Journal: Nature Communications

Article Title: IFN-β is a macrophage-derived effector cytokine facilitating the resolution of bacterial inflammation

doi: 10.1038/s41467-019-10903-9

Figure Lengend Snippet: Non-phagocytic resolution phase macrophages express IFN-β. a , b Male mice were injected intraperitoneally with zymosan A (1 mg/mouse) followed by an injection of PKH2-PCL at 62 h. After 4 h, the peritoneal cells were recovered and immuno-stained for F4/80 and CD11b. Then, F4/80 + macrophages were sorted based on the extent of PKH2-PCL acquisition (PKH2 + /− populations; >98% purity) using the FACSAria III sorter (illustrated in ( a ). The collected cells were immediately used for RNA extraction (with RNA integrity value above 7.5), and a gene expression microarray analysis was performed using Illumina hiSeq 2500. Differential gene expression analysis and gene ontology (GO) enrichment were performed for genes that were significantly upregulated ( b , left panel) or downregulated ( b , right panel) in non-phagocytic/satiated (PKH2-PCL lo ) macrophages in comparison to phagocytic (PKH2-PCL hi ) ones. The results indicate the statistical significance of the GO term and the percentage of enrichment is presented. c – e Expression of IFN-β and ISG15 in sorted satiated and phagocytic macrophages. Representative results ( c ) and mean ± SEM ( d , e ) for three independent experiments. * P < 0.05 (Student’s t test). g , h Peritoneal exudates were collected from unchallenged mice (0 h) or following peritonitis for 4–96 h. IFN-β content in cell-free fluids was determined by ELISA ( f ). Results are mean ± SEM from three (24, 72, 96 h) or four (0, 4, 48 h) mice. * P < 0.05, ** P < 0.01, *** P < 0.005 (Tukey’s HSD). Alternatively, resolution phase macrophages were recovered 66 h post peritonitis initiation (PPI) and incubated with TGF-β (5 ng/ml), poly (I:C) (4 μg/ml) or apoptotic cells (AC, at a ratio of 1:5) for 24 h. Culture supernatants were then collected and IFN-β content was measured ( g ). Culture media from apoptotic cells served as control. Results are representative from three independent experiments. * P < 0.05, ** P < 0.01, *** P < 0.005 (Tukey’s HSD). Source data are provided as a Source Data file

Article Snippet: Peritoneal exudates and bronchoalveolar lavage fluid were collected at the indicated times and the levels of IFN-β in cell-free fluids were determined by VeriKine-HS Mouse Interferon Beta Serum ELISA Kit (Pestka Biomedical Laboratories, Inc).

Techniques: Injection, Staining, RNA Extraction, Gene Expression, Microarray, Comparison, Expressing, Enzyme-linked Immunosorbent Assay, Incubation, Control

Journal: Nature Communications

Article Title: IFN-β is a macrophage-derived effector cytokine facilitating the resolution of bacterial inflammation

doi: 10.1038/s41467-019-10903-9

Figure Lengend Snippet: IFN-β favors macrophage reprogramming during the resolution of inflammation. a – d Macrophages were recovered from peritoneal exudates of male Ifnb +/+ or Ifnb − / − mice at 48–66 h PPI and cultured with LPS (1 μg/ml) for 24 h. Culture supernatants were then collected and levels of IL-10 ( a ), IL-6 ( b ), IL-12 ( c ) and CCL3 ( d ) were determined by selective ELISAs. Results are means ± SEM from four independent experiments. * P < 0.05, *** P < 0.005 (Tukey’s HSD). e – f Macrophages were recovered from peritoneal exudates of Ifnb +/+ mice at 48–66 h PPI and cultured with mouse IFN-β or IFN-α (20 ng/ml each) for 48 h. Then, culture supernatants were collected and levels of IL-10 ( e ) and IL-12 ( f ) were determined by ELISA. Results are means ± SEM (n = 4). *** P < 0.005 (Tukey’s HSD). g Macrophages were recovered from peritoneal exudates of Ifnb +/+ mice 48–66 h PPI and incubated with IFN-β (20 ng/ml) for 48 h. The cells were then immunostained for F4/80 and CD11b and the percentage of CD11b low macrophages was determined by flow cytometry. Results are means ± SEM from three independent experiments. *** P < 0.005 (Tukey’s HSD). h – i Mice undergoing peritonitis were treated with IFN-β (20 ng/mouse, i.p.) or vehicle at 24 h PPI. Peritoneal macrophages were collected at 48 h PPI, lysed and immunoblotted for 12/15-LO, arginase 1, ISG15 and GAPDH. Representative blots ( h ) and densitometry analysis (means ± SEM) ( i ) for three independent experiments. * P < 0.05 (Student’s t test). Source data are provided as a Source Data file

Article Snippet: Peritoneal exudates and bronchoalveolar lavage fluid were collected at the indicated times and the levels of IFN-β in cell-free fluids were determined by VeriKine-HS Mouse Interferon Beta Serum ELISA Kit (Pestka Biomedical Laboratories, Inc).

Techniques: Cell Culture, Enzyme-linked Immunosorbent Assay, Incubation, Flow Cytometry

Journal: Molecular medicine reports

Article Title: Serum protein microarray analysis of patients with preeclampsia.

doi: 10.3892/mmr.2012.864

Figure Lengend Snippet: Figure 1. RayBio® Human Cytokine Antibody Microarray (AAH-CYT-G1000), including two slides: series 6 (60 cytokines) and series 7 (60 cytokines). A total of 60 antibodies against cytokines and chemokines were placed on the microarray. (A) Representative membrane protein microarrays were incubated with the serum of 5 preeclamptic subjects (top; A), and 3 healthy pregnant subjects (bottom; A). (B) Preeclampsic women showed significantly increased serum levels of TNF-R1, Axl and TIMP-2 when compared to healthy pregnant women. (C) The names and locations of each cytokine/chemokine custom spots are listed.

Article Snippet: Serum was diluted to 1:3 and probed for the cytokine profile using the RayBio Human Cytokine Antibody Array kit according to the manufacturer's instructions (No. AAH-CYT-G1000; RayBiotech, Norcross, GA, USA).

Techniques: Microarray, Membrane, Incubation

Journal: Molecular cell

Article Title: The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma

doi: 10.1016/j.molcel.2022.03.019

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mesenchymal Stem Cell Growth Kit for Adipose and Umbilical-derived MSCs - Low Serum , ATCC , Cat# PCS-500-040.

Techniques: Microarray, Recombinant, Sample Purification, Isolation, Derivative Assay, shRNA, Construct, CRISPR, Plasmid Preparation, Software

Journal: Molecular cell

Article Title: The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma

doi: 10.1016/j.molcel.2022.03.019

Figure Lengend Snippet: A. Experimental schematic to profile BAF complex localization and other chromatin changes in hTERT-MSCs upon 24 hours adipogenesis. B. edgeR analysis of differential occupancy of BAF complexes (SMARCA4) on the genome upon 24 hours adipogenesis. C. HOMER motif analysis of sites that gain BAF complex (SMARCA4) occupancy upon 24 hours adipogenesis. D. Heatmap of SMARCA4, CEBPB, H3K27ac, and ATAC-seq peaks over sites that gain BAF complex (SMARCA4) occupancy upon 24 hours adipogenesis (“SMARCA4 targets”). E. Experimental schematic to define the specific role for BAF complexes in adipogenesis using small molecule-mediated inhibition of BAF complex ATPase activity with compound 12 (CMP12). F. Heatmap of SMARCA4, CEBPB, H3K27ac, and ATAC-seq peaks upon DMSO or CMP12 treatment in base or adipogenic media for 24 hours over SMARCA4 gained sites in the DMSO adipogenesis condition. G. Comparison of changes in RNA in the CMP12 and DMSO treatment conditions upon adipogenesis. Dark blue circles are genes that are not as up-regulated or are more down-regulated upon adipogenesis with CMP12 treatment compared to DMSO (CMP12-attenuated gene). Light blue circles are a subset of CMP12-attenuated genes that are also nearest to sites that gain BAF complexes (SMARCA4) upon adipogenesis in the DMSO condition (CMP12-attenuated gene and SMARCA4 target). H. Gene ontology analysis of CMP12-attenuated gene and SMARCA4 targets. I. Heatmap of logFC in expression of genes in DMSO and CMP12 conditions upon adipogenesis. J. Track examples at the CD36, ELOVL6 and WNT5A loci. See also Figure S4.

Article Snippet: Mesenchymal Stem Cell Growth Kit for Adipose and Umbilical-derived MSCs - Low Serum , ATCC , Cat# PCS-500-040.

Techniques: Inhibition, Activity Assay, Comparison, Expressing

Journal: Molecular cell

Article Title: The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma

doi: 10.1016/j.molcel.2022.03.019

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mesenchymal Stem Cell Growth Kit for Adipose and Umbilical-derived MSCs - Low Serum , ATCC , Cat# PCS-500-040.

Techniques: Microarray, Recombinant, Sample Purification, Isolation, Derivative Assay, shRNA, Construct, CRISPR, Plasmid Preparation, Software

Journal: Reproductive Biology and Endocrinology : RB&E

Article Title: A promising future for endometriosis diagnosis and therapy: extracellular vesicles - a systematic review

doi: 10.1186/s12958-022-01040-y

Figure Lengend Snippet: Key characteristics of studies of extracellular vesicles in endometriosis

Article Snippet: Shan 2021 [ ] , Human ( n = 5 for RNA seq, n = 80 for validation) , Human ( n = 6 for RNA seq, n = 80 for validation) , Serum , ExoRNeasy Serum/Plasma Midi Kit (#76,214, Qiagen) , Yes , lncRNAs (seq) Ten lncRNAs validated with RT-qPCR , Potential diagnostic marker RP3-399L15.2 AUC 0.86, Sn 67%, Sp 98%. Using combination of RP3-399L15.2 and CH507-513H4.6 AUC 0.90, Sn 80%, Sp 85%. , Not discussed, but potential therapeutic targets , Not discussed , Endometriomas only.

Techniques: Diagnostic Assay, Isolation, Derivative Assay, Migration, Biomarker Discovery, Activity Assay, Inhibition, Expressing, Over Expression, Clinical Proteomics, Control, RNA Sequencing, Marker, In Vivo, In Vitro, Microarray, Cell Culture

Journal: BioMed Research International

Article Title: MicroRNAs as Salivary Markers for Periodontal Diseases: A New Diagnostic Approach?

doi: 10.1155/2016/1027525

Figure Lengend Snippet: Comparison of methods from current investigations regarding miRNAs in periodontal disease.

Article Snippet: Zahran et al. 2015 [ ] , 20 healthy controls, 40 potentially malignant disorders, 20 OSCC, 20 recurrent aphthous stomatitis , Unstimulated saliva supernatant , miRNeasy serum/plasma extraction kit (Qiagen) , — , RT-qPCR SYBR green PCR kit (Qiagen) , SNORD68 , One-way ANOVA, F -test, Dunnett t -test, Scheffe's multiple comparison, two-tailed tests , miR-21, miR-184, miR-145.

Techniques: Comparison, RNA Extraction, Biomarker Discovery, Control, In Vitro, Microarray, Isolation, TaqMan microRNA Assay, SYBR Green Assay, Labeling, Real-time Polymerase Chain Reaction, Virus, Quantitative RT-PCR, In Vivo, Expressing, Mann-Whitney U-Test

Journal: BioMed Research International

Article Title: MicroRNAs as Salivary Markers for Periodontal Diseases: A New Diagnostic Approach?

doi: 10.1155/2016/1027525

Figure Lengend Snippet: Comparison of methods for salivary miRNA diagnosis.

Article Snippet: Zahran et al. 2015 [ ] , 20 healthy controls, 40 potentially malignant disorders, 20 OSCC, 20 recurrent aphthous stomatitis , Unstimulated saliva supernatant , miRNeasy serum/plasma extraction kit (Qiagen) , — , RT-qPCR SYBR green PCR kit (Qiagen) , SNORD68 , One-way ANOVA, F -test, Dunnett t -test, Scheffe's multiple comparison, two-tailed tests , miR-21, miR-184, miR-145.

Techniques: Comparison, Biomarker Discovery, Extraction, Control, Marker, Isolation, Mann-Whitney U-Test, TaqMan microRNA Assay, TLDA Assay, Expressing, Microarray, Lysis, SYBR Green Assay

Journal: International Journal of Molecular Sciences

Article Title: Targeting CD177: A Novel Therapeutic Strategy for NLRP3-Associated Autoinflammatory Diseases

doi: 10.3390/ijms27062841

Figure Lengend Snippet: CD177 is elevated in patients with NLRP3-AID. ( A ) Venn diagram shows the results of the transcriptome sequencing analysis. ( B ) Heatmap shows differentially expressed genes. ( C ) Flow cytometry detects the expression of CD177 in peripheral blood of NLRP3 mutant patient (PT) and healthy controls (H). ( D ) GEPIA analysis of the expression of CD177 in different immune cells in peripheral blood. ( E ) qPCR assay detects CD177 expression in peripheral blood neutrophils. ( F , G ) qPCR assay detects the expression of CD177 in neutrophils from two healthy controls (H3 and H4) treated with NLRP3 agonist (Nigericin) or NLRP3 inhibitor (CY-09). ( H – K ) qPCR assay detects the expression of IL-1β, IL-6, TNFα and IL-18 in neutrophils from HCs treated with Nigericin or CY-09. ( L ) GEPIA analysis of the expression correlation between CD177 and IL-1β. ( M ) qPCR assay examines the expression of CD177 in MCF-7 cells transfected with CD177 siRNA or negative control siRNA. ( N ) Western blot analysis of CD177 protein levels in MCF-7 cells transfected with CD177 siRNA or negative control siRNA. ( O ) The mRNA levels of IL-1β, IL-6, TNFα and IL-18 in MCF-7 cells transfected with CD177 siRNA or negative control siRNA. qPCR Data are shown as mean ± s.d. Student’s t -test was used. Statistical significance was determined as * p < 0.05; *** p < 0.001.

Article Snippet: The levels of IL-1β and IL-6 in the serum were detected using mouse-specific IL-6 (CSB-E04639m, Cusabio, Wuhan, China) and IL-1β (CSB-E08054m, Cusabio, Wuhan, China) detection kits according to the manufacturer’s instructions.

Techniques: Sequencing, Flow Cytometry, Expressing, Mutagenesis, Transfection, Negative Control, Western Blot

Journal: International Journal of Molecular Sciences

Article Title: Targeting CD177: A Novel Therapeutic Strategy for NLRP3-Associated Autoinflammatory Diseases

doi: 10.3390/ijms27062841

Figure Lengend Snippet: NLRP3 mutant mice exhibit phenotypic heterogeneity despite identical genotypes. ( A ) Images of wild-type ( Nlrp3 +/+ ) mice and NLRP3 mutant ( Nlrp3 L573W/+ ) mice with different inflammatory states. Notably, both mild and severe phenotypic groups are confirmed to be heterozygous for the p.L573W mutation. ( B ) Body weight of wild-type mice, NLRP3 mutant (Nlrp3 L573W/+) mice with different inflammatory states (weight measured starting from day 12, every other day). ( C ) Flow cytometry analysis of neutrophils in mouse peripheral blood ( n = 6 per group). ( D – F ) Histopathological detection of mouse tissues (skin, liver, spleen) showing varying degrees of inflammatory infiltration, Scale bars: 400 μm, 100 μm. ( G – I ) Immunohistochemical detection of mouse tissues (skin, liver, spleen) showing differences in neutrophil marker Ly6G expression, Scale bars: 200 μm, 50 μm. ( J ) Cytokine microarray in serum of wild-type mice and NLRP3 mutant mice with different inflammatory states. ( K , L ) Flow cytometry detection of IL-1β and IL-6 protein expression in mouse peripheral blood cells ( n = 6 per group). ( M – O ) qPCR detection of IL-1β, IL-6, and TNFα mRNA expression levels in mouse skin, liver, and spleen tissues ( n = 3). qPCR Data are shown as mean ± s.d. Student’s t -test was used. Statistical significance was determined as ** p < 0.01; *** p < 0.001; ns, not significant. CD177 expression is elevated in NLRP3 mutant mice and correlates with disease severity.

Article Snippet: The levels of IL-1β and IL-6 in the serum were detected using mouse-specific IL-6 (CSB-E04639m, Cusabio, Wuhan, China) and IL-1β (CSB-E08054m, Cusabio, Wuhan, China) detection kits according to the manufacturer’s instructions.

Techniques: Mutagenesis, Flow Cytometry, Immunohistochemical staining, Marker, Expressing, Microarray

Journal: International Journal of Molecular Sciences

Article Title: Targeting CD177: A Novel Therapeutic Strategy for NLRP3-Associated Autoinflammatory Diseases

doi: 10.3390/ijms27062841

Figure Lengend Snippet: Targeted IL-6 therapy is ineffective for NLRP3 mutation-induced AID. ( A – G ) Flow cytometry detection of neutrophil, IL-1β, IL-6 and CD177 protein expression in peripheral blood of NLRP3 mutant severe mice treated with or without IL-6 antibody ( n = 7). ( H – K ) qPCR detection of IL-1β, IL-6, TNFα and CD177 mRNA expression levels in skin, liver, and spleen tissues of NLRP3 mutant severe mice treated with or without IL-6 antibody ( n = 3). ( L – N ) Histopathological detection of mouse tissues (skin, liver, spleen), Scale bars: 400 μm, 100 μm. ( O – Q ) Immunohistochemical detection of Ly6G levels in mouse skin, liver, spleen tissues, Scale bars:200 μm, 50 μm. qPCR Data are shown as mean ± s.d. Student’s t -test was used. Statistical significance was determined as * p < 0.05; ** p < 0.01; *** p < 0.001; ns, not significant.

Article Snippet: The levels of IL-1β and IL-6 in the serum were detected using mouse-specific IL-6 (CSB-E04639m, Cusabio, Wuhan, China) and IL-1β (CSB-E08054m, Cusabio, Wuhan, China) detection kits according to the manufacturer’s instructions.

Techniques: Mutagenesis, Flow Cytometry, Expressing, Immunohistochemical staining

Journal: International Journal of Molecular Sciences

Article Title: Targeting CD177: A Novel Therapeutic Strategy for NLRP3-Associated Autoinflammatory Diseases

doi: 10.3390/ijms27062841

Figure Lengend Snippet: Targeting CD177 suppresses the expression of IL-1β. ( A , B ) Flow cytometry detection of IL-1β protein expression levels in peripheral blood of mice treated with either IL-1β antibody or CD177 siRNA ( n = 6). ( C ) ELISA detection of serum IL-1β protein levels in mice treated with either IL-1β antibody or CD177 siRNA ( n = 3). ( D , E ) Flow cytometry detection of IL-6 protein expression levels in peripheral blood of mice treated with either anti-IL-1β antibody or CD177 siRNA ( n = 6). ( F ) ELISA detection of serum IL-6 protein levels in mice treated with either IL-1β antibody or CD177 siRNA ( n = 3). ( G – I ) qPCR detection of IL-6, IL-1β, and TNFα mRNA expression levels in mouse skin, liver, and spleen tissues ( n = 3). ( J ) Schematic diagram shows the role of CD177 in the development of NLRP3 mutation-related autoinflammation. qPCR Data are shown as mean ± s.d. Student’s t -test was used. Statistical significance was determined as ** p < 0.01; *** p < 0.001.

Article Snippet: The levels of IL-1β and IL-6 in the serum were detected using mouse-specific IL-6 (CSB-E04639m, Cusabio, Wuhan, China) and IL-1β (CSB-E08054m, Cusabio, Wuhan, China) detection kits according to the manufacturer’s instructions.

Techniques: Expressing, Flow Cytometry, Enzyme-linked Immunosorbent Assay, Mutagenesis

Journal: Nature Communications

Article Title: CD8 + T cell loss induces autoinflammation in inborn errors of cell death

doi: 10.1038/s41467-026-70317-2

Figure Lengend Snippet: a , b Schematic diagram showing serum cytokine microarray analysis of continuous P2’s serum samples before (PS1 and PS2) or after (PS3, flare; PS4 and PS5, non-flare) the onset of recurrent fever ( a ). PCA analysis of sample variance determined by semi-quantitative 174 cytokines antibody array on serum samples of C1-C3 from three unaffected controls and PS1-PS5 from P2 ( b ). c–e The integrated relative MFI plots of P2’s serum cytokine levels. 26 cytokines peaked in PS3 were enrich in group 1 (left), 24 cytokines higher than control were enriched in group 2 (right) ( c ). The relative MFI was calculated by normalizing the average MFI of the unaffected controls ( n = 3) to 0, and setting the largest MFI to 1 or the smallest MFI to −1 across 5 samples from P2. Boxplots exhibiting expression scores of cytokines of group 1 ( d ) and group 2 ( e ) in indicated cell with Seurat AddModuleScore function. The cell number of each subtype (listed in the “Methods” section), was employed for p value calculations. Boxes show the median (center line), 25th and 75th percentiles (upper and lower hinges), and whiskers extend to 1.5× the interquartile range, representing the maximum and minimum values. f Average expression values (arcsinh transformed) of cl. Casp-3 across identified peripheral immune cell lineages in PBMCs freshly isolated from four unaffected controls (C) and two patients (P, 1 sample from P1 and 2 samples from P2) by mass cytometry by time-of-flight (CyTOF) analysis. g–j Representative contour plots of cl. Casp-3 ( g , h ) and histograms of total RIPK1, pRIPK1(S166) levels ( i , j ) in CD4 + T and CD8 + T cells in freshly isolated PBMCs from unaffected controls (for cl. Casp-3, n = 12; for pRIPK1(S166), n = 10) and patients ( n = 4 for P1 and P2) (left). Summary histograms of cl. Casp-3 and pRIPK1(S166) (right) were shown. k Representative histogram and statistical analysis of surface CD69 expression on CD3 + T cells from unaffected controls ( n = 7) and two patients ( n = 3 for P1 and P2). l Serum IFNγ, sCD25, sCD95 and CD95L of unaffected controls (for IFNγ, n = 9; for sCD25, n = 15; for sCD95 and CD95L, n = 10), two patients (for IFNγ, P1, n = 5, P2 = 6; for sCD25, P1, n = 5, P2, n = 4; for sCD95, P1 and P2, n = 7; for CD95L, P1 = 7; P2 = 8) and their parents (for IFNγ and sCD25, n = 7; for sCD95 and CD95L, n = 6) as well as two CRIA syndrome patients ( n = 6) determined by ELISA. T denotes 10 ng ml -1 TNF; S denotes 250 nM SM164; Z denotes 25 μM z-VAD-fmk. All histogram graphs show mean ± SD. P values were determined by two-tailed unpaired t-test. Data in g–k were pooled from two independent experiments.

Article Snippet: Human or mouse serum cytokines were measured by enzyme-linked immunosorbent assay (ELISA) (Multi Sciences: 70-EK1280, 70-EK194, 70-EK182HS, 70-EK106HS, 70-EK191, 70-EK180HS, 70-EK1F01, 70-EK1F02, EK206HS, EK282HS/2) according to the manufacturer’s instructions.

Techniques: Microarray, Ab Array, Control, Expressing, Transformation Assay, Isolation, Mass Cytometry, Enzyme-linked Immunosorbent Assay, Two Tailed Test

Journal: Nature Communications

Article Title: CD8 + T cell loss induces autoinflammation in inborn errors of cell death

doi: 10.1038/s41467-026-70317-2

Figure Lengend Snippet: a Schematic diagram of T cell-MDM co-culture system. b , c qRT-PCR analysis of TNF, IL1B and IL6 mRNA levels in GM-CSF-activated monocytes derived macrophages (MDMs) co-cultured with or without T cells for 6 h. GM-CSF-activated MDMs generated from ( b , left) unaffected control 1 (C1) or ( b , right) unaffected control 3 (C3) or P1 ( c ) were co-cultured with donor-matched T cells as well as T cells from other unaffected controls (C2 and C4) or patients as indicated. d Dot plot of IFNG, TNF in cell subtypes found in scRNA-seq of PBMCs from three unaffected controls and two patients. e Representative histograms and statistical analysis of TNF and IFNγ expression in CD8 + T cells in PBMCs isolated from unaffected controls ( n = 6) and patients ( n = 3 from P1 and P2) treated with 10 ng ml -1 TNF (T) with or without 250 nM SM-164 (S), 25 μM z-VAD-fmk (Z) for 24 h. f , T cells isolated from P2 were co-cultured with MDMs generated from unaffected control in the presence of 10 μg ml -1 adalimumab, 10 μg ml -1 emapalumab alone or in combination for 6 h. TNF, IL1B and IL6 mRNA levels of MDMs were analyzed by qRT-PCR. g Experimental timeline for generation of lineage negative bone marrow cells (Lin - BMs)-transplanted mice with conditional overexpression of human WT or mutated RIPK1 K377E or R390G in CD8 + T cell- or myeloid cell-specific lineage. h, i ELISA measurement of serum Tnf and Il6 levels in mice specifically overexpressing WT or mutated hRIPK1 in ( h ) CD8 + T cells (EV, n = 5; WT, K377E and R390G n = 7) or ( i ) myeloid cells (EV, n = 5; WT, K377E and R390G n = 6). All histogram graphs show mean ± SD. P values were determined by one-way ANOVA with Tukey’s multiple comparisons test. Data in b , c , and f show the means ± SD of technical triplicates. The results shown in b were derived from two independent experiments using cells from different donors. The experiment in ( c , h , i , f ) is representative of two independent experiments. Data in e were pooled from two independent experiments.

Article Snippet: Human or mouse serum cytokines were measured by enzyme-linked immunosorbent assay (ELISA) (Multi Sciences: 70-EK1280, 70-EK194, 70-EK182HS, 70-EK106HS, 70-EK191, 70-EK180HS, 70-EK1F01, 70-EK1F02, EK206HS, EK282HS/2) according to the manufacturer’s instructions.

Techniques: Co-Culture Assay, Quantitative RT-PCR, Derivative Assay, Cell Culture, Generated, Control, Expressing, Isolation, Over Expression, Enzyme-linked Immunosorbent Assay

Journal: Cells

Article Title: Clinical Value and Molecular Function of Circulating MicroRNAs in Endometrial Cancer Regulation: A Systematic Review

doi: 10.3390/cells11111836

Figure Lengend Snippet: Conservation, extraction, and analysis of the miRs.

Article Snippet: [ ] , Serum , −20 °C , Norgen Total RNA Purification Kit , Human miRNA microarray chip analysis (Agilent-070156 Human) , Reaction mix.

Techniques: Extraction, Microarray, Clinical Proteomics, Reverse Transcription, Isolation, Sequencing, SYBR Green Assay, TaqMan microRNA Assay, cDNA Synthesis, RNA Extraction, Purification, Library Quantification

Journal: Cell Research

Article Title: Conversion of hepatoma cells to hepatocyte-like cells by defined hepatocyte nuclear factors

doi: 10.1038/s41422-018-0111-x

Figure Lengend Snippet: HNF1A, HNF4A and FOXA3 induce HCC cell reprogramming. a The experimental design for the induction of rHeps. HCC cells were infected with adenovirus expressing HNF1A, HNF4A and FOXA3 (each at MOI = 10). rHeps were characterized 10–14 days after induction. b Hepatic gene expression in HCCLM3 cells induced by different adenoviruses expressing HNF1A, HNF4A or FOXA3 (n = 3). Data are normalized to 3F (HNF1A, HNF4A and FOXA3). c Hepatic gene expression gradually increased during conversion of HCCLM3 cells to rHeps. Expression levels of the indicated genes were analyzed by real-time PCR (n = 3). Data are normalized to day 0. d Hepatocyte-like morphology of rHeps derived from HCCLM3 cells observed by fluorescence microscopy. Scale bar in white, 100 µm. e Expression of ALB and AFP in rHeps derived from HCCLM3 cells was analyzed by RT–PCR (left), and ALB secretion was measured by ELISA (right) (n = 3). Primary human hepatocytes (PHHs) cultured for 2 days were used as positive control. f Global gene expression profile analysis of rHeps derived from HCCLM3 cells and Ad-GFP-treated control cells by cDNA microarray. PHHs were used as the positive control. Hierarchical clustering showed that rHeps grouped together with PHHs. * indicates P < 0.05

Article Snippet: Human albumin ELISA Human albumin was measured by the Human Albumin ELISA Quantitation kit (Assay Pro) according to the manufacturer’s instructions.

Techniques: Infection, Expressing, Gene Expression, Real-time Polymerase Chain Reaction, Derivative Assay, Fluorescence, Microscopy, Reverse Transcription Polymerase Chain Reaction, Enzyme-linked Immunosorbent Assay, Cell Culture, Positive Control, Control, Microarray

Journal: Cell Research

Article Title: Conversion of hepatoma cells to hepatocyte-like cells by defined hepatocyte nuclear factors

doi: 10.1038/s41422-018-0111-x

Figure Lengend Snippet: Transplanted rHeps reconstructed the hepatic plate and liver lobules. a Respective HCCLM3-derived rHeps and control cells (1.5 × 107) were transplanted into the livers of Fah−/−Rag2−/− mice through spleen injection. Scale bars, 100 µm. b H&E and immunohistochemical staining of human Fah, ALB and AAT in the livers of rHep recipient Fah−/−Rag2−/− mice. c Human ALB levels in the sera of rHep-transplanted Fah−/−Rag2−/− (F/R) mice were measured by ELISA. The sera from normal human and F/R mice were used as positive and negative controls, respectively. d Fah staining of the repopulated rHeps in Fah−/−Rag2−/− mice. Images of different section areas were merged into one using Adobe Photoshop CS5 (Adobe Systems). e The percentage of Fah-positive rHeps in the liver of each rHep recipient mouse was calculated and shown. f The Kaplan-Meier survival curve of Fah−/−Rag2-/- mice that were transplanted with PHHs, control cells or rHep cells after NTBC removal. * indicates P < 0.05

Article Snippet: Human albumin ELISA Human albumin was measured by the Human Albumin ELISA Quantitation kit (Assay Pro) according to the manufacturer’s instructions.

Techniques: Derivative Assay, Control, Injection, Immunohistochemical staining, Staining, Enzyme-linked Immunosorbent Assay

Journal: Cell Reports

Article Title: Cross-reactivity of glycan-reactive HIV-1 broadly neutralizing antibodies with parasite glycans

doi: 10.1016/j.celrep.2022.110611

Figure Lengend Snippet: Binding of HIV-1 bnAbs to S. mansoni parasite-derived glycans on glycan microarrays (A) Synthetic glycan microarray displaying S. mansoni -derived N -glycans and fragment structures as previously described ( Brzezicka et al., 2015 ; Echeverria et al., 2018 ). No high-mannose glycan structures are present on this array. Glycans bound by the HIV-1 bnAbs PGT121, PGT151, and PGT123 are displayed. Mammalian “self” and “non-self” glycans are shown in gray and blue, respectively. Binding is reported in relative fluorescence units (RFU). Each histogram represents the average RFU values for four replicates spots and the error bars represent the SD of the mean. A full list of glycan structures present on the synthetic glycan array can be found in Figure S1 . (B) Shotgun glycan microarray of S. mansoni -extracted glycans as previously described ( De Boer et al., 2007 ; van Diepen et al., 2012 , ). Binding of HIV-1 bnAbs PGT121, PGT151, and PGT128 determined. Each line represents the average mean fluorescence intensity (MFI) values for three replicates spots. Glycans bound are displayed on the right and mammalian “self” glycans and non-mammalian “non-self” glycan motifs are indicated. The life stage and type of glycan ( N -, O -, or glycosphingolipid [GSL] glycan) are reported. Glycan structures with “s” indicate structures only found on the shotgun glycan microarray. Man, green circle; GlcNAc, blue square; GalNAc, yellow square; Gal, yellow circle; sialic acid, purple diamond; fucose, red triangle; xylose, star.

Article Snippet: Serum/plasma samples were inactivated with TritonX (0.1%) and diluted to 1:100 before adding to the wells. mAbs were used at 50 μg/mL in sample diluent (ab108769, Abcam) and serum standards provided in the Human Anti- Schistosoma mansoni IgG ELISA Kit (ab108769, Abcam) were used as controls.

Techniques: Binding Assay, Derivative Assay, Microarray, Fluorescence

Journal: Cell Reports

Article Title: Cross-reactivity of glycan-reactive HIV-1 broadly neutralizing antibodies with parasite glycans

doi: 10.1016/j.celrep.2022.110611

Figure Lengend Snippet: Cross-reactivity of HIV-1 bnAbs with S. mansoni (A) Western blot of S. mansoni -soluble cercariae antigen (SCA) and adult worm antigen (AWA) (both at 25 μg per lane) with glycan-binding bnAbs 2G12, PGT128, PGT121, and PGT151 and V3-specific mAb F425-b4e8 (all at 50 μg/mL). A control western blot stained with sera from S. mansoni -infected humans or rabbits immunized with SCA/AWA is shown in A. Binding of HIV-1 bnAbs to recombinant gp120 is shown in B. (B) Optical density at 450 nm of 2G12, PGT128, PGT121, and PGT151 (at 50 μg/mL) determined by ELISA using S. mansoni -soluble egg antigen (SEA), SCA, and AWA. V3-specific mAb F425-b4e8 and CD4-bnAb VRC01 (at 50 μg/mL), as well as healthy human serum, and S. mansoni -positive human serum as positive control. Error bars represent data from repeated experiments. The horizontal dotted line indicates the cut-off for the positive control provided with the assay kit (see ). Bar graphs show the mean of the OD values from at least 3 repeat experiments, and the error bars represent the SD. (C–F) Binding of HIV-1 bnAbs to S. mansoni cercariae. HIV-1 bnAbs binding was detected with Alexa Fluor 488 (green), actin was detected with rhodamine (red), and DNA was stained with DAPI (blue). Black and white images show projections of bnAb staining only, while colored images show overlays. (C) Binding of 2G12 to S. mansoni cercariae. 2G12 bound to putative ciliated sensory papillae ( 1 ), superficial neural projections ( 2 ), and the duct opening on the oral sucker and dotted fractions of glycoprotein on the oral sucker ( 3 ). (D) Binding of PGT128 to S. mansoni cercariae. PGT128 recognized spines, ciliated sensory papillae, and basement membrane/tegument/glycocalyx structures ( 1 ), similar to ConA ( A). PGT128 also recognized surface motifs (spines, ciliated sensory papillae, and basement membrane/tegument/glycocalyx structures) above the actin layer ( 2 ) and the duct opening on the oral sucker and dotted fractions of glycoprotein on the oral sucker ( 3 ). (E) Binding of PGT121 to S. mansoni cercariae. PGT121 recognizes the pre- and post-acetabular gland system, which is sits interior of the parasite ( 1 ) and surface motifs of ciliated sensory papillae and basement membrane/tegument/glycocalyx structures above the actin layer ( 2 ). The green arrow indicates ciliated sensory papillae reaching outside while being anchored to the outer surface by actin (red arrow). PGT121 also bound the duct opening on the oral sucker and dotted fractions of glycoprotein, co-locating with actin on the oral sucker ( 3 ). (F) Binding of PGT151 to S. mansoni cercariae. PGT151 recognized surface motifs of ciliated sensory papillae above the actin layer with high intensity ( 1 ) and ciliated tufts of the flame cells and on the protone phridial tubules ( 2 ). Binding of glycan-independent HIV-1 bnAbs F425-b4e8 and VRC01 is shown in A and S6B. Confocal microscopy staining was performed twice on different cercariae preparations. Representative images are shown from one experiment.

Article Snippet: Serum/plasma samples were inactivated with TritonX (0.1%) and diluted to 1:100 before adding to the wells. mAbs were used at 50 μg/mL in sample diluent (ab108769, Abcam) and serum standards provided in the Human Anti- Schistosoma mansoni IgG ELISA Kit (ab108769, Abcam) were used as controls.

Techniques: Western Blot, Binding Assay, Staining, Infection, Recombinant, Enzyme-linked Immunosorbent Assay, Positive Control, Confocal Microscopy

Journal: Cell Reports

Article Title: Cross-reactivity of glycan-reactive HIV-1 broadly neutralizing antibodies with parasite glycans

doi: 10.1016/j.celrep.2022.110611

Figure Lengend Snippet: Analysis of HIV-1 neutralization and S. mansoni seroprevalence in IAVI Protocol C donors (A) Comparison of neutralization score between donors with S. mansoni SEA seroreactivity (SH1) and no seroreactivity (SH0) at different time points after HIV-1 infection (TP2, TP3, and the time point with highest neutralization score [Best]). Neutralization score (Score) is a numerical representation of neutralization breadth and potency against a HIV-1 cross-clade virus panel and categorized by “TOP” (score ≥ 1), “MEDIUM” (score < 1 and ≥0.5), and “WEAK” (score < 0.5) as determined by Landais et al. ( Landais et al., 2016 ). Groups were compared using a chi-square test, but no statistical differences were observed. (B) Distribution of neutralizing epitopes targeted in sera (as determined by serum mapping studies; Landais et al., 2016 ) across S. mansoni status is displayed in a bar chart with the sum of each specificity overall. Single specificities are displayed in orange, while the distribution of mixed specificities is stacked on top in blue. (C) Comparison of geometric mean ID 50 at TP3, the number of viruses neutralized (breadth) at TP3, neutralization score at TP3, best neutralization score (from all time points in the study) ( Landais et al., 2016 ), CD4 count at setpoint (cells per microliter), viral load (log RNA copies per milliliter) at setpoint, and time to ART in years from setpoint between donors with S. mansoni seroreactivity (SH1) and no S. mansoni seroreactivity (SH0). p values (Mann-Whitney test) are reported as follows: not significant (ns), ∗ p < 0.0332, ∗∗ p < 0.0021, ∗∗∗ p < 0.0002, and ∗∗∗∗ p < 0.00001. Additional cohort analysis can be found in Figures S7 A–S7C.

Article Snippet: Serum/plasma samples were inactivated with TritonX (0.1%) and diluted to 1:100 before adding to the wells. mAbs were used at 50 μg/mL in sample diluent (ab108769, Abcam) and serum standards provided in the Human Anti- Schistosoma mansoni IgG ELISA Kit (ab108769, Abcam) were used as controls.

Techniques: Neutralization, Infection, MANN-WHITNEY

Journal: Cell Reports

Article Title: Cross-reactivity of glycan-reactive HIV-1 broadly neutralizing antibodies with parasite glycans

doi: 10.1016/j.celrep.2022.110611

Figure Lengend Snippet: Cross-reactivity of N332/V3 PCDN76-lineage mAbs with S. mansoni isolates (A) Binding of PCDN76 38A and 38B and their less mutated precursors UCA-P, UCA-S, 22A, and 22C to recombinant JR-CSF gp120 was measured using ELISA. Experiments were performed in duplicate and repeated twice. A representative dataset is shown. Error bars represent the range of the value for experiments performed in duplicate (not shown when smaller than symbol size). (B) Binding of PCDN76 38A and 38B and their less mutated Ab precursors to S. mansoni SEA, SCA, and AWA on ELISA (at 50 μg/mL). N -glycan-independent HIV-1 mAbs F425-b4e8 and VRC01 were used as negative controls and S. mansoni -positive human serum as positive control. Error bars represent data from repeated experiments. Bar graphs show the mean of the OD values from at least 3 repeat experiments, and the error bars represent the SD. (C–H) Binding of less mutated PCDN76 precursors (UCA-P, UCA-S, 22A, 22C, and 38A) to S. mansoni cercariae. HIV-1 mAbs were detected with Alexa Fluor 488 (green), actin was detected with rhodamine (red), and DNA was stained with DAPI (blue). Black and white images show projections of mAb staining only, while colored images show overlays. (C) UCA-P recognizes superficial neural projections and ciliated sensory papillae ( 1 ), similar to 2G12. UCA-P recognized motifs of superficial neural projections and ciliated sensory papillae are located above the actin layer ( 2 ). Similar to 2G12, UCA-P displays binding to duct opening on the oral sucker ( 3 ). (D) UCA-S recognizes surface motifs (spines, ciliated sensory papillae, and basement membrane/tegument/glycocalyx structures) above the actin layer ( 1 ), and basement membrane/tegument/glycocalyx structures similar to ConA and PGT128 ( 2 ). (E) 16A binds to glycoproteins on the body, which could be ciliated tufts of the flame cells and/or ciliated regions on the protone phridial tubules and to ciliated sensory papillae on the tail and the body ( 1 ). Furthermore, binding to the duct opening on the oral sucker is observed ( 2 ). (F) 22A recognizes spines, ciliated sensory papillae and basement membrane/tegument/glycocalyx structures, similar to ConA and PGT128 ( 1 ). 22A recognizes surface motifs (spines, ciliated sensory papillae and basement membrane/tegument/glycocalyx structures) above the actin layer ( 2 ). 22A binds dotted fractions of glycoprotein on the oral sucker ( 3 ). (G) 22C recognizes spines, ciliated sensory papillae, and basement membrane/tegument/glycocalyx structures ( 1 ). (H) 38A recognizes spines, ciliated sensory papillae, and basement membrane/tegument/glycocalyx structures. Confocal images showing staining of PGT128 and PCDN76 38B are shown in Figures S6 C and S6D, respectively. Confocal microscopy staining was performed twice on different cercariae preparations. Representative images are shown from one experiment.

Article Snippet: Serum/plasma samples were inactivated with TritonX (0.1%) and diluted to 1:100 before adding to the wells. mAbs were used at 50 μg/mL in sample diluent (ab108769, Abcam) and serum standards provided in the Human Anti- Schistosoma mansoni IgG ELISA Kit (ab108769, Abcam) were used as controls.

Techniques: Binding Assay, Recombinant, Enzyme-linked Immunosorbent Assay, Positive Control, Staining, Confocal Microscopy

Journal: Cell Reports

Article Title: Cross-reactivity of glycan-reactive HIV-1 broadly neutralizing antibodies with parasite glycans

doi: 10.1016/j.celrep.2022.110611

Figure Lengend Snippet:

Article Snippet: Serum/plasma samples were inactivated with TritonX (0.1%) and diluted to 1:100 before adding to the wells. mAbs were used at 50 μg/mL in sample diluent (ab108769, Abcam) and serum standards provided in the Human Anti- Schistosoma mansoni IgG ELISA Kit (ab108769, Abcam) were used as controls.

Techniques: Recombinant, Plasmid Preparation, Enzyme-linked Immunosorbent Assay, Infection, Software, Microarray, Microscopy, Imaging

Journal: iScience

Article Title: Combination of serum human satellite RNA and miR-21-5p levels as a biomarker for pancreatic cancer

doi: 10.1016/j.isci.2023.106021

Figure Lengend Snippet:

Article Snippet: Total RNA was extracted from 200 μL of the serum using the miRNeasy Serum/Plasma Advanced Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

Techniques: Reverse Transcription, Microarray, Software