Journal: BMC Cancer

Article Title: Role of Cancer Associated Fibroblast (CAF) derived miRNAs on head and neck malignancies microenvironment: a systematic review

doi: 10.1186/s12885-025-13965-9

Figure Lengend Snippet: Summary characteristics of included studies

Article Snippet: Jin Yang1 – Et al [ ] , 2021 , china , In vitro (human) and In vivo (animal) , oral squamous cell carcinoma (OSCC) , In vitro case sample: 1. 6 OSCC patients (were obtained from the West China Hospital of Stomatology at Sichuan University during 2017–2019; The OSCC patients were 45–63 years old, experienced no relapses, and underwent no preoperative chemotherapy and/or radiotherapy.) 2. The human OSCC cell lines Cal-27, UMSCC-1, HSC-2, and FaDu were purchased from ATCC or obtained from the State Key Laboratory of Oral Diseases In vitro control sample: 1. 6 patients who received third molar extraction as normal controls 2. Cal-27 cells were used alone as the control group in this study In vivo case sample: Four- to six-week-old BALB/c nude mice, half male and half female, were purchased from Charles River (Beijing, China) , 1. Clinical tissue sample collection and primary cell culture 2. Plasmid construction and cell transfection 3. Cell lines and mice 4. RNA isolation, RNA sequencing, and qRT-PCR 5. Immunohistochemistry and immunofluorescence 6. Histology and immunohistochemistry 7. Western blotting 8. RNA-FISH and luciferase reporter assays 9. Bioinformatic analysis 10. Statistical analysis , Using siRNA to knock down lncRNA H19 suppressed the MAPK signaling pathway and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) and miR-675-5p. Additionally, the lncRNA H19/miR-675-5p/PFKFB3 axis was found to promote the glycolysis pathway in oral cancer-associated fibroblasts (CAFs), confirmed through luciferase reporter system assays and treatment with a specific miRNA inhibitor miR-675-5p/PFKFB3 act as key regulators in lncRNA H19-mediated glycolysis in oral CAFs , The lncRNA H19 was found to be a crucial lncRNA in oral cancer-associated fibroblasts (CAFs) and was simultaneously increased in both oral cancer cell lines and CAFs. Using small interfering RNA (siRNA) techniques, we found that reducing lncRNA H19 levels impacted the growth, movement, and glucose metabolism of oral cancer-associated fibroblasts (CAFs). The study introduces a novel approach to analyzing glucose metabolism in oral cancer-associated fibroblasts (CAFs), potentially offering a unique biomarker for oral squamous cell carcinoma (OSCC) diagnosis and a fresh target for anti-tumor treatment.

Techniques: In Vitro, Control, Formalin-fixed Paraffin-Embedded, Expressing, Quantitative RT-PCR, Cell Culture, Transfection, Western Blot, Migration, Biomarker Discovery, Isolation, Purification, Reverse Transcription, Polymerase Chain Reaction, Over Expression, Labeling, Transmission Assay, Electron Microscopy, RNA Extraction, Sequencing, Quantitative Proteomics, Real-time Polymerase Chain Reaction, Immunofluorescence, Immunohistochemistry, Luciferase, Gene Expression, Disruption, Reporter Assay, Immunodepletion, Amplification, Immunocytochemistry, Flow Cytometry, Derivative Assay, Immunohistochemical staining, Extraction, Microarray, Contraction Assay, Comparison, In Vivo, Ex Vivo, Staining, Invasion Assay, Tube Formation Assay, Fluorescence, In Situ Hybridization, Reverse Transcription Polymerase Chain Reaction, Inhibition, Apoptosis Assay, Enzyme-linked Immunosorbent Assay, Produced, Phospho-proteomics, Transformation Assay, Activation Assay, Cell Isolation, Transduction, Stable Transfection, DNA Methylation Assay, Cell Migration Assay, Plasmid Preparation, Zymography, Functional Assay, Translocation Assay, Clinical Proteomics, Construct, MTT Assay, Co-culture Assay, Pull Down Assay, Immunoprecipitation, Tumorigenicity Assay, Transferring, RNA Sequencing, Knockdown, Small Interfering RNA, Immunostaining, Protein-Protein interactions, Gradient Centrifugation, CCK-8 Assay, Injection, Protein Extraction

Journal: Nature protocols

Article Title: Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays

doi: 10.1038/nprot.2009.183

Figure Lengend Snippet: A schematic outlining the steps of an array paint experiment. (a) Derivative chromosomes are isolated from a cell line by chromosome sorting (Steps 1–22), the derivative chromosomes are then amplified using a GenomePlex Complete Whole Genome Amplification Kit, (Steps 23–38) and the derivative chromosome amplified DNA is fluorescently labeled in Cy3 or Cy5 (Steps 39–54). (b) The fluorescently labeled derivative DNA is hybridized onto a microarray using Agilent SureHyb chamber (Steps 55–80) (picture courtesy of Agilent). (c) The microarray is scanned (Steps 81–83). (d) The features on the microarray are analyzed, the log2 ratio of Cy5/Cy3 intensity is calculated for each oligonucleotide and plotted against the base-pair chromosome position (Steps 84–85). The top schematic represents the data for one parent chromosome (chr A), whereas the lower schematic represents the other parent chromosome (chr B). The transition from a high (red spots) to a low log2 ratio (green spots) indicates a chromosome breakpoint. If a feature sequence spans a chromosome breakpoint, the ratio will be close to 0 (orange spots).

Article Snippet: Agilent aCGH Wash Buffer 1 (Agilent, cat. no. 5188-5221) Agilent aCGH Wash Buffer 2 (Agilent, cat. no. 5188-5222) EQUIPMENT 0.22-μm syringe filter (Nalgene, cat. no. 190-2520) 20-μm mesh filter (Celltrics, Partec, cat. no. 04-004-2325) MoFlo High Performance Cell Sorter equipped with two water-cooled lasers (Coherent, Innova 300 series) 1.5-ml microfuge tubes Benchtop microfuge Heat block Thermal cycler Microcon YM-30, 30 kDa, sample reservoirs and tubes (Millipore, cat. no. 42422) NanoDrop 2000 Spectrophotometer (Thermo Scientific) Hybridization Gasket Slide Kit (5) for 1 microarray per slide format (Agilent, cat. no. G2534-60003) Hybridization Chamber Kit (Agilent, cat. no. G2534A) Blunt forceps (supplied with hybridization chamber) Human Genome CGH Microarray Kit 244A, consists of 5 microarrays (Agilent, cat. no. G4411B) DNA Microarray Hybridization Oven (Agilent, cat. no. G2545A) set to 65 °C, 20 rpm Hybridization Oven Rotator Rack (Agilent, cat. no. G2530-60029) Three glass troughs One slide rack Microarray Scanner (we used Agilent G2565CA but G2565BA can be used, Agilent) Slide holders supplied with scanner Feature Extraction 9.5 or 10.5 software and Agilent Scan Control software—both supplied with scanner DNA Analytics 4.0 (Agilent, cat. no. G4172AA) Freely available ‘R’ software Summit v3.1 (analysis software from Dako/Beckman Coulter) REAGENT SETUP Cell culture medium Supplement 500 ml of RMPI 1640 or DMEM with 15% (vol/vol) fetal calf serum and antibiotics.

Techniques: Isolation, Amplification, Whole Genome Amplification, Labeling, Microarray, Sequencing

Journal: Nature protocols

Article Title: Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays

doi: 10.1038/nprot.2009.183

Figure Lengend Snippet: Troubleshooting table.

Article Snippet: Agilent aCGH Wash Buffer 1 (Agilent, cat. no. 5188-5221) Agilent aCGH Wash Buffer 2 (Agilent, cat. no. 5188-5222) EQUIPMENT 0.22-μm syringe filter (Nalgene, cat. no. 190-2520) 20-μm mesh filter (Celltrics, Partec, cat. no. 04-004-2325) MoFlo High Performance Cell Sorter equipped with two water-cooled lasers (Coherent, Innova 300 series) 1.5-ml microfuge tubes Benchtop microfuge Heat block Thermal cycler Microcon YM-30, 30 kDa, sample reservoirs and tubes (Millipore, cat. no. 42422) NanoDrop 2000 Spectrophotometer (Thermo Scientific) Hybridization Gasket Slide Kit (5) for 1 microarray per slide format (Agilent, cat. no. G2534-60003) Hybridization Chamber Kit (Agilent, cat. no. G2534A) Blunt forceps (supplied with hybridization chamber) Human Genome CGH Microarray Kit 244A, consists of 5 microarrays (Agilent, cat. no. G4411B) DNA Microarray Hybridization Oven (Agilent, cat. no. G2545A) set to 65 °C, 20 rpm Hybridization Oven Rotator Rack (Agilent, cat. no. G2530-60029) Three glass troughs One slide rack Microarray Scanner (we used Agilent G2565CA but G2565BA can be used, Agilent) Slide holders supplied with scanner Feature Extraction 9.5 or 10.5 software and Agilent Scan Control software—both supplied with scanner DNA Analytics 4.0 (Agilent, cat. no. G4172AA) Freely available ‘R’ software Summit v3.1 (analysis software from Dako/Beckman Coulter) REAGENT SETUP Cell culture medium Supplement 500 ml of RMPI 1640 or DMEM with 15% (vol/vol) fetal calf serum and antibiotics.

Techniques: Incubation, Isolation, Staining, Fluorescence, Negative Control, Produced, Labeling, Microarray, Hybridization

Journal: Science Progress

Article Title: Role of thrombus-derived exosomal lncRNA LOC101928697 in regulating endothelial function via FUS protein interaction in myocardial infarction

doi: 10.1177/00368504251372111

Figure Lengend Snippet: Analysis of the correlation between FUS protein and myocardial infarction. (a) Enrichment Analysis Bar Plot based on differential gene expression profiles in lncRNA microarray analysis.(b) Detection information about lncRNA LOC101928697 binding to FUS proteins in AnnoLnc2 database. (c) Detection information about lncRNA LOC101928697 binding to FUS protein in RBPDP database. (d) Scores in the RPISeq database on the model of lncRNA LOC101928697 binding to FUS protein. (e-g) Prediction information about lncRNA LOC101928697 binding to FUS protein in catRAPID website, (e) Statistical map information about protein and RNA binding sites, (f) Total scoring information, and (g) Interaction map showing the interaction region between protein and RNA. (h-i) Analyses about bioinformatics techniques based on GSE163772 in the GEO database, where (h) is a statistical map of FUS gene expression in endothelial cells of a mouse model of myocardial infarction, and (i) A scatter plot about the correlation between the level of FUS gene expression and the disease state (control vs. myocardial infarction).

Article Snippet: After extensive washing, the bound proteins were eluted, separated by SDS-PAGE, and analyzed by Western blot using anti-FUS antibody (Proteintech, Cat No. 11570-1-AP, dilution 1:5000) to detect the enrichment of FUS protein.

Techniques: Gene Expression, Microarray, Binding Assay, RNA Binding Assay, Control

Journal: Science Progress

Article Title: Role of thrombus-derived exosomal lncRNA LOC101928697 in regulating endothelial function via FUS protein interaction in myocardial infarction

doi: 10.1177/00368504251372111

Figure Lengend Snippet: Interaction of exosomal lncRNA LOC101928697 with FUS proteins. (a and b) The western blot detection of FUS protein expression in each group of cells and the statistical graph. (c) Statistical graph of RT-qPCR to detect the expression of FUS at the mRNA level in each group of cells. (d) The fluorescence graph of fluorescence in situ hybridization (FISH) experiment. In which FUS was labeled with green fluorescence, lncRNA LOC101928697 was labeled with red fluorescence, and the nucleus was labeled with blue fluorescence (20×). (e) Western blot detection of FUS protein following RNA pull-down using sense or antisense LOC101928697 transcripts. (f) Quantification of FUS protein enrichment in sense RNA pull-down versus antisense control, based on densitometric analysis. (g-h) Western blot detection of FUS protein expression in each group of cells after knockdown or overexpression of lncRNA LOC101928697 and the statistical graphs. (i) Statistical graph of mRNA level expression of FUS in each group of cells after knockdown or overexpression of lncRNA LOC101928697 by RT-qPCR assay. a p < 0.05 compared to control group. b p < 0.05 compared to exosome group. c p < 0.05 compared to siRNA + exosome group.

Article Snippet: After extensive washing, the bound proteins were eluted, separated by SDS-PAGE, and analyzed by Western blot using anti-FUS antibody (Proteintech, Cat No. 11570-1-AP, dilution 1:5000) to detect the enrichment of FUS protein.

Techniques: Western Blot, Expressing, Quantitative RT-PCR, Fluorescence, In Situ Hybridization, Labeling, Protein Enrichment, Control, Knockdown, Over Expression

Journal: Aquaculture (Amsterdam, Netherlands)

Article Title: Evaluation of a high-EPA oil from transgenic Camelina sativa in feeds for Atlantic salmon ( Salmo salar L.): Effects on tissue fatty acid composition, histology and gene expression

doi: 10.1016/j.aquaculture.2015.03.020

Figure Lengend Snippet: Summary of the results of microarray analysis.

Article Snippet: Microarray hybridisations were performed in SureHyb hybridisation chambers in a DNA Microarray Hybridisation Oven (Agilent Technologies).

Techniques: Microarray

Journal: European Journal of Inflammation

Article Title: Human interaction targets of SARS-COV-2 spike protein: A systematic review

doi: 10.1177/1721727X221095382

Figure Lengend Snippet: Basic characteristics of the included studies.

Article Snippet: Y. M. Hu , The in vitro antiviral activity of lactoferrin against common human coronaviruses and SARS-CoV-2 was mediated by targeting the heparan sulfate co-receptor , Human RD, Huh-7 cell, HEK293T cell, HCT-8 cell, Caco-2 cell, Calu-3 cell, and MRC-5 cell lines , Immunofluorescence, differential scanning fluorimetry, real-time PCR , ACE2 , lactoferrin (LF) had broad-spectrum antiviral activity against SARS-CoV-2, HCoV-OC43, HCoV-NL63, and HCoV-229E in cell culture, and bovine lactoferrin (BLF) was more potent than human lactoferrin. BLF bound to heparan sulfate proteoglycans (HSPGs), thereby blocking viral attachment to the host cell. The antiviral activity of BLF could be antagonized by the HSPG mimetic heparin. The antiviral activity of LF was synergistic with remdesivir in cell culture. The N-terminal positively charged region in BLF (residues 17–41) conferred the binding to HSPGs , ( ) .

Techniques: Expressing, Sequencing, Binding Assay, Mutagenesis, Flow Cytometry, Activity Assay, Enzyme-linked Immunosorbent Assay, Microneutralization Assay, Spectroscopy, Immunohistochemistry, Western Blot, Infection, Single Vesicle Fusion Assay, Activation Assay, Pull Down Assay, Affinity Chromatography, Immunofluorescence, Staining, Cell Culture, In Situ, Microarray, In Vitro, RNA Extraction, Functional Assay, Coagulation, Ex Vivo, Transgenic Assay, Transduction, Microscopy, Generated, Protein Binding, Blocking Assay, Isolation, RNA Sequencing Assay, Methylation, Mass Spectrometry, Purification, Neutralization, Imaging, Co-culture Assay, Luciferase, Titration, Depletion Assay, Chromatography, Inhibition, Next-Generation Sequencing, TCID50 Assay, Co-Immunoprecipitation Assay, Transmission Assay, Plaque Assay, Derivative Assay, Immunostaining, SPR Assay, Concentration Assay, Plasmid Preparation, Digital PCR, Real-time Polymerase Chain Reaction, In Vivo, Immunoprecipitation, Cell Attachment Assay, Marker, Variant Assay, Immunohistochemical staining, In Situ Hybridization, Protease Inhibitor, Transfection, Recombinant, Immunohistofluorescence, cDNA Library Assay, Labeling, Microscale Thermophoresis, Cytotoxicity Assay, Conjugation Assay, Raman Spectroscopy, Affinity Precipitation, Fluorescence, Förster Resonance Energy Transfer, Tube Formation Assay, DNA Methylation Assay, Peptide Microarray, TUNEL Assay, Kinase Assay, Confocal Microscopy, Endocytosis Assay, Affinity Purification, Over Expression, Proliferation Assay, Clone Assay, Transcomplementation Assay, Cell-Cell Fusion Assay, Silver Staining, Cell Adhesion Assay, Construct, Electron Microscopy, Produced, shRNA, Angiogenesis Assay, Far Western Blot, Dot Blot, Negative Staining, Enzymatic Assay, Multicolor Immunofluorescence Staining, CRISPR, Modification, XTT Assay