple types of solid tumors. While MDSCs were initially characterized to inhibit T cells and NK cells through the upregulation of iNOS and arginase-1 and production of Nitric Oxide, reactive oxygen species, TGF-β, and IL-10, there is now growing literature that MDSCs can promote cancer progression through other mechanisms. Here we propose that myeloid-intrinsic inflammasome activation plays a direct role in tumor progression. To investigate this, in vitro tumor proliferation studies were performed and show that CD11b+, Ly6C+ monocytic MDSCs isolated from tumor bearing mice promote inflammasome-dependent proliferation of multiple murine tumor cell lines. Mass cytometry and RNA sequencing data of human Head & Neck Squamous Cell Carcinoma patient samples indicate that the total myeloid immune infiltrate can differ greatly among patients. In cases where the T cell immune infiltrate is low, we propose that the infiltrating myeloid cells are utilizing inflammasome signaling to promote tumor progression. These results provide a greater understanding of the role of inflammasome signaling in MDSC-mediated immunosuppression within the tumor microenvironment which will allow for a better understanding of the function of MDSCs in cancer and identification of potential targetable components of MDSC signaling for cancer therapeutics.
The fate of leukemia-specific CD8+ T cell clones is dictated by antigen specificity and the mechanism of cognate antigen presentation
Authors: Chen Xiufen , Flood Blake , MacNabb Brendan , Blazar Bruce R. , Kline Justin 
Published: January 2023

Abstract
We previously demonstrated that high-affinity leukemia-specific CD8+ T cells are deleted in leukemia-bearing hosts in a manner that depends on cross-presentation of the antigen by splenic Batf3-lineage dendritic cells. Here, we generated a T cell receptor transgenic mouse strain (Tg101) that expresses TCR-α and -β chains from a CD8+ T cell clone specific for a native H-2Kb-restricted antigen on C1498 leukemia cells. In naïve mice, Tg101 T cells demonstrate no evidence of self-reactivity, arguing that the Tg101 antigen is leukemia-specific. In leukemia-bearing mice, high-affinity 2C CD8+ T cells specific for the H-2Kb-restricted model antigen, SIYRYYGL, encounter antigen rapidly (day 3–4) via its cross-presentation by splenic CD8a+ DCs, proliferate briefly, and are largely deleted by day 12. Conversely, antigen encounter by Tg101 CD8+ T cells in mice with leukemia is delayed (day 8–10), and primarily occurs in the liver - a prominent site of leukemia progression. Subsequently, Tg101 T cells expand, upregulate expression of co-inhibitory receptors, including PD-1, LAG-3, TIM-3 and TIGIT, and produce effector cytokines poorly, consistent with the acquisition of a dysfunctional state. Surprisingly, in vivo antigen encounter by Tg101 T cells occurs independently of CD11c+ cells, indicating that the Tg101 antigen is poorly cross-presented. Rather, the antigen is directly presented to Tg101 T cells by C1498 cells. Collectively, our data reveal that CD8+ T cell tolerance is effectively generated in leukemia-bearing animals. However, the nature of the leukemia antigen and the context in which it is presented are critical factors in dictating the underlying mechanism of tolerance that ensues. A search for the Tg101 antigen is ongoing.
Influence of immune-checkpoint inhibitor and HLA-G in patients with Cervical Cancer
Authors: CRISPIM-FREITAS JANAINA C. O. , Morais Rayanne S. P. , Oliveira Valéria S. , Sadissou Ibrahim , Palomino Gustavo M. , Cobucci Ricardo N. O. , Lira George A. , Carvalho Kleyton T. C. , Silva Emanuelly B. O. , Silva Norma L. , Donadi Eduardo A. 
Published: January 2023

Abstract
A better understanding of the role of Immune checkpoint inhibitors (ICI) and immunoregulatory genes HLA-G is essential for the development of immunotherapeutic strategies in cancer. This study aims to evaluate the influence of CTLA-4, PD-1 and polymorphisms of HLA-G and soluble HLA-G (sHLA-G) in patients with cervical cancer (CC), different degrees of Cervical Intraepithelial Neoplasia (CIN), and healthy control (HC). One hundred and seventy-four (174) non-pregnant Brazilian women, sexually active, older than 18 years, were evaluated. These patients were stratified according to the results of the anatomopathological examination in: CC group n=24, Low-grade squamous intraepithelial lesions (LSIL) n=66, High-grade squamous intraepithelial lesions (HSIL) n=84. HC group consisted of 47 women without cytological and/or colposcopic abnormalities detected. The peripheral blood of these patients was collected for analysis of CTLA-4, PD-1 and HLA-G polymorphisms using real-time PCR. The analysis indicated a significantly higher 14bpDel allele frequency in CC when compared to HC group (P=0.030, OR=1.71, 95%CI 1.01–2.74). Moreover, the 14bpDel/Del genotype frequency was also significantly higher in patients with CC group (P = 0.035, OR=2.23, 95%CI 1.05–4.97). Qualitative analysis revealed that the production of sHLA-G is detectable in 52.03% (n=77) of all patients groups and 34.29 %(n=12) in HC groups. This analysis revealed a trend of significance (P= 0.063; OR=2.08, 95%CI=0.96–4.48) in CC group. The polymorphisms of CTLA-4 and 14 bp HLA-G are associated with a significantly increased risk of CC. HLA-G 14bp Del/Del polymorphism, and the serum sHLA-G can act as a promising biomarker for might be a genetic risk factor for CC.
Patient-derived, vaccine-elicited MUC1 antibodies mediate immune effector functions against cancer cells
Authors: Miller Michelle L , Lohmueller Jason , Ricci Eric , Lu William , Finn Olivera J 
Published: January 2023

Abstract
Cancer cells undergo changes that the immune system recognizes, and this can be leveraged for therapy. Antibodies specific for such changes can exert anti-tumor effects via multiple mechanisms, including blocking oncogenic signaling, serving as Trojan horses carrying toxic compounds, coordinating innate immune engagement for cytotoxicity through cellular and non-cellular means, and promoting antigen uptake to jumpstart adaptive immunity for durable protection. We analyzed 12 high-affinity fully human IgG1 monoclonal antibodies that recognize a tumor-specific hypoglycosylated form of Mucin-1 (MUC1) that is overexpressed in &gt;80% of all cancers. These antibodies are unique and different from humanized murine anti-MUC1 mAbs, having undergone selection and affinity maturation in individuals receiving the MUC1-100mer peptide vaccine (Lohmueller et al. Sci. Rep. 2016). Importantly, in all vaccinated individuals that generated antibodies to MUC1, there have been no adverse events in 8 years, increasing the likelihood that as therapeutic agents they would be safe. To test their immune effector capacity, we used these human anti-MUC1 antibodies in in vitro antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP) and complement-dependent cytotoxicity (CDC) assays with different huMUC1-expressing cell lines, immune effector cells and serum. Several of the anti-MUC1 antibodies can mediate ADCC by NK cells and ADCP by macrophages, although there was very little or no CDC function. Notably, unlike in published studies on rituximab and alemtuzumab, the amount of antibody binding to cancer cells (MUC1) did not always correlate with increased effector function.
Bortezomib improves antitumor CD8+ T cell function by modulating miR-155 and its targets
Authors: Renrick Ariana N , Thounaojam Menaka , Chaudhuri Evan , Dash Chandravanu , Shanker Anil 
Published: January 2023

Abstract
The immunosuppressive tumor microenvironment dampens host antitumor immunity by multiple mechanisms including interfering with various cell signaling pathways that aid in the differentiation and function of immune cells. We have taken an immunotherapeutic approach in order to strengthen antitumor immunity in mice bearing solid tumors, specifically breast tumors. In doing so, we observed that treatment with bortezomib, an FDA-approved proteasome inhibitor, has the ability to increase CD8+T lymphocyte IFNγ secretion and expression of effector molecules, perforin, granzyme-B and the T-box transcription factor eomesodermin. In order to understand the molecular mechanism(s) of how bortezomib works to improve antitumor immunity we sought to explore its effects on miRNA expression as well as function. We found that treatment of wild-type or tumor-bearing BALB/c mice with bortezomib modulated the expression of various miRNAs in CD8+T cells. From miRNA array data, we identified miR-155 as one prominent modulator of antitumor CD8+T cell immune functions. miR-155 has been accredited to controlling CD8+T cell responses by regulating interferon signaling in viral infections and cancer. We are currently elucidating the mechanisms of bortezomib-mediated effects on miR-155 and its targets, such as suppressor of cytokine signaling 1 (SOCS1) and inositol polyphosphate-5-phosphatase (SHIP1) that are associated with T cell function. These data provide novel insights on using bortezomib not only as an agent to sensitize tumors to cell death, but also to provide lymphocyte-stimulatory effects that could overcome immunosuppressive actions of tumor on antitumor T cell function.
Getting in the groove: Editing of MHC-I antigen repertoires by molecular chaperones is governed by a network of protein dynamics
Authors: Sgourakis Nikolaos , McShan Andrew , Natarajan Kannan , Jiang Jiansheng , Park Jihye , Overall Sarah , Toor Jugmohit S , Kumirov Vlad , Flores-Solis David , Badstubner Mareike , Kovrigin Evgenii L , Bagshaw Clive R , Pallesen Jesper , Procko Erik , Margulies David H 
Published: January 2023

Abstract
Molecular chaperones TAPBPR (TAP-binding protein related) and tapasin associate with class-I major histocompatibility complex (MHC-I) molecules to promote optimization (editing) of peptide cargo. Using solution NMR, we investigate the molecular mechanism of peptide exchange performed by the 90 kDa chaperone protein complex. We identify TAPBPR-induced conformational changes on conserved MHC-I surfaces, consistent with our independently determined X-ray structure of the empty complex. Conformational dynamics present in the empty MHC-I are stabilized by TAPBPR in a peptide-deficient complex, and become progressively dampened with increasing peptide occupancy. Incoming peptides are recognized by the chaperoned groove according to the global stability of the final pMHC-I product, and anneal in a native-like conformation. Our results demonstrate an inverse relationship between MHC-I occupancy by peptide and the affinity of TAPBPR for such pMHC-I molecules, where the lifetime of transiently bound peptides controls the dynamic regulation of a conformational switch, located near the TAPBPR binding site, which triggers TAPBPR release. We further discuss the role of protein dynamics in shaping chaperone specificity towards different human and murine class-I MHC allotypes, and present the high-resolution cryoEM structure of a human A*02/TAPBPR complex with novel insights into the antigen editing mechanism. These results suggest a similar mechanism for the editing function of tapasin in the peptide-loading complex, and provide a molecular blueprint for the design of novel chaperones with tailored antigen editing functions.
The gut microbiota from lupus-prone B6. Sle1.Sle2.Sle3 (TC) induces inflammation via a mechanism other than bacterial translocation
Authors: Brown Josephine Michelle , Choi Seung-Chul , Morel Laurence 
Published: January 2023

Abstract
The lupus-prone microbiota from TC mice induces autoimmunity when transferred to germ-free B6 mice and broad-spectrum antibiotic treatment attenuates autoimmunity in TC mice, demonstrating a microbiota involvement in inflammation. Aged TC mice show colon inflammation relative to B6 controls Fecal blood was detected in approximately 30% of aged TC mice tested, whereas B6 mice were negative. Based on these findings, we sought to understand if compromised barrier integrity could account for the proinflammatory nature of the TC microbiota. Serum endotoxin and intestinal tight junction protein expression were similar between TC and B6 controls, and serum FITC levels were lower in TC mice following FITC-dextran gavage. Colony growth was found in about 30% of aged TC liver and mesenteric lymph node homogenates, but not in the tissues of pre-autoimmune TC mice. The TC bacterial colonies were identified as Staphylococcus xylosus, a non-pathogenic commensal. These findings suggest that TC mice do not have a compromised intestinal barrier, and that the bacterial translocation that occurs in a minority of TC mice only after the onset of autoimmunity is a consequence, rather than a cause of autoimmunity. Therefore, the inflammatory nature of the TC microbiota is likely related to immune activation starting in the gut itself through the production of specific metabolites.
Type II Cytokines in the Thymic Microenvironment Influence T cell Negative Selection in Type One Diabetes
Authors: Cattin-Roy Alexis N , Ukah Tobechukwu Kenneth , Zaghouani Habib 
Published: January 2023

Abstract
From an autoimmunity perspective type II cytokines, such as IL-4 and IL-13, are viewed as anti-inflammatory because of their ability to foster peripheral tolerance. This report provides evidence that credits these cytokines with yet another attribute that pertains to central T cell tolerance. Specifically, a subset of early thymic progenitors (ETPs) which expresses the IL-4Rα/IL-13Rα1 heteroreceptor (HR) adopts a pattern of lineage commitment with guidance from IL-4/IL-13 in the thymic microenvironment. Indeed, IL-4 and IL-13 direct HR+ ETPs towards the myeloid lineage by inhibiting their T cell potential and promoting maturation towards dendritic cells (DCs). Given that DCs can contribute to negative selection of self-reactive T cells, IL-4 and IL-13 in the microenvironment would impact the development of autoreactive T cells in two ways: diminished T cell generation from ETPs and elimination of self-reactive lymphocytes by DC-driven negative selection. This postulate is supported by findings indicating that in the C57BL/6 mouse strain, where IL-4 and IL-13 are readily available in the thymic microenvironment, HR+ ETPs give rise to myeloid cells that contribute to negative T cell selection leading to resistance against experimental allergic encephalomyelitis (EAE). In contrast, in NOD mice IL-4 and IL-13 availability is limited and HR+ETPs give rise to T cells; perhaps leading to diminished negative selection of T cells with diabetogenic potential and higher susceptibility to type 1 diabetes (T1D). These previously unrecognized observations extend the function of type II cytokines to central tolerance and offer a possible link of the environment to the development of autoimmunity as envisioned by hygiene hypothesis theories.
Involvement of CCR5 in bone resorption associated to apical periodontitis
Authors: De Rossi Andiara , Alves Sandra Yasuyo Fukada , Nelson-Filho Paulo , Silva Raquel Assed B , Silva Lea Assed Bezerra 
Published: January 2023

Abstract
The involvement of Cysteine-cysteine chemokine receptor 5 (CCR5) in the protection or stimulation of bone resorption associated with apical periodontitis that occur as consequence of endodontic infection has not yet been elucidated. The present study proposes to characterize the involvement of CCR5 in the genesis and progression of apical periodontitis, using animals deficient for this molecule. Experimental induction of periapical lesions was performed in CCR5 −/− (knockout) or wild type transgenic mice through the coronary opening of the lower 1st molars and exposure of the root canals to the oral environment for their contamination. After the death of the animals (at 0, 7, 21 and 42 days), the samples obtained in different experimental periods were evaluated by conventional microscopy and fluorescence (morphometry and characterization of the lesions), histoenzimology (TRAP for osteoclasts), immunohistochemistry, immunofluorescence and real-time PCR, to characterize the inflammatory cell in the presence or absence of CCR5 (neutrophils, macrophages and CD4 and CD8 lymphocytes), expression of cytokines (IL-1±, TNF-±, IFN-³, IL 4, IL-6 and IL-10), their ligands (RANTES and MIP- 1±) and factors involved in bone formation and resorption (RUNX2, NFATc1, ALP, RANK, RANKL, OPG and cathepsin K) and infection of tissues. Our results shows that CCR5 knockout mice developed more extense and severe inflammation and alveolar bone destruction at periapical region at 21 and 42 days after endodontic infection. It was concluded that CCR5 deficiency results in development of more severe periapical alveolar bone resorption associated to endodontic infection.