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: 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