Journal: EMBO Molecular Medicine

Article Title: Cancer cell adaptation to hypoxia involves a HIF‐GPRC5A‐YAP axis

doi: 10.15252/emmm.201708699

Figure Lengend Snippet: A SILAC‐based proteomics data identify known (red) and novel (green) hypoxia‐induced proteins in SW620 cells. One‐sample t ‐test was performed. B Western blotting confirmed GPRC5A as a hypoxia‐induced protein in SILAC lysates. C Validation of GPRC5A Western blot data using siRNA. *Non‐specific band of ˜60 kDa not depleted by GPRC5A siRNA. D Confocal microscopy showing plasma membrane GPRC5A expression in hypoxic SW620 cells (scale bars: 75 μm). E Western blotting showing GPRC5A upregulation by hypoxia in a panel of colorectal tumour cell lines. F Basal & hypoxia‐induced GPRC5A protein expression was decreased by HIF‐1/2α depletion. G Depletion of HIF‐1β decreased GPRC5A protein upregulation in hypoxia. H Hypoxia mimetic DMOG induced HIF‐1/2α, CA9 and GPRC5A protein expression. Dual HIF‐1/2α depletion reduced GPRC5A induction by DMOG. I qRT–PCR demonstrating that GPRC5A mRNA was upregulated by hypoxia ( n = 3). GPRC5A was normalised to HPRT (error bars ± SD). J qRT–PCR demonstrating that HIF‐1/2α depletion decreased GPRC5A induction during hypoxia ( n = 3). GPRC5A was normalised to HPRT (error bars ± SD). K ChIP‐PCR analyses identify HIF‐1α binding to the GPRC5A promoter region containing a putative optimal HRE (error bars ± SD, n = 3). Data information: Asterisks (*) indicate non‐specific band. Level adjustments were made to images in Adobe Photoshop post‐acquisition for clarity (equal changes applied to the entire image). Representative examples of n = 3 independent experiments are shown. Source data are available online for this figure.

Article Snippet: The human colorectal tumour cell lines Caco2, DLD1, HT29, HCT15, HCT116, LOVO, LS174T, RKO, SW480 and SW620 were obtained from the American Type Culture Collection (ATCC; Rockville, USA).

Techniques: Multiplex sample analysis, Western Blot, Biomarker Discovery, Confocal Microscopy, Clinical Proteomics, Membrane, Expressing, Quantitative RT-PCR, Binding Assay

Journal: EMBO Molecular Medicine

Article Title: Cancer cell adaptation to hypoxia involves a HIF‐GPRC5A‐YAP axis

doi: 10.15252/emmm.201708699

Figure Lengend Snippet: A, B Expression of CA9 and GPRC5A in formalin‐fixed paraffin‐embedded hypoxic SW620 cells by IHC. Reduced CA9 and GPRC5A expressions with siRNA confirm antibody specificity (scale bars: 200 μm). C IHC analysis of serial sections from human colorectal tissue from patients with mesenteric ischaemia (strangulated colon). GPRC5A is co‐expressed with CA9 in the colonic epithelial cells (scale bars: 50 μm). D Quantitative RT–PCR analysis of mouse intestinal tissue. Gene expression was normalised to housekeeping gene Tbp . Raw data from three independent experiments ( n = 3 mice) are shown (error bars ± SEM). E Tg[ fli1 :eGFP; vhl −/− ] and Tg[ fli1 :eGFP] zebrafish embryos (5 days post‐fertilisation) demonstrate excessive angiogenesis and increased expression of HIF target genes (scale bars: 100 μm). F gprc5ba was induced in vhl mutant zebrafish embryos and fli1 :eGFP zebrafish embryos exposed to 5% O 2 (vs. normoxia) for 24 h (RT–PCR). G, H Bioinformatic analysis of transcriptomics dataset GSE24551. Gene set analyses reveal GPRC5A mRNA strongly correlated with HIF/hypoxia gene signatures. GSEA datasets used were Semenza_HIF1_Targets (M12299) Broad_Hallmark_Hypoxia (M5891). Analysis was performed using R2 ( http://r2.amc.nl ). I Kaplan–Meier curve following analysis of transcriptomics dataset GSE24551. Event‐free survival is significantly reduced in patients with tumours expressing high levels of GPRC5A mRNA. Analysis was performed using R2 ( http://r2.amc.nl ). Data information: Level adjustments were made to images in Adobe Photoshop post‐acquisition for clarity (equal changes applied to the entire image). Representative examples of n = 3 independent experiments are shown. Source data are available online for this figure.

Article Snippet: The human colorectal tumour cell lines Caco2, DLD1, HT29, HCT15, HCT116, LOVO, LS174T, RKO, SW480 and SW620 were obtained from the American Type Culture Collection (ATCC; Rockville, USA).

Techniques: Expressing, Formalin-fixed Paraffin-Embedded, Quantitative RT-PCR, Gene Expression, Mutagenesis, Reverse Transcription Polymerase Chain Reaction

Journal: EMBO Molecular Medicine

Article Title: Cancer cell adaptation to hypoxia involves a HIF‐GPRC5A‐YAP axis

doi: 10.15252/emmm.201708699

Figure Lengend Snippet: A Lentivirally transduced and puromycin‐selected SW620:GPRC5A si1R cells were doxycycline‐induced (2.5 μg/ml) for 48 h and flow‐sorted (BD Influx) based on medium/high TurboGFP expression (note that pCW57‐GFP‐2A‐GPRC5A si1R uses the P2A self‐cleaving peptide to produce separate TurboGFP and GPRC5A si1R cDNA). Pre‐ and post‐flow‐sorted profiles are shown, confirming near 100% expression. Related to Figs D, and H, I, and L. B Confirmation of TurboGFP expression in doxycycline (2.5 μg/ml)‐treated SW620:GPRC5A si1R cells. Phase contrast and green (TurboGFP) images were obtained using the IncuCyte ZOOM live cell imaging system (scale bars: 300 μm). Level adjustments were made to images in Adobe Photoshop post‐acquisition for clarity (equal changes applied to the entire image). Related to Figs D, and H, I, and L. C Western blotting confirms GPRC5A overexpression in doxycycline‐treated SW620:GPRC5A si1R cells. Cells were treated for 72 h with doxycycline (2.5 μg/ml) in normoxia prior to harvest. Related to Figs D, and H, I, and L. Asterisk (*) indicates non‐specific band. D Optimisation of the violet ratiometric membrane asymmetry apoptosis assay for flow cytometry. SW620 cells were treated for 24 h with the pan‐BCL2 family inhibitor ABT‐737 (10 μM). Live, dead and apoptotic cells were gated using FlowJo (v10). A representative example is shown. Related to Fig E. Source data are available online for this figure.

Article Snippet: The human colorectal tumour cell lines Caco2, DLD1, HT29, HCT15, HCT116, LOVO, LS174T, RKO, SW480 and SW620 were obtained from the American Type Culture Collection (ATCC; Rockville, USA).

Techniques: Expressing, Live Cell Imaging, Western Blot, Over Expression, Membrane, Apoptosis Assay, Flow Cytometry

Journal: NPJ Precision Oncology

Article Title: GD2 CAR T cells against human glioblastoma

doi: 10.1038/s41698-021-00233-9

Figure Lengend Snippet: a Representative phase contrast microscopy pictures of patient-derived primary glioblastoma cells (C3, C6, C10, and C12) showing different morphological features (upper row). GD2 surface expression (solid histograms) in selected primary glioblastoma samples and isotype control (open histograms) measured by flow cytometry (lower row). b GD2 is extensively expressed in patient tumor resections by immunohistochemistry (middle column) and immunofluorescence (right column) stains, on the left column H&E staining. c Cartoon representing the second-generation anti-GD2 CAR structure. d Glioblastoma cell lines (dsRED T98G GD2 high , dsRED A172 GD2 low ) and e patient-derived primary glioblastoma cells (dsRED C3, dsRED C6, dsRED C10, and dsRED C12) co-cultures at 2:1 E:T ratio with GD2 CAR T and GFP control T cells derived from five PBMC donors (# n ). After 48 h tumor cell viability is calculated by fluorescence viability assay as reported in “Methods”. Data are shown as mean ± SD from six technical replicates; p values are calculated by an unpaired two-tailed t -test.

Article Snippet: GSC media is composed of DMEM-F12 (Gibco, Sigma-Aldrich, Saint Louis, MO, USA; #21331-020/046) supplemented with B27 1× (ThermoFisher Scientific, MA, USA; #12587010), EGF (20 ng/mL, PeproTech, London, UK; #AF-100-15), bFGF (20 ng/mL, PeproTech; #AF-100-18B), 1% glutamine (EuroClone, Pero, MI, Italy; #ECB3000D), and 1% penicillin–streptomycin (CarloErba, Milano, Italy; #FA30WL0022100), while commercially available glioblastoma cell lines (T98G ATCC® CRL-1690 TM and A172 ATCC® CRL-1620, Manassas, Virginia, USA) were maintained in DMEM-F12 with 10% FBS (Carlo Erba; #FA30WS181B500), 1% glutamine (EuroClone), and 1% penicillin–streptomycin (CarloErba).

Techniques: Microscopy, Derivative Assay, Expressing, Control, Flow Cytometry, Immunohistochemistry, Immunofluorescence, Staining, Fluorescence, Viability Assay, Two Tailed Test

Journal: NPJ Precision Oncology

Article Title: GD2 CAR T cells against human glioblastoma

doi: 10.1038/s41698-021-00233-9

Figure Lengend Snippet: Glioblastoma cells (dsRED C3, dsRED C6, dsRED C10, and dsRED C12) co-cultures with GD2 CAR T and GFP control T cells at three different E:T ratios. After 24, 48, and 72 h tumor viability is calculated by fluorescence viability assay as reported in “Methods”. Representative bar graphs from PBMC donor #4 are reported. Data are shown as mean ± SD from six technical replicates; p values are calculated by unpaired two-tailed t -test.

Article Snippet: GSC media is composed of DMEM-F12 (Gibco, Sigma-Aldrich, Saint Louis, MO, USA; #21331-020/046) supplemented with B27 1× (ThermoFisher Scientific, MA, USA; #12587010), EGF (20 ng/mL, PeproTech, London, UK; #AF-100-15), bFGF (20 ng/mL, PeproTech; #AF-100-18B), 1% glutamine (EuroClone, Pero, MI, Italy; #ECB3000D), and 1% penicillin–streptomycin (CarloErba, Milano, Italy; #FA30WL0022100), while commercially available glioblastoma cell lines (T98G ATCC® CRL-1690 TM and A172 ATCC® CRL-1620, Manassas, Virginia, USA) were maintained in DMEM-F12 with 10% FBS (Carlo Erba; #FA30WS181B500), 1% glutamine (EuroClone), and 1% penicillin–streptomycin (CarloErba).

Techniques: Control, Fluorescence, Viability Assay, Two Tailed Test

Journal: NPJ Precision Oncology

Article Title: GD2 CAR T cells against human glioblastoma

doi: 10.1038/s41698-021-00233-9

Figure Lengend Snippet: Representative fluorescence micrographs highlight a robust cluster activation and killing activity of GD2 CAR T population against primary glioblastoma cells. This feature was never evident in GFP T control cells. DsRED C3 glioblastoma (red) cells in co-culture with GD2 CAR T (green) and GFP T control cells (green) at 2:1 and 5:1 E:T ratios at 24, 48, 72, and 96 h. The scale bar: 400 µm.

Article Snippet: GSC media is composed of DMEM-F12 (Gibco, Sigma-Aldrich, Saint Louis, MO, USA; #21331-020/046) supplemented with B27 1× (ThermoFisher Scientific, MA, USA; #12587010), EGF (20 ng/mL, PeproTech, London, UK; #AF-100-15), bFGF (20 ng/mL, PeproTech; #AF-100-18B), 1% glutamine (EuroClone, Pero, MI, Italy; #ECB3000D), and 1% penicillin–streptomycin (CarloErba, Milano, Italy; #FA30WL0022100), while commercially available glioblastoma cell lines (T98G ATCC® CRL-1690 TM and A172 ATCC® CRL-1620, Manassas, Virginia, USA) were maintained in DMEM-F12 with 10% FBS (Carlo Erba; #FA30WS181B500), 1% glutamine (EuroClone), and 1% penicillin–streptomycin (CarloErba).

Techniques: Fluorescence, Activation Assay, Activity Assay, Control, Co-Culture Assay

Journal: NPJ Precision Oncology

Article Title: GD2 CAR T cells against human glioblastoma

doi: 10.1038/s41698-021-00233-9

Figure Lengend Snippet: a Glioblastoma cells (dsRED C6) co-cultures with either autologous or allogeneic GD2 CAR T and GFP control T cells at 5:1 E:T ratios. After 48 and 72 h tumor viability is calculated by fluorescence assay as reported in “Methods”. Data are shown as mean ± SD from three technical replicates; p values are calculated by unpaired two-tailed t -test. b Representative fluorescence micrographs show clusters of activation and killing activity of GD2 CAR T cells. GFP T cell population show an absence of reactivity of autologous cytotoxic lymphocytes. DsRED C6 glioblastoma (red) cells in co-culture with GD2 CAR T (green) and GFP T control cells (green) at 5:1 E:T ratio at 24, 48, and 72 h. The scale bar: 1000 µm.

Article Snippet: GSC media is composed of DMEM-F12 (Gibco, Sigma-Aldrich, Saint Louis, MO, USA; #21331-020/046) supplemented with B27 1× (ThermoFisher Scientific, MA, USA; #12587010), EGF (20 ng/mL, PeproTech, London, UK; #AF-100-15), bFGF (20 ng/mL, PeproTech; #AF-100-18B), 1% glutamine (EuroClone, Pero, MI, Italy; #ECB3000D), and 1% penicillin–streptomycin (CarloErba, Milano, Italy; #FA30WL0022100), while commercially available glioblastoma cell lines (T98G ATCC® CRL-1690 TM and A172 ATCC® CRL-1620, Manassas, Virginia, USA) were maintained in DMEM-F12 with 10% FBS (Carlo Erba; #FA30WS181B500), 1% glutamine (EuroClone), and 1% penicillin–streptomycin (CarloErba).

Techniques: Control, Fluorescence, Two Tailed Test, Activation Assay, Activity Assay, Co-Culture Assay

Journal: NPJ Precision Oncology

Article Title: GD2 CAR T cells against human glioblastoma

doi: 10.1038/s41698-021-00233-9

Figure Lengend Snippet: Co-culture supernatants of glioblastoma cell lines (dsRED T98G GD2 high , dsRED A172 GD2 low ) and primary glioblastoma cells (dsRED C3, dsRED C6, dsRED C10 and dsRED C12) with either GD2 CAR T or GFP control T cells (donor #4) at 2:1 E:T ratio are assessed for cytokine release at 48 h and 7days. Cytokine profile is measured by multiplex Luminex system, and the concentration level is reported as pg/mL. a Granzyme B. b MIP-1α. c IFNγ. d TNFα. e sFAS-Ligand. f TRAIL. g GM-CSF. h IL-6. i CD137. l TGF β1. Data are shown as mean ± SD from two technical replicates; p values are calculated by unpaired two-tailed t -test. NS not significant.

Article Snippet: GSC media is composed of DMEM-F12 (Gibco, Sigma-Aldrich, Saint Louis, MO, USA; #21331-020/046) supplemented with B27 1× (ThermoFisher Scientific, MA, USA; #12587010), EGF (20 ng/mL, PeproTech, London, UK; #AF-100-15), bFGF (20 ng/mL, PeproTech; #AF-100-18B), 1% glutamine (EuroClone, Pero, MI, Italy; #ECB3000D), and 1% penicillin–streptomycin (CarloErba, Milano, Italy; #FA30WL0022100), while commercially available glioblastoma cell lines (T98G ATCC® CRL-1690 TM and A172 ATCC® CRL-1620, Manassas, Virginia, USA) were maintained in DMEM-F12 with 10% FBS (Carlo Erba; #FA30WS181B500), 1% glutamine (EuroClone), and 1% penicillin–streptomycin (CarloErba).

Techniques: Co-Culture Assay, Control, Multiplex Assay, Luminex, Concentration Assay, Two Tailed Test

Journal: NPJ Precision Oncology

Article Title: GD2 CAR T cells against human glioblastoma

doi: 10.1038/s41698-021-00233-9

Figure Lengend Snippet: a Representative fluorescence microscopy images of glioblastoma spheroids alone (upper row) or in co-culture with either GD2 CAR T (bottom row) or GFP control T cells (middle row) at 2:1 E:T ratio. CAR T cells antitumor activity is monitored at 24, 48, 72, and 96 h. Tumor cells in red, GD2 CAR T cells and GFP control T cells in green. The scale bar is 1000 µm. b Representative fluorescence microscopy images of primary C3 glioblastoma cells forming a tissue-like structure in VITVO ® 3D bioreactor at 72 h and 5 days (left row) and then in co-culture with GD2 CAR T (right row) and GFP control T cells (middle row) at 5:1 E:T ratio. A fluorescence-based live/dead assay is used to monitor the cytotoxic effect of CAR T cells at 72 h and 5 days (living cells in green, dead cells in red). The scale bar: 1000 µm.

Article Snippet: GSC media is composed of DMEM-F12 (Gibco, Sigma-Aldrich, Saint Louis, MO, USA; #21331-020/046) supplemented with B27 1× (ThermoFisher Scientific, MA, USA; #12587010), EGF (20 ng/mL, PeproTech, London, UK; #AF-100-15), bFGF (20 ng/mL, PeproTech; #AF-100-18B), 1% glutamine (EuroClone, Pero, MI, Italy; #ECB3000D), and 1% penicillin–streptomycin (CarloErba, Milano, Italy; #FA30WL0022100), while commercially available glioblastoma cell lines (T98G ATCC® CRL-1690 TM and A172 ATCC® CRL-1620, Manassas, Virginia, USA) were maintained in DMEM-F12 with 10% FBS (Carlo Erba; #FA30WS181B500), 1% glutamine (EuroClone), and 1% penicillin–streptomycin (CarloErba).

Techniques: Fluorescence, Microscopy, Co-Culture Assay, Control, Activity Assay, Live Dead Assay

Journal: NPJ Precision Oncology

Article Title: GD2 CAR T cells against human glioblastoma

doi: 10.1038/s41698-021-00233-9

Figure Lengend Snippet: a Representative images of histological specimens immune-labeled with anti-human mitochondrial (MIT) monoclonal antibody (brown: DAB) confirmed the engraftment of intracranial injected patient-derived glioblastoma C12.FFLuc cells (T) in mouse brain (B). The scale bar: 100 µm. b Hematoxylin and eosin staining show the high infiltrative capacity of C12.FFLuc tumor cells (T) in mouse brain (B). First column, the scale bar is 1000 µm. Second and third columns, the scale bar: 100 µm. All sections were derived from formalin-fixed paraffin-embedded brains of euthanized mice at the initial signs of distress and weight loss of up to 30%.

Article Snippet: GSC media is composed of DMEM-F12 (Gibco, Sigma-Aldrich, Saint Louis, MO, USA; #21331-020/046) supplemented with B27 1× (ThermoFisher Scientific, MA, USA; #12587010), EGF (20 ng/mL, PeproTech, London, UK; #AF-100-15), bFGF (20 ng/mL, PeproTech; #AF-100-18B), 1% glutamine (EuroClone, Pero, MI, Italy; #ECB3000D), and 1% penicillin–streptomycin (CarloErba, Milano, Italy; #FA30WL0022100), while commercially available glioblastoma cell lines (T98G ATCC® CRL-1690 TM and A172 ATCC® CRL-1620, Manassas, Virginia, USA) were maintained in DMEM-F12 with 10% FBS (Carlo Erba; #FA30WS181B500), 1% glutamine (EuroClone), and 1% penicillin–streptomycin (CarloErba).

Techniques: Labeling, Injection, Derivative Assay, Staining, Formalin-fixed Paraffin-Embedded

Journal: Cell systems

Article Title: Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells

doi: 10.1016/j.cels.2020.10.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Human: SKMEL28, Melanoma Cell Line , MGH Cancer Center, primary source ATCC , CLS Cat# 300337/p495_SK-MEL-28, RRID:CVCL_0526.

Techniques: Formalin-fixed Paraffin-Embedded, Recombinant, Gene Expression, RNA Sequencing, Quantitative Proteomics, Phospho-proteomics, Software, Mass Spectrometry, Targeted Proteomics, Over Expression, Knockdown, Stable Transfection, Expressing, CRISPR, High Throughput Screening Assay, Microscopy, Live Cell Imaging, Cytometry, Staining

Journal: Cell systems

Article Title: Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells

doi: 10.1016/j.cels.2020.10.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Human: A-375 (A375), Melanoma Cell Line , MGH Cancer Center, primary source ATCC , ATCC Cat# CRL-1619, RRID:CVCL_0132.

Techniques: Formalin-fixed Paraffin-Embedded, Recombinant, Gene Expression, RNA Sequencing, Quantitative Proteomics, Phospho-proteomics, Software, Mass Spectrometry, Targeted Proteomics, Over Expression, Knockdown, Stable Transfection, Expressing, CRISPR, High Throughput Screening Assay, Microscopy, Live Cell Imaging, Cytometry, Staining

Journal: Cell systems

Article Title: Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells

doi: 10.1016/j.cels.2020.10.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Experimental Models: Cell Lines Human: A-375 (A375), Melanoma Cell Line MGH Cancer Center, primary source ATCC ATCC Cat# CRL-1619, RRID:CVCL_0132 Human:C32, Melanoma Cell Line MGH Cancer Center, primary source ATCC ATCC Cat# CRL-1585, RRID:CVCL_1097 Human: K2, Melanoma Cell Line MGH Cancer Center, primary source ATCC RRID:CVCL_AT85 Human: MMAc-SF (MMACSF), Melanoma Cell Line MGH Cancer Center, primary source RIKEN BioResource Center RCB Cat# RCB1200, RRID:CVCL_1420 Human: MZ-MEL-7 (MZ7MEL), Melanoma Cell Line MGH Cancer Center, primary source Johannes Gutenberg University Mainz RRID:CVCL_1436 Human: RVH-421 (RVH421), Melanoma Cell Line MGH Cancer Center, primary source ATCC RRID:CVCL_1672 Human: SKMEL28, Melanoma Cell Line MGH Cancer Center, primary source ATCC CLS Cat# 300337/p495_SK-MEL-28, RRID:CVCL_0526 Human: WM115, Melanoma Cell Line MGH Cancer Center, primary source ATCC ATCC Cat# CRL-1675, RRID:CVCL_0040 Human: HEK293T, Cell Line ATCC ATCC Cat# CRL-3216, RRID:CVCL_0063 A375_aEGFR1 (A375 with constitutive EGFR overexpression by CRISPRa; sgRNA1) This work N/A A375_aEGFR2 (A375 with constitutive EGFR overexpression by CRISPRa; sgRNA2) This work N/A A375_iEGFR (A375 with constitutive EGFR knockdown by CRISPRi; sgRNA1) This work N/A A375 stably expressing ERK-KTR:CFP reporter This work N/A Oligonucleotides See Table S2 for oligonucleotide sequences This work N/A Recombinant DNA psPAX2 Addgene Cat# 12260 pCMV-VSV-G Addgene Cat# 8454 pMH0001, expresses dCas9-BFP-KRAB, for CRISPRi Addgene Cat# 85969 pHRdSV40-dCas9–10xGCN4_v4-P2A-BFP, expresses dCas9 tagged with 10 copies of the GCN4 peptide v4 and BFP, for CRISPR a Addgene Cat# 60903 pHRdSV40-scFv-GCN4-sfGFP-VP64-GB1-NLS, expresses an antibody that binds to the GCN4 peptide from the SunTag system, and is fused to VP64, for CRISPRa Addgene Cat# 60904 pU6-sgRNA EF1Alpha-puro-T2A-BFP Addgene Cat# 60955 4_pPB_ERKKTRmTq2_H2BVenus_mCherryGemin, fluorescent reporter for H2B(Venus), ERK:TTR (mTurquoise), Geminin (mCherry) Fallahi-Sichani et al., 2017 N\A pCMV_hyPBase Fallahi-Sichani et al., 2017 N\A Software and Algorithms PySB, open-source programming framework for Systems Biology modelling in Python Lopez et al., 2013 http://pysb.org/ eBNG, energy-based modeling in BioNetGen Sekar et al., 2017 https://github.com/RuleWorld/bionetgen Amici (Advanced Multilanguage Interface to CVODES and IDAS) framework used for parameter estimation Fröhlich et al., 2017 https://github.com/ICB-DCM/AMICI Pypesto, a widely applicable and highly customizable toolbox for parameter estimation.

Techniques: Formalin-fixed Paraffin-Embedded, Recombinant, Gene Expression, RNA Sequencing, Quantitative Proteomics, Phospho-proteomics, Software, Mass Spectrometry, Targeted Proteomics, Over Expression, Knockdown, Stable Transfection, Expressing, CRISPR, High Throughput Screening Assay, Microscopy, Live Cell Imaging, Cytometry, Staining

Journal: Cell systems

Article Title: Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells

doi: 10.1016/j.cels.2020.10.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Human: HEK293T, Cell Line , ATCC , ATCC Cat# CRL-3216, RRID:CVCL_0063.

Techniques: Formalin-fixed Paraffin-Embedded, Recombinant, Gene Expression, RNA Sequencing, Quantitative Proteomics, Phospho-proteomics, Software, Mass Spectrometry, Targeted Proteomics, Over Expression, Knockdown, Stable Transfection, Expressing, CRISPR, High Throughput Screening Assay, Microscopy, Live Cell Imaging, Cytometry, Staining