Journal: Cell reports

Article Title: Nanoparticle-based itaconate treatment recapitulates low-cholesterol/low-fat diet-induced atherosclerotic plaque resolution

doi: 10.1016/j.celrep.2024.114911

Figure Lengend Snippet:

Article Snippet: Direct-zol RNA Miniprep Kit , Zymo Research , R2054.

Techniques: Purification, Plasmid Preparation, Produced, Recombinant, Concentration Assay, Saline, Labeling, Membrane, Enzyme-linked Immunosorbent Assay, Quantitation Assay, Phospholipid Assay, BIA-KA, RNAscope, HD Assay, Polymer, Sequencing, Expressing, Software, Microscopy

Journal: Journal of the Royal Society Interface

Article Title: Testing the reproducibility and robustness of the cancer biology literature by robot

doi: 10.1098/rsif.2021.0821

Figure Lengend Snippet: The list of repeatable results. These drugs were found to produce statistically significant changes in the expression of the genes. Human reading—what was found by human annotators: text—is the direction of change of gene expression (↑ increase, stimulation; ↓ decrease, inhibition); MCF7—whether the change was found using the MCF7 cell line; MDA—whether the change was found using the MDA-MB-231 cell line. Text mining—the direction of change of gene expression identified automatically by the computer. MCF7—the results of the robotic experiments using the MCF7 cell line. MDA—the results of the robotic experiments using the MDA-MB-231 cell line. Team 1—the statistical significance found by team 1; team 2—the statistical significance found by team 2; sign—the direction of change of gene expression.

Article Snippet: Thermo Fisher single-tube Taqman gene expression assays: AKT1, Hs00178289_m1; ATF4, Hs00909569_g1; BIRC5, Hs00977611_g1; BRCA1, Hs01556193_m1; BRCA2, Hs00609073_m1; CASP3, Hs00234387_m1; CCND1, Hs00765553_m1; CTNNB1, Hs00355049_m1; EGFR, Hs01076092_m1; ERBB2, Hs01001580_m1; ERBB3, Hs00176538_m1; ERBB3, Hs00951444_m1; ERBB3, Hs00951455_m1; ESR1, Hs01046812_m1; ESR1, Hs01046816_m1; HDAC1, Hs00606262_g1; HIF1A, Hs00153153_m1; HSP90, Hs00743767_sH; IL-8, Hs00174103_m1; MAPT, Hs00902194_m1; MELK, Hs01106440_m1; MMP-2, Hs01548727_m1; MMP-9, Hs00234579_m1; MTOR, Hs00234508_m1; NF-KB1, Hs00765730_m1; p21, Hs00355782_m1; p27, Hs01597588_m1; p300, Hs00914223_m1; p53, Hs01034249_m1; PDK1, Hs01561850_m1; PGR, Hs00172183_m1; PTEN, Hs02621230_s1; RASSF1, Hs00176538_m1; STAT3, Hs00374280_m1; STK11, Hs00975988_m1; TNF, Hs01113624_g1; TXNIP, Hs00197750_m1; uPA, Hs01547054_m1; VEGFA, Hs00900055_m1.

Techniques: Expressing, Gene Expression, Inhibition

Journal: Journal of the Royal Society Interface

Article Title: Testing the reproducibility and robustness of the cancer biology literature by robot

doi: 10.1098/rsif.2021.0821

Figure Lengend Snippet: The list of statements about the effect of a drug on gene expression levels (textual propositions) tested for reproducibility and robustness.

Article Snippet: Thermo Fisher single-tube Taqman gene expression assays: AKT1, Hs00178289_m1; ATF4, Hs00909569_g1; BIRC5, Hs00977611_g1; BRCA1, Hs01556193_m1; BRCA2, Hs00609073_m1; CASP3, Hs00234387_m1; CCND1, Hs00765553_m1; CTNNB1, Hs00355049_m1; EGFR, Hs01076092_m1; ERBB2, Hs01001580_m1; ERBB3, Hs00176538_m1; ERBB3, Hs00951444_m1; ERBB3, Hs00951455_m1; ESR1, Hs01046812_m1; ESR1, Hs01046816_m1; HDAC1, Hs00606262_g1; HIF1A, Hs00153153_m1; HSP90, Hs00743767_sH; IL-8, Hs00174103_m1; MAPT, Hs00902194_m1; MELK, Hs01106440_m1; MMP-2, Hs01548727_m1; MMP-9, Hs00234579_m1; MTOR, Hs00234508_m1; NF-KB1, Hs00765730_m1; p21, Hs00355782_m1; p27, Hs01597588_m1; p300, Hs00914223_m1; p53, Hs01034249_m1; PDK1, Hs01561850_m1; PGR, Hs00172183_m1; PTEN, Hs02621230_s1; RASSF1, Hs00176538_m1; STAT3, Hs00374280_m1; STK11, Hs00975988_m1; TNF, Hs01113624_g1; TXNIP, Hs00197750_m1; uPA, Hs01547054_m1; VEGFA, Hs00900055_m1.

Techniques: Gene Expression

Journal: Journal of the Royal Society Interface

Article Title: Testing the reproducibility and robustness of the cancer biology literature by robot

doi: 10.1098/rsif.2021.0821

Figure Lengend Snippet: The list of major robust results. In major robustness the original textual statement was about neither MCF7 nor MDA-MB-231 cells. Notes: In one case, ↑PTEN/resveratrol, we see a consistently opposite effect in both MCF7 and MDA-MB-231 cells to that observed in the paper in MCF7 cells. This observation does not invalidate the replicability of the original result, but it does raise questions about its reproducibility. PTEN (phosphatase and tensin homologue) acts as a tumour suppressor gene. Up to 70% of primary prostate tumours lose one PTEN allele and retain the other copy [ 36 ]. Resveratrol (3,5,4′-trihydroxy-trans-stilbene) is a stilbenoid, a natural plant product. Resveratrol is associated with possible life longevity. The inhibition of PTEN by resveratrol is potentially of clinical concern.

Article Snippet: Thermo Fisher single-tube Taqman gene expression assays: AKT1, Hs00178289_m1; ATF4, Hs00909569_g1; BIRC5, Hs00977611_g1; BRCA1, Hs01556193_m1; BRCA2, Hs00609073_m1; CASP3, Hs00234387_m1; CCND1, Hs00765553_m1; CTNNB1, Hs00355049_m1; EGFR, Hs01076092_m1; ERBB2, Hs01001580_m1; ERBB3, Hs00176538_m1; ERBB3, Hs00951444_m1; ERBB3, Hs00951455_m1; ESR1, Hs01046812_m1; ESR1, Hs01046816_m1; HDAC1, Hs00606262_g1; HIF1A, Hs00153153_m1; HSP90, Hs00743767_sH; IL-8, Hs00174103_m1; MAPT, Hs00902194_m1; MELK, Hs01106440_m1; MMP-2, Hs01548727_m1; MMP-9, Hs00234579_m1; MTOR, Hs00234508_m1; NF-KB1, Hs00765730_m1; p21, Hs00355782_m1; p27, Hs01597588_m1; p300, Hs00914223_m1; p53, Hs01034249_m1; PDK1, Hs01561850_m1; PGR, Hs00172183_m1; PTEN, Hs02621230_s1; RASSF1, Hs00176538_m1; STAT3, Hs00374280_m1; STK11, Hs00975988_m1; TNF, Hs01113624_g1; TXNIP, Hs00197750_m1; uPA, Hs01547054_m1; VEGFA, Hs00900055_m1.

Techniques: Inhibition, Activation Assay, Over Expression, Membrane, Polymer, Binding Assay

Journal: Cell

Article Title: Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

doi: 10.1016/j.cell.2021.11.017

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: In brief, digested cells were seeded in 3-dimensional (3D) Growth-factor Reduced Matrigel (Corning), fed with human complete organoid medium containing Advanced DMEM/F12 (GIBCO), 10 mM HEPES (GIBCO), 1x GlutaMAX (GIBCO), 500 nM A83-01 (Tocris), 50 ng/mL mEGF (Peprotech), 100 ng/mL mNoggin (Peprotech), 100 ng/mL hFGF10 (Peprotech), 10 nM hGastrin I (Sigma), 1.25 mM N-acetylcysteine (Sigma), 10 mM Nicotinamide (Sigma), 1x B27 supplement (GIBCO), RSPONDIN-1 conditioned media 10% final, WNT3A conditioned media 50% final, 100 U/mL penicillin/streptomycin (GIBCO), and 1x Primocin (Invivogen) , and maintained at 37°C in 5% CO 2 .

Techniques: Polymer, Recombinant, Amplification, Reverse Transcription, Membrane, DNA Library Preparation, Picogreen Assay, Software, Imaging

Journal: Cell Reports Medicine

Article Title: Single extracellular vesicle detection assay identifies membrane-associated α-synuclein as an early-stage biomarker in Parkinson’s disease

doi: 10.1016/j.xcrm.2025.101999

Figure Lengend Snippet:

Article Snippet: Purmorphamine , Tocris , Cat# 4551.

Techniques: Virus, Recombinant, Electron Microscopy, Bicinchoninic Acid Protein Assay, Software, Membrane, Polymer, Lysis, Extraction, Western Blot, Conjugation Assay

Journal: The Journal of Biological Chemistry

Article Title: Polymer-based antibody mimetics (iBodies) target human PD-L1 and function as a potent immune checkpoint blocker

doi: 10.1016/j.jbc.2024.107325

Figure Lengend Snippet: Chemical structure of the N -(2-hydroxypropyl)methacrylamide (HPMA) copolymer carrier called iBody and its functional ligands. A , general design of iBodies. iBodies can carry various ligands, for example a fluorophore ( yellow ), an affinity anchor ( blue ) and a targeting ligand ( green ). B and C , anti-human PD-L1 iBodies (α-hPD-L1 iBodies) were synthesized by decorating HPMA copolymers (pHPMA) with the PD-L1-targeting ligand WL12 (iBody 1 and iBody 2), a biotin affinity anchor (iBody 1 and iBody 3) and an ATTO488 fluorophore (iBody 1 and iBody 3).

Article Snippet: DNA encoding extracellular domain (residues 19–239) of human PD-L1 was amplified by PCR from pCMV3-full-length human PD-L1 plasmid (Sino Biological Inc. cat# HG10084-CH), and subcloned into pTT28 vector (National Research Council of Canada) between Nhe I and AgeI restriction sites.

Techniques: Functional Assay, Synthesized

Journal: The Journal of Biological Chemistry

Article Title: Polymer-based antibody mimetics (iBodies) target human PD-L1 and function as a potent immune checkpoint blocker

doi: 10.1016/j.jbc.2024.107325

Figure Lengend Snippet: The characterization and composition of anti-hPD-L1 iBodies

Article Snippet: DNA encoding extracellular domain (residues 19–239) of human PD-L1 was amplified by PCR from pCMV3-full-length human PD-L1 plasmid (Sino Biological Inc. cat# HG10084-CH), and subcloned into pTT28 vector (National Research Council of Canada) between Nhe I and AgeI restriction sites.

Techniques: Negative Control

Journal: The Journal of Biological Chemistry

Article Title: Polymer-based antibody mimetics (iBodies) target human PD-L1 and function as a potent immune checkpoint blocker

doi: 10.1016/j.jbc.2024.107325

Figure Lengend Snippet: Binding characteristics of α-PD-L1 iBodies and WL12 to immobilized rhPD-L1. A–C , determination of EC 50 for iBody 1 and WL12 in a sandwich ELISA. Dilution series of iBody 1 (biotinylated and carrying WL12), iBody 3 (negative control, lacking the PD-L1-targeting ligand), biotinylated WL12 and ATTO488-WL12 were incubated in the presence or absence of 100 ng of directly immobilized rhPD-L1. The interaction for biotinylated WL12 and iBodies was detected by addition of Neutravidin-HRP and subsequent measurement of relative luminescence, whereas for ATTO-WL12, the detection was carried out by measuring the fluorescence intensity. EC 50 was calculated using a 4-parameter logistic function in GraphPad Prism 9.0.0. D , kinetic parameters of the interaction of iBody 2 with immobilized rhPD-L1. SPR was performed using three concentrations of iBody 2 (carrying the PD-L1-targeting ligand only) in the presence of immobilized rhPD-L1. The negative control (25 nM Ctrl, black ) contains the highest concentration of iBody 2 in the absence of rhPD-L1. Kinetic parameters were calculated by fitting the curves using a one-to-one model in TraceDrawer v.1.5 software. Data are representative of three independent experiments.

Article Snippet: DNA encoding extracellular domain (residues 19–239) of human PD-L1 was amplified by PCR from pCMV3-full-length human PD-L1 plasmid (Sino Biological Inc. cat# HG10084-CH), and subcloned into pTT28 vector (National Research Council of Canada) between Nhe I and AgeI restriction sites.

Techniques: Binding Assay, Sandwich ELISA, Negative Control, Incubation, Fluorescence, Concentration Assay, Software

Journal: The Journal of Biological Chemistry

Article Title: Polymer-based antibody mimetics (iBodies) target human PD-L1 and function as a potent immune checkpoint blocker

doi: 10.1016/j.jbc.2024.107325

Figure Lengend Snippet: iBodies bind to membrane-bound hPD-L1. A , flow cytometry analysis of iBody 1 (carrying WL12, biotin and ATTO488) and iBody 3 (mock polymer, carrying biotin and ATTO488) binding to hPD-L1-transfected and wild-type (hPD-L1 and WT) CHO cells. Cells were measured on a BD LSRFortessa flow cytometer, gated for single cells, and analyzed with FlowJo 10.4.1( Fig. S4 ). EC 50 was calculated from the median fluorescence intensity (MFI) using a 4-parameter logistic function in GraphPad Prism 9.0.0 (representative of two experiments). B , flow cytometry analysis of ATTO488-WL12 using the same cell lines and methods (representative of two experiments). C , visualization of hPD-L1 expression on hPD-L1-transfected and wild-type CHO cells. Cells were fixed with 2% formaldehyde (30 min, RT), blocked with 1% BSA (2 h, RT), and stained with 10 nM of iBody 1 or iBody 3 or Alexa Fluor 488-conjugated α-hPD-L1 antibody or the control antibody (Ctrl Ab; Alexa Fluor 488-conjugated mouse IgG1 kappa, clone: P3.6.2.8.1) were added directly to seeded CHO cells transfected or untrasnfected with PD-L1 (1 h, RT). Cells were washed, nuclei were stained with 2 μg/ml Hoechst 33342 and visualized using a Zeiss confocal microscope. Scale bar = 20 μm. The figure shows representative data out of two experiments. D , detection of hPD-L1 expression on cancer cell lines. A panel of cancer cell lines was stained with 100 nM iBody 1 ( red ), 100 μl of 1:100 FITC-conjugated α-PD-L1 antibody (clone 29E.2A3, green) or 100 nM iBody 3 ( blue ) and 15 ug/ml control antibody (Ctrl Ab; mouse FITC-conjugated IgG2b, clone MPC-11, yellow ) or without staining ( grey ). Adherent cells were trypsinized and washed alongside with suspension cells and stained for 30 min at 4 °C. Cells were washed, measured on a BD LSRFortessa flow cytometer, and gated for single cells ( Fig. S7 ). The data were analyzed with FlowJo 10.4.1.

Article Snippet: DNA encoding extracellular domain (residues 19–239) of human PD-L1 was amplified by PCR from pCMV3-full-length human PD-L1 plasmid (Sino Biological Inc. cat# HG10084-CH), and subcloned into pTT28 vector (National Research Council of Canada) between Nhe I and AgeI restriction sites.

Techniques: Membrane, Flow Cytometry, Polymer, Binding Assay, Transfection, Fluorescence, Expressing, Staining, Microscopy, Suspension

Journal: The Journal of Biological Chemistry

Article Title: Polymer-based antibody mimetics (iBodies) target human PD-L1 and function as a potent immune checkpoint blocker

doi: 10.1016/j.jbc.2024.107325

Figure Lengend Snippet: α-hPD-L1 iBodies restore activation of PD-1/PD-L1-suppressed Jurkat T cells. A , schematic illustration of the cellular model for in vitro evaluation of α-PD-L1 compounds (created in biorender.com ). B , PD-L1-overexpressing Raji B cells were pre-incubated with a dilution series of α-PD-L1 compounds in the presence of 25 pg/ml SEE for 1 h and then co-cultured in a 1:1 ratio with PD-1-overexpressing Jurkat T cells for 24 h. Supernatants were collected, and IL-2 levels were measured using ELISA. EC 50 was calculated using a 4-parameter logistic function in GraphPad Prism 9.0.0. Data are representative of five independent experiments performed in duplicates, with error bars indicating the standard deviation. C , PD-L1-overexpressing Raji B cells were pre-incubated with 2 nM of α-PD-L1 compounds in the presence of 25 pg/ml SEE for 1 h and then co-cultured in a 1:1 ratio with PD-1-overexpressing Jurkat T cells for 18 h. Cells were collected and stained with BV421-conjugated anti-human CD69 antibody. The isotype control antibody (100 ng) was used to stain the iBody 2-treated sample. Cells were measured with a BD LSRFortessa instrument ( Fig. S9 ). Data are represented as median fluorescence intensity (MFI). Error bars indicate the standard deviation. D , histograms indicate the percentage of CD69-expressing cells (gated above the basal CD69 expression in the absence of SEE; no SEE). Data were analyzed with FlowJo 10.4.1 and are representative of three independent experiments performed in duplicates. MFI comparison was carried out using a one-way ANOVA test in GraphPad Prism 9.0.0. ∗∗ indicates p -value < 0.01; ns = not significant.

Article Snippet: DNA encoding extracellular domain (residues 19–239) of human PD-L1 was amplified by PCR from pCMV3-full-length human PD-L1 plasmid (Sino Biological Inc. cat# HG10084-CH), and subcloned into pTT28 vector (National Research Council of Canada) between Nhe I and AgeI restriction sites.

Techniques: Activation Assay, In Vitro, Incubation, Cell Culture, Enzyme-linked Immunosorbent Assay, Standard Deviation, Staining, Fluorescence, Expressing, Comparison