Journal: Cell Death & Disease

Article Title: Obesity impairs cardiolipin-dependent mitophagy and therapeutic intercellular mitochondrial transfer ability of mesenchymal stem cells

doi: 10.1038/s41419-023-05810-3

Figure Lengend Snippet: Key resources table.

Article Snippet: 39 , RNeasy Mini Kit (250) , Qiagen , 74106.

Techniques: Recombinant, Control, Staining, Isolation, Enzyme-linked Immunosorbent Assay, Live Dead Assay, TUNEL Assay, ATP Assay, Protease Inhibitor, cDNA Synthesis, Saline, Purification

Journal: STAR Protocols

Article Title: CyTOF protocol for immune monitoring of solid tumors from mouse models

doi: 10.1016/j.xpro.2022.101949

Figure Lengend Snippet: Representative surface staining panel design—Mouse immune panel

Article Snippet: Maxpar® X8 Antibody Labeling Kit, 167Er—4 Rxn , Standard BioTools , 201167A.

Techniques: Staining, Marker

Journal: STAR Protocols

Article Title: CyTOF protocol for immune monitoring of solid tumors from mouse models

doi: 10.1016/j.xpro.2022.101949

Figure Lengend Snippet:

Article Snippet: Maxpar® X8 Antibody Labeling Kit, 167Er—4 Rxn , Standard BioTools , 201167A.

Techniques: Blocking Assay, Purification, Recombinant, Staining, Sterility, Antibody Labeling, Software, Transferring, Microscopy

Journal: Cell reports

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina

doi: 10.1016/j.celrep.2024.114005

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Micro BCA TM Protein Assay Kit , ThermoFisher Scientific , Cat# #23235 RRID: N/A.

Techniques: Control, Affinity Purification, Recombinant, Bicinchoninic Acid Protein Assay, Western Blot, Electron Microscopy, RNAscope, Multiplex Assay, Mass Spectrometry, Mutagenesis, Software, Microscopy

Journal: Nature neuroscience

Article Title: Control of tumor-associated macrophages and T cells in glioblastoma via AHR and CD39

doi: 10.1038/s41593-019-0370-y

Figure Lengend Snippet: a, Left: representative immunofluorescence images of tissue array from human gliomas stained for TMEM119 (red), CD68 (green), CD39 (cyan) and nuclei (blue). Scale bars, 20 μm. Right: quantification of the total number of CD39+ CD68+ TMEM119Neg cells in 33 glioma samples classified as grade 1 (n = 2), grade 2 (n = 14), grade 3 (n = 8) or grade 4 (n = 9). Kruskal–Wallis test. b, Flow cytometry analysis of CD39 expression in peripheral infiltrated macrophages in TAMs (LinNeg CD11b+ CD45Hi) gated from WT and AHRLysM mice 17 days after GL261 cell implantation (n = 3 independent mice). Representative histogram shown on the left and quantification analysis on the right. c, AHR recruitment to the Entpd1 promoter as assessed by ChIP in KYN- or TCM-stimulated BMDMs in the presence or absence of an AHR inhibitor (n = 3 technical replicates). d, Relative expression of luciferase activity in HEK293 cells transfected with a luciferase reporter driven by the ENTPD1 promoter alone, or with a construct coding for AHR, and stimulated TCM for 24 h. RPMI condition was the reference sample (n = 3 technical replicates). e, Representative images from intracranial tumors in WT and CD39LysM mice 21 days after GL261-luciferase cell implantation (n = 4 independent mice). f, Survival curve analysis of WT and CD39LysM mice implanted intracranially with GL261-luciferase cells (n = 8 independent mice). g,h, Total number of TILs (CD3+ CD8+) (g) and percentage of IFN-γ+ cells in TILs (h) gated from WT and CD39LysM mice 15 days after GL261-luciferase cell implantation (n = 3 independent mice). i–k, Nanostring analysis of sorted CD8+ TILs from WT and CD39LysM mice 15 days after GL261-luciferase cell implantation (pool of 5 mice per group). Heatmap of gene expression for all genes (i) and of T cell dysfunction-related genes (j). k, Ratio of the expression of genes related to CD8+ T cell dysfunction in WT and CD39LysM mice. l–n, Naive CD8+ T cells purified using beads activated with anti-CD3 and anti-CD28 monoclonal antibodies in the presence or absence of adenosine for 48 h (n = 3 technical replicates for all analyses). Expression levels of T cell effector and dysfunction genes were analyzed by qPCR (l), frequency of IFN-γ+ cells in CD8+ T cells by FACS (m) and cytokines production by ELISA (n). Data in b–h and l–n are representative of two independent experiments; similar results were obtained. Data in a–e, g, h, l–n are shown as mean ± s.e.m. P values were determined by two-sided Student’s t-tests (b, e, g, h, l–n) or one-way ANOVA (a, c and d), and survival analysis was performed using a Kaplan–Meier plot using a log-rank (Mantel–Cox) test (f).

Article Snippet: The following primary antibodies were used in this study: mouse anti-L-KYN (1:100; no. IS003 clone 3D4-F2, ImmuSmol); goat anti-CD14 (1:100; no. LS-B3012–50, LifeSpan Biosciences); rabbit anti-TMEM119 (1:500; no. ab185333, Abcam); mouse anti-CD39 (1:100; no. 328202, Biolegend); goat anti-AHR (1:100; no. ab186070, Abcam); mouse anti-AHR (1:100; no. ab2769, Abcam); mouse anti-CD68 (1:100; no. ab955, Abcam); rabbit anti-CD8 (0.175 μg ml −1 ; no. 790–4460, Ventana Labs); rabbit anti-CD4 (0.5 μg ml −1 ; no. 790–4423, Ventana Labs); and rat anti-CD3 (1.2 μg ml −1 ; no. MCA1477, Bio-Rad).

Techniques: Immunofluorescence, Staining, Flow Cytometry, Expressing, Luciferase, Activity Assay, Transfection, Construct, Purification, Enzyme-linked Immunosorbent Assay

Journal: Frontiers in Immunology

Article Title: Allergic T H 2 Response Governed by B-Cell Lymphoma 6 Function in Naturally Occurring Memory Phenotype CD4 + T Cells

doi: 10.3389/fimmu.2018.00750

Figure Lengend Snippet: Role of Bcl6-mediated MPT cell functions in NAT H 2 differentiation in an allergic murine model. [ (A) top] Mixture of purified KJ1-26 − MPT cells ( Bcl6 -WT or Bcl6 -KO) and KJ1-26 + WT naïve CD4 + T cells were transferred into BALB/c nu/nu mice intravenously (day 0). These mice were immunized with alum-conjugated OVA and then intratracheally challenged with OVA. [ (A) bottom] Absolute cell numbers of Neu, Eos, AM, and Lym in BALF, (B) hematoxylin and eosin-stained, formalin-fixed lung sections (magnification: 200×), and (C) T H 2 cytokine levels in the BALF of recipient mice 48 h after the last OVA challenge. (D) Relative Il4, Il5 , and Il13 expression mRNA in splenic KJ1-26 + T cells restimulated with anti-CD3 monoclonal antibodies 5 days after the last challenge. (E) OVA-specific IgE antibody titers in sera from each recipient of Bcl6 -WT NAT H 2 cells, plus MPT H 2 cells transferred from Bcl6 -TG, Bcl6 -WT, or Bcl6 -KO mice 2 days after the last challenge. All results are representative of four independent experiments with similar outcomes. Data are presented as the mean ± SEM ( n = 5–7). * P < 0.05, ** P < 0.01, comparison between two groups is indicated. AM, alveolar macrophages; BALF, bronchoalveolar lavage fluid; Bcl6, B-cell lymphoma 6; Eos, eosinophils; KJ + , KJ1-26-positive; KO, knockout; Lym, lymphocytes; MPT cell, memory phenotype CD4 + T cell; MPT H 2 cell, MPT cell-derived T H 2 cell; NAT H 2 cell; naïve CD4 + T cell-derived T H 2 cell; Neu, neutrophils; NS, not significant; OVA, ovalbumin; TG, transgenic; WT, wild-type.

Article Snippet: IgE anti-OVA Abs were detected using a mouse anti-OVA IgE Antibody Assay Kit (Chondrex, Redmond, WA, USA).

Techniques: Purification, Staining, Expressing, Knock-Out, Derivative Assay, Transgenic Assay

Journal: Frontiers in Immunology

Article Title: Circulating and Salivary Antibodies to Fusobacterium nucleatum Are Associated With Cystic Pancreatic Neoplasm Malignancy

doi: 10.3389/fimmu.2020.02003

Figure Lengend Snippet: Circulating plasma antibody reactivity to oral commensals identified in pancreatic tumor lesions. Plasma diluent (1/300) from patients with histology verified pancreas tissues: IPMN with low grade dysplasia (LGD-IPMN), IPMN with high grade dysplasia or with invasive cancer (HGD-IPMN + Cancer), or benign tumors/non-IPMN (Control) was tested in duplicates in ELISA plates coated with indicated antigen in (A–F) (bacteria: 5 × 10E7 CFU/ml, peptide 10 μg/mL). The total plasma IgG level is shown in (G) . Internal control Mean OD absorbance values of duplicates are shown. Statistical analysis was performed using the Kolmogorov–Smirnov test, ** p < 0.01, *** p < 0.001, and **** p < 0.0001.

Article Snippet: Total levels of salivary IgA and plasma IgG antibodies were measured using Human IgA/IgG ELISA Kit (Novus Biologicals, Colorado, United States) according to the manufacturer’s instructions.

Techniques: Clinical Proteomics, Control, Enzyme-linked Immunosorbent Assay, Bacteria

Journal: Frontiers in Immunology

Article Title: Circulating and Salivary Antibodies to Fusobacterium nucleatum Are Associated With Cystic Pancreatic Neoplasm Malignancy

doi: 10.3389/fimmu.2020.02003

Figure Lengend Snippet: Salivary IgA antibody reactivity to oral commensals quantified by ELISA using saliva diluent (1/16) from indicated patient group. Salivary IgA reactivity to F. nucleatum , the Fap2 mimotope, and S. gordonii (A,B,F) in HG-IPMN/Cancer patients is significantly increased compared to other groups. The differences in antibody levels against bacterial antigens of G. adiacens, S. anginosus , and E. coli (C,D,E) were insignificant between groups. Total plasma IgA level did not differ between the groups (G) . Statistical analysis was performed using the Kolmogorov–Smirnov test, * p < 0.05 and ** p < 0.01.

Article Snippet: Total levels of salivary IgA and plasma IgG antibodies were measured using Human IgA/IgG ELISA Kit (Novus Biologicals, Colorado, United States) according to the manufacturer’s instructions.

Techniques: Enzyme-linked Immunosorbent Assay, Clinical Proteomics

Journal: Frontiers in Immunology

Article Title: Circulating and Salivary Antibodies to Fusobacterium nucleatum Are Associated With Cystic Pancreatic Neoplasm Malignancy

doi: 10.3389/fimmu.2020.02003

Figure Lengend Snippet: Correlation between circulating plasma (A) or salivary (B) antibody reactivity to F. nucleatum and Fap2 mimotope, or between circulating plasma antibody and salivary antibodies to either of antigen (C,D) . Competitive ELISA (E) with saliva samples with or without antigen pre-absorption as indicated for 2 h, then subjected to Fap2 mimotope ELISA test. Statistical analysis was performed using two-tailed Pearson correlation test and Wilcoxon test for two related samples. ** p < 0.01, ns = not significant.

Article Snippet: Total levels of salivary IgA and plasma IgG antibodies were measured using Human IgA/IgG ELISA Kit (Novus Biologicals, Colorado, United States) according to the manufacturer’s instructions.

Techniques: Clinical Proteomics, Competitive ELISA, Enzyme-linked Immunosorbent Assay, Two Tailed Test