bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alcohol abstinence partially restores peripheral mucosal-associated invariant T cells in patients with alcoholic hepatitis
Authors: Li Wei , Lin Edward , Liangpunsakul Suthat , Rane Susimita , Lan Jie , Chalasani Sai , Puri Puneet , Kamath Patrick , Sanyal Arun , Shah Vijay , Katz Barry , Radaeva Svetlana , Crabb David , Chalasani Naga , Yu Qigui 
Published: January 2023

Abstract
Alcoholic hepatitis (AH) develops in a small percentage of heavy drinkers. The adaptive immune system of AH patients is hyper-activated, yet dysregulated and ineffective against infectious diseases. Mucosal-associated invariant T (MAIT) cells are innate-like lymphocytes that are found in liver, intestinal mucosa, and peripheral blood and contribute to protection against infectious diseases. To determine whether MAIT cells were dysregulated in heavy drinkers and the effect of alcohol abstinence on MAIT cell recovery, we compared peripheral MAIT cells between AH patients and heavy drinkers without liver disease (HDC) at baseline and 6- and 12-month followup. At baseline, AH patients had severely reduced frequency of MAIT cells than HDC and healthy donor controls (HC), whereas MAIT cell frequency was not significantly different between HDC and HC. In addition, MAIT cells in AH patients expressed higher levels of the activation markers (CD69, CD38, and HLA-DR) as well as the immune checkpoint inhibitor PD-1. Multiplex immunoassays showed that plasma levels of several cytokines related to MAIT cell activation were elevated in AH patients (IFN-s, IL-7, IL-15, IL-17, IL-18, and IL-23, and TNF-a). In AH patients, the frequency MAIT cells and CD38-expressing MAIT cells correlated with levels of several cytokines and AST. At followup, AH patients had increased MAIT cell frequency and decreased MAIT cell activation with cessation of alcohol. However, abstinent AH patients still had higher levels of CD38-expressing MAIT cells than HDC at 6-month followup.

Conclusion
Blood MAIT cells were severely reduced and were dysregulated in AH patients and alcohol abstinence partially reversed abnormalities in MAIT cell frequency and phenotype.
BCAS2 is a neuron protector to inhibit microgliosis
Authors: CHEN SHOW LI. 
Published: January 2023

Abstract
Breast carcinoma amplified sequence 2(BCAS2) is involved in Prp19/CDC5 Lspliceosome complex for regulation of RNA splicing. Exon array analysis indicated that β-catenin was one of BCAS2-targeted gene. Disruption of Wnt/β-catenin signaling is involved in several neurodegenerative diseases such as Alzheimer’s disease (AD). Current report of other group demonstrated that the RNA expression of BCAS2 is reduced in the microarray analysis of AD patients. Recently, we used the Cre/loxP system driven by CaMKIIα to generate BCAS2 conditional knock out (cKO) in postnatal forebrain, which causes microcephaly-like, dendritic malformation, poor learning and memory phenotypes partly reasons from down-regulation of β-catenin. In this study, the reactive gliosis in cKO mice was extensively measured and compared with WT mice. The selective microgliosis was found in the cornu ammonis1 stratumradiatum (CA1 Rad) and dentate gyrus molecular layer (DG Mo) but did not exhibit astrogliosis in cKO compared with WT mice, which confirmed depletion of BCAS2 in the forebrain caused neural defect. Lithium, an inhibitor of glycogen synthase kinase-3β (GSK-3β). Lithium treatment to cKO mice could improve their spatial learning and memory capability using passive avoidance and Morris water maze; and reduced selective microgliosis in the molecular layer (DG Mo)compared with untreated cKO mice. Taken together, BCAS2 may be a neuron protective factor to inhibit microgliosis.
Evaluation of the pig-tailed macaque (Macaca nemestrina) as a model of human Staphylococcus aureus nasal carriage
Authors: Cole Amy Liese , Cosgrove-Sweeney Yvonne , Lasseter Amanda G. , Gray Justin M. , Beavis Ashley C. , Chong Christine , Hajheidari Safarali V. , Beyene Alex , Patton Dorothy L. , Cole Alexander M. 
Published: January 2023

Abstract
Staphylococcus aureus (SA) nasal carriage is a common condition effecting both healthy and immunocompromised populations, and provides a reservoir for dissemination of potentially infectious strains by casual contact. Factors regulating the onset and duration of nasal SA colonization are mostly unknown, and a human-relevant animal model is needed. Here, we screened 17 pig-tailed macaques (Macaca nemestrina) for SA carriage, and 14 of 17 animals tested positive in the nose at one or both screening sessions (8 weeks apart), while the other three animals were negative in the nose but positive in the pharynx at least once. Similar to humans, SA colonization was densest in the nose, and treatment of the nostrils with mupirocin ointment effectively cleared the nostrils and 6 extra-nasal body sites. Experimental nasal SA colonization was established with 104 CFU/nostril, and both autologous and non-autologous strains survived over 40 days without any apparent adverse effects. A human nasal SA isolate (D579/ST398) was carried in 4 of 6 animals for over three weeks. Nostrils that did eradicate experimentally applied SA exhibited neutrophilic innate immunity marked by elevated nasal IL-1β, IL-8, and MCP-1, and a 10-fold decreased IL-1RA:IL-1β ratio within 7 days post-inoculation, analogous to the human condition. Taken together, pig-tailed macaques represent a physiological model of human SA nasal carriage with utility for testing natural colonization and decolonization mechanisms, and novel classes of anti-SA therapeutics.
Sirt1-mediated metabolic modulation of Aicda, class-switch DNA recombination and somatic hypermutation
Authors: Gan Huoqun , shen Tian , Sanchez Helia , Xu Zhenming , Zan Hong , Casali Paolo 
Published: January 2023

Abstract
Maturation of the antibody response entails Ig somatic hypermutation (SHM) and class switch DNA recombination (CSR). SHM and CSR perfect the antigen-binding activity and diversify the effector functions of antibodies. By showing that histone deacetylase (HDAC) inhibitors selective for class I/II HDACs dampened SHM/CSR by decreasing activation induced cytidine deaminase (AID) expression through upregulation of miRNAs that target Aicda, we have outlined an important role of Zn-dependent HDACs in the modulation of the antibody response. Here we have shown that the NAD+-dependent Class III HDAC Sirt1 also plays an important role in the regulation of SHM and CSR. B cells undergoing CSR/SHM profoundly downregulated Sirt1. Sirt1 deletion in AID-expressing B cells of AicdacreSirt1fl/fl mice, led to increased CSR and SHM in response to NP-CGG, as a result of upregulated AID expression, without altering Prdm1 expression. Sirt1-deficient B cells reduced DNA methylation in the Aicda promoter and hyperacetylated p65, thus activating the canonical NF-kB pathway, which mediates Aicda activation, in absence of any change in DNA methylation of the Prdm1 promoter or histone acetylation of the Aicda or Prdm1 promoter. Increased glucose concentration, which reduced NAD+ Sirt1 co-factor, led to hyperacetylated p65 and Aicda upregulation. Conversely, the NAD+ Sirt1 co-factor or SRT1720 small molecule, a specific Sirt1 activator, dampened Aicda expression and CSR once added to B cells. Thus, our findings outline an important B cell-intrinsic role of Sirt1 in the modulation of the antibody response. Such a role is independent from and may be in addition to the histone deacetylation activity of this Class III HDAC in immune cells other than B lymphocytes.
IL-5 signaling protects mice against mortality from acute lung injury
Authors: Hrusch Cara L. , Mills Kathleen A.M. , Krishack Paulette A. , Decker Donna M. , Blaine Kelly M. , Sperling Anne I. 
Published: January 2023

Abstract
Acute respiratory distress syndrome (ARDS) affects almost 200,000 people in the US each year with a mortality rate of 20–40%. ARDS occurs as a result of acute lung injury (ALI)-induced damage to pulmonary epithelium and/or endothelium. In a bleomycin model of ALI, we previously have shown that ICOS−/− mice, which have defective type-2 immune responses, are more susceptible to death. However, exogenous treatment of these mice with IL-5 reduces lung edema and mortality. We hypothesized that IL-5 signaling is necessary for survival from ALI and examined how mice deficient in IL-5Rα respond during ALI. IL-5Rα−/− mice had significantly increased lung edema at day 5 post-bleomycin challenge compared to WT mice (P=0.014), and had 100% mortality by day 15 (P=0.0002). IL-5Rα−/− mice had severely reduced numbers of lung eosinophils before and after challenge compared to WT mice, suggesting that eosinophils may provide protection from ALI. However, we found no difference in survival between eosinophil-deficient PHIL mice and WT mice (P=0.36). In WT mice, IL-5Rα was constitutively expressed by lung eosinophils and neutrophils. However, bleomycin challenge upregulated the receptor on myeloid cells and epithelial cells, indicating that IL-5 may regulate multiple cell populations during inflammation. Our study demonstrates that IL-5 is a critical mediator of protection against lung injury by maintaining barrier function in the lung. Surprisingly, eosinophils may not be required for the protective effect, and our data suggests that many lung cell types are capable of responding to IL-5 in the context of ALI. Thus, IL-5 may be a novel therapeutic strategy to protect against lung injury following pulmonary infection, sepsis, or trauma.
Protection from lethal Flu infections: lessons from a systemic lupus mouse model
Authors: Abboud Georges , Choi Seung-Chul , Titov Anton , Li Wei , Morel Laurence 
Published: January 2023

Abstract
Patients with systemic lupus erythematosus (SLE) are more susceptible to infections than healthy subjects but it is unknown whether this is due to disease or treatment. Using mice expressing three SLE susceptibility loci (triple congenics hereafter called TC mice) we unexpectedly found that these mice are resistant to an otherwise lethal respiratory Flu PR8 (H1N1) infection. At the naïve state, TC mice had not only more activated plasmacytoid dendritic cells, inflammatory monocytes and natural killer cells but also more activated CD8+ and CD4+ T cells with higher TNF and IFNg-producing capacity than C57BL/6J controls. At the primary effector phase following intranasal Flu PR8 infection, TC mice mounted poor antibody responses but their Flu-specific CD8+ T cell responses were greater effectors at the membrane level (higher frequencies of KLRG1+IL7R− and KLRG1+IL7R+) and at the transcriptional level (higher T-bet expression) than CD8+ T cells from C57BL/6J counterparts. PR8-immune TC mice also developed more functional Flu-specific CD8+ T cell responses than C57BL/6J mice following to a heterosubtypic Flu X-31 (H3N2) challenge. While immunosuppressive treatments of SLE in patients might be responsible of mounting poor anti-microbial immune responses, lessons from this SLE mouse model could be taken to prevent and protect against severe Flu infections.
Toll-like receptor-4-interacting surfactant protein-A-derived peptide reduces inflammation in a mouse model of intratracheal lipopolysaccharide challenge.
Authors: Awasthi Shanjana , Kumar Gaurav , Xie Jun , Beierle Jacob , Awasthi Vibhudutta , Ramani Vijay , Singh Bhupinder , Breshears Melanie , Kosanke Stanley 
Published: January 2023

Abstract
Acute lung injury is characterized by inflammation and respiratory failure. In this work, we evaluated the effect of Toll-like receptor 4 (TLR4)-interacting SPA4 peptide on inflammatory and physiological parameters in cells and in mice against lipopolysaccharide (LPS). Cellular toxicity was assessed using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Binding of SPA4 peptide was studied in cells transiently transfected with a plasmid DNA encoding TLR4. We assessed the changes in the levels of cytokines and chemokines in supernatants of cells treated with SPA4 peptide simultaneously or post-LPS challenge. The extent of lung edema, levels of cytokines and chemokines, and changes in lung histopathology, blood gas and electrolytes, and serum lactate levels, were then determined after SPA4 peptide treatment in a mouse model of acute lung inflammation and injury induced by intratracheal LPS challenge. Our results demonstrate that the SPA4 peptide is not toxic, and binds to TLR4 at the cellular level. A significant reduction was observed in secreted levels of LPS-induced cytokines and chemokines in cell-free supernatants. Correspondingly, the levels of TNF-α, IL-1β, IL-6, MIP-2, KC, and MCP-1 were reduced in bronchoalveolar lavage fluids of SPA4 peptide-treated mice. Moreover, SPA4 peptide treatment attenuated the LPS-induced pulmonary inflammation, lung edema, serum lactate, and blood gas and electrolyte parameters. Together, our results suggest that the SPA4 peptide treatment can help control lung inflammation and injury.
Versatile system for single cell acquisition and analysis
Authors: Ma Zhongcai , Kudo Lili C. , Karsten Stanislav L. 
Published: January 2023

Abstract
Single cell analysis (SCA) has become an essential part of basic and clinical research. A prerequisite to SCA studies is the isolation of individual cells from cell cultures. There are commercially available technologies including laser based systems and cell sorting instruments. However, they are typically complex and expensive making integration within standard lab/clinical sample processing workflows difficult. We have developed a universal platform for rapid acquisition of single cells from cultures and deposition into the single wells for further molecular analysis or clonal expansion. The instrument may also be used for tissue microdissection and measurements of individual cell adhesion. The main working principle is based on the capillary based vacuum pulse assisted technology (CTAS; UP8797644). Developed instrument collects individual cells from any adherent cultures grown in standard cell culture dishes in as small as 15 nl volume. It may be used with a wide range of inverted microscopes, so that the cells of interest can be identified based on morphology, location or fluorescent label. Automatic extraction and deposition algorithms were developed for acquisition of targeted cells and tissue regions of interest. Here, individual cells were collected from human neuroblastoma SH-SY5Y, CHO, and 3T3 cell lines. Collected cells were dispensed immediately into individual wells for clonal expansion. Clonal expansion and trypan blue assay revealed minimal effect on cellular viability (up to 99% when compared to controls). The benefits of the proposed technology include cost-efficiency, simple operation, complete workflow, and compatibility with a wide range of inverted microscopes and standard culture dishes.
Rapid cell fractionation of whole immune organs using a novel microfluidic device
Authors: Pradhan Isha , Cohen Henry , Wong-Noonan Stephanie , Wells Derrick , Lakomy Robert , Tajima Asako , Bai Shi , Rudert William , Boehm Bernhard O. , Trucco Massimo , Hou Han Wei , Fan Yong 
Published: January 2023

Abstract
Separation and isolation of specific cell populations from solid immune organs are essential steps in immunological research. While antibody-labeling based cell sorting techniques, such as FACS, offer the possibility of isolating rare cells from a large background population, the cost and lengthy preparation time associated with these approaches remain burdensome for many researchers. Here, we report a rapid partitioning method that allows the separation of immune cells based on their size and density using a novel, spiral designed, microfluidic device (MFD) (Hou et al., 2016)
Representing less than 0.5% of the total thymic cells, thymic epithelial cells (TECs) are critical for the generation of diverse T cell populations, essential for acquired immunity. Due to their rarity, separating TECs from the large pool of thymocytes is challenging. Using a MFD, we achieved substantial enrichment of TECs (up to 20X), high cell recovery (&gt;2.5X of the traditional density gradient method) and excellent cell viability (&gt;90%) within 7 minutes/thymus. High-purity TEC populations were obtained through further depletion of CD45+ thymic stromal cells using MACS. Thymus organoids reconstructed with TECs can support the development of both CD4+ and CD8+ T cells in vitro, proving the function of the isolated TECs.
In addition, MFD could also be utilized to separate immune cell subtypes from spleen and lymph nodes. Notably, significant enrichment of CDllc+ MHCII+ dendritic cells (~15X) was achieved without RBC lysis and antibody labeling. In conclusion, our data suggest that the MFD partitioning method is efficient and cost-effective for rapid size-based separation of immune cells from primary and secondary immune organs for downstream applications.
A novel high-throughput method for quantification of microbiota distribution at the single cell level using high dynamic range DNA barcoding
Authors: Shiroguchi Katsuyuki , Jin Jianshi , Takeuchi Tadashi , Miyauchi Eiji , Ohno Hiroshi 
Published: January 2023

Abstract
In the bacteria-host interaction, the dynamics of microbiota contributes to the development of many diseases, e.g., infectious diseases, gastrointestinal cancers, autoimmune diseases, etc. The mechanisms behind the dynamics of microbiota remain unknown, and one of them is cell-cell interaction among the bacteria within microbiota. In order to investigate the mechanisms, a method to characterize the microbiota, including identification of species and the cell-number distribution of all species, is required. However, the current techniques measure the distribution of 16S rRNA copies, which is different from the cell-number distribution, since different bacterium has different 16S rRNA copies on its genome. Here we are developing a novel high-throughput bacterial counting/identification method by 16S rRNA sequencing and our developed cell barcoding. To validate this method, we measured a known ten bacterial community, and successfully identified their correct 16S rRNA sequences. This method identifies sequences independently of database and distinguishes single-base difference, so that it can identify unregistered 16S rRNA sequences as well. Based on these identified 16S rRNA sequences, we quantified the cell numbers of each bacterium. The results were consistent with the cell numbers measured under a microscope. Furthermore, we applied this method for studying the murine gut bacterial microbiota, and we found significant changes between the large intestine and the cecum. We also identified unregistered 16S rRNA sequences in both samples. This method offers a high-throughput experimental way that directly counts each bacterium in a bacterial community including unregistered bacteria at the cell level.
Standardized oligo barcode antibody conjugates, and Veri-Cells™ PBMC for multiplex immunophenotyping and CITE-Seq
Authors: Li Cheng-Rui , Yeung Bertrand , Zhao Xinfang , Divekar Anagha , Monell Craig , Yang Xifeng 
Published: January 2023

Abstract
The CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) platform is a recent advance in single cell analysis, which is based on high-throughput single cell sequencing (scSeq) and combines measurements of cellular proteins and transcriptomes. This platform will potentially transform how complex cell populations (lineage differentiation or tumor infiltrating lymphocytes) are studied. Published data indicated that CITE-Seq analysis on cell surface marker expression are comparable to multi-color flow cytometry, but provides superior capacity in multiplexing to the latter. Currently, individual investigators use their choice of oligo bar-codes for different protein markers and there is no available control. This will make comparison of data from different studies difficult in the future. The availability of standardized oligonucleotide bar-code labeled antibodies as well as control cells will enable reliable comparison data from longitudinal studies or among different studies. FlexSeq™ is our new product line, in which monoclonal antibodies are conjugated with unique oligonucleotide bar-codes. We provide standardized bar-coding system and ready to use oligo-antibody conjugates to support CITE-Seq based multiplex immunophenotyping. Veri-Cells™ is our proprietary lyophilized cell product that can be used as a control for detection of cell surface and intracellular flow cytometry. In this study, we validate the application of FlexSeq™ products in CITE-Seq platform, and compare Veri-Cells™ PBMC with freshly isolated PBMC in the assays.
Enhanced cell growth with physiologically relevant media supplements.
Authors: Naser Lisa , Master Alyssa M. 
Published: January 2023

Abstract
Recent advances in genetic engineering have resulted in exponential growth in cell therapy technologies. This has led to a need for corresponding advances in the cell culture media that is used to recover, sustain and expand these important cells. Cell therapy researchers and manufacturers alike, have spent valuable time and money to optimize media formulations to enhance cell proliferation while maintaining functional capabilities of stem cells and immune cells. Proliferation rates and cell robustness often suffer in serum free media (SFM) or chemically defined formulations due to the lack of physiologically relevant protein sources and concentrations. Physiologix™ XF Human Growth Factor Concentrate (hGFC) is a cell culture media supplement that can be used in place of serum supplements with traditional basal media such as RPMI 1640 or DMEM/F12. In this study, hGFC was compared to various serum free media. CD4+ T cells, bone marrow derived mesenchymal stem cells (BM-MSC) and induced pluripotent stem cells (iPSC) were cultured in the presence of hGFC or SFM. All cell types had preferentially higher cell count when grown in the presence of hGFC than in their corresponding SFM. In addition to this, CD4+ T cell function was examined by looking at cytokine profiles, activation markers CD25 and CD69, and exhaustion marker PD-1. Cells showed higher capability for activation in presence of hGFC. They also exhibited greater ability for exhaustion under constant stimulation, which is indicative of a more physiologically relevant response to constant stress. The implications of this data are particularly important for those in cell therapy manufacturing where cell proliferation rate and viability are critical.