KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti-phospho-p44/42 MAPK (ERK1/2) (Thr202/Tyr204) | Cell Signaling Technology | Cat# 4370; RRID:AB_2315112 |
| Rabbit polyclonal anti-p44/42 MAPK (ERK1/2) | Cell Signaling Technology | Cat# 9102; RRID:AB_330744 |
| Rabbit polyclonal anti-phospho-AKT (Ser473) | Cell Signaling Technology | Cat# 9271; RRID:AB_329825 |
| Rabbit polyclonal anti-Akt | Cell Signaling Technology | Cat# 9272; RRID:AB_329827 |
| Mouse monoclonal anti-Vinculin | Sigma-Aldrich | Cat# V9131; RRID:AB_477629 |
| Mouse monoclonal anti-c-K-Ras (Ab-1) (234-4.2) | Millipore | Cat# OP24; RRID:AB_2134115 |
| Mouse monoclonal anti-A-Raf (A-5) | Santa Cruz Biotechnology | Cat# sc-166771; Lot# A2617; RRID:AB_2060508 |
| Mouse monoclonal anti-Raf-B (F-7) | Santa Cruz Biotechnology | Cat# sc-5284; Lot# A0617; RRID:AB_626760 |
| Mouse monoclonal anti-Raf-1 (E-10) | Santa Cruz Biotechnology | Cat# sc-7267; Lot# I0117; RRID:AB_628196 |
| Rabbit polyclonal anti-phospho-MEK1 (Ser298) | Cell Signaling Technology | Cat# 9128; RRID:AB_330810 |
| Mouse monoclonal anti-MEK1/2 (L38C12) | Cell Signaling Technology | Cat# 4694; RRID:AB_10695868 |
| Rabbit monoclonal anti-c-Myc (D84C12) XP | Cell Signaling Technology | Cat# 5605; RRID:AB_1903938 |
| Rabbit polyclonal anti-phospho-p90RSK (Thr359/Ser363) | Cell Signaling Technology | Cat# 9344; RRID:AB_331650 |
| Rabbit monoclonal anti-RSK1/2/3 | Cell Signaling Technology | Cat# 9355; RRID:AB_659900 |
| Rabbit monoclonal anti-p27 kip1 | Cell Signaling Technology | Cat# 3688; RRID:AB_2077836 |
| Rabbit polyclonal anti-BAD | Cell Signaling Technology | Cat# 9292; RRID:AB_331419 |
| Rabbit monoclonal anti-Bim (C34C5) | Cell Signaling Technology | Cat# 2933; RRID:AB_1030947 |
| Rabbit monoclonal anti-E-Cadherin (24E10) | Cell Signaling Technology | Cat# 3195; RRID:AB_2291471 |
| Rabbit monoclonal anti-vimentin (D21H3) XP | Cell Signaling Technology | Cat# 5741; RRID:AB_10695459 |
| Rabbit polyclonal anti-phospho-FoxO1 (Thr24)/FoxO3a (Thr32) Antibody | Cell Signaling Technology | Cat# 9464; RRID:AB_329842 |
| Rabbit polyclonal anti-phospho-FoxO1 (Ser256) | Cell Signaling Technology | Cat# 9461; RRID:AB_329831 |
| Rabbit monoclonal anti-FoxO3a (D19A7) | Cell Signaling Technology | Cat# 12829; RRID:AB_2636990 |
| Rabbit monoclonal anti-phospho-c-Raf (Ser338) (56A6) | Cell Signaling Technology | Cat# 9427; RRID:AB_2067317 |
| Rabbit polyclonal anti-phospho-Cofilin (Ser3) | Cell Signaling Technology | Cat# 3311; RRID:AB_330238 |
| Rabbit polyclonal anti-Cofilin (D3F9) XP | Cell Signaling Technology | Cat# 5175; RRID:AB_10622000 |
| Rabbit monoclonal anti-phospho-RSK1 p90 (T359 + S363) antibody [E238] | Abcam | Cat# ab32413; RRID:AB_2181172 |
| Anti-RSK1 | Eli Lilly and Company | Cat# 334G |
| Mouse monoclonal anti-phospho-p44/42 MAPK (ERK1/2) (Thr202/Tyr204) (E10) | Cell Signaling Technology | Cat# 9106; RRID:AB_331768 |
| Rabbit monoclonal anti-p44/42 MAPK (Erk1/2) (137F5) | Cell Signaling Technology | Cat# 4695; RRID:AB_390779 |
| Rabbit polyclonal anti-phospho-S6 Ribosomal Protein (Ser240/244) | Cell Signaling Technology | Cat# 2215; RRID:AB_331682 |
| Mouse monoclonal anti-S6 Ribosomal Protein (54D2) | Cell Signaling Technology | Cat# 2317; RRID:AB_2238583 |
| Mouse monoclonal anti-β-actin | Sigma-Aldrich | Cat# A5441; RRID:AB_476744 |
| Bacterial and Virus Strains | ||
| DH5α | Thermo Fisher | Cat# 18258012 |
| Biological Samples | ||
| HPAF-II KRAS mutant PDAC rat xenograft tumor tissue | Provided by Eli Lilly | Star methods section of this paper |
| CFPAC-1 KRAS mutant PDAC rat xenograft tumor tissue | Provided by Eli Lilly | Star methods section of this paper |
| SW1990 KRAS mutant PDAC rat xenograft tumor tissue | Provided by Eli Lilly | Star methods section of this paper |
| Chemicals, Peptides, and Recombinant Proteins | ||
| BGB-283 (RAF family kinases and EGFR inhibitor) | Selleckchem | Cat# S7926 |
| BVD-523 (ERK1/2 inhibitor) | Provided by Biomed | Biomed |
| Valley Discoveries | Valley Discoveries | |
| Erlotinib (EGFR inhibitor) | Selleckchem | Cat# S7786 |
| FRAX-597 (PAK1/2/3 inhibitor) | Selleckchem | Cat# S7271 |
| LY3009120 (pan-RAF inhibitor) | Provided by Eli Lilly | Provided by Eli Lilly |
| LY3214996 (ERK1/2 inhibitor) | Provided by Eli Lilly | Provided by Eli Lilly |
| MK-2206 (AKT1/2/3 inhibitor) | Selleckchem | Cat# S1078 |
| SCH772984 (ERK1/2 inhibitor) | Selleckchem | Cat# S7101 |
| Trametinib (MEK1/2 inhibitor) | Selleckchem | Cat# S2673 |
| Vemurafenib (BRAF inhibitor) | Selleckchem | Cat# S1267 |
| Critical Commercial Assays | ||
| CellTiter-Glo Luminescent Cell Viability Assay | Promega | Cat# G7570 |
| RealTime-Glo MT Cell Viability Assay | Promega | Cat# G9711 |
| CellTox Green Cytotoxicity Assay | Promega | Cat# G8741 |
| TACS® Annexin V-FITC in situ apoptosis detection kit | Trevigen, Inc. | Cat# 4830 |
| Deposited Data | ||
| CRISPR | This paper | Star methods section of this paper |
| Drug sensitivity resistance testing (DSRT) | This paper | Star methods section of this paper |
| Reverse phase protein array (RPPA) | This paper | Star methods section of this paper |
| RNA sequencing | EMBL-EBI European Nucleotide Archive (ENA) database - https://www.ebi.ac.uk/ena/ | PRJEB38063 |
| Multiplexed kinase inhibitor beads and mass spectrometry (MIB/MS) | This paper | Star methods section of this paper |
| Experimental Models: Cell Lines | ||
| Human: HPAC (pancreatic adenocarcinoma) | ATCC | Cat# CRL-2119, RRID:CVCL_3517 |
| Human: MIA PaCa-2 (pancreatic ductal adenocarcinoma) | ATCC | CRM-CRL-1420, RRID:CVCL_0428 |
| Human: PANC-1 (pancreatic ductal adenocarcinoma) | ATCC | Cat# CRL-1469, RRID:CVCL_0480 |
| Human: Pa01C (pancreatic ductal adenocarcinoma) | (Jones et al., 2008) | (Jones et al., 2008) |
| Human: Pa02C (pancreatic ductal adenocarcinoma) | (Jones et al., 2008) | (Jones et al., 2008) |
| Human: Pa03C (pancreatic ductal adenocarcinoma) | (Jones et al., 2008) | (Jones et al., 2008) |
| Human: Pa04C (pancreatic ductal adenocarcinoma) | (Jones et al., 2008) | (Jones et al., 2008) |
| Human: Pa14C (pancreatic ductal adenocarcinoma) | (Jones et al., 2008) | (Jones et al., 2008) |
| Human: Pa16C (pancreatic ductal adenocarcinoma) | (Jones et al., 2008) | (Jones et al., 2008) |
| Human: A549 (lung adenocarcinoma) | ATCC | Cat# CCL-185, RRID:CVCL_0023 |
| Human: NCI-H358 (minimally invasive lung adenocarcinoma) | ATCC | Cat# CRL-5807, RRID:CVCL_1559 |
| Human: SW900 (squamous cell lung carcinoma) | ATCC | ATCC Cat# HTB-59, RRID:CVCL_1731 |
| Human: SW620 (Colon adenocarcinoma) | ATCC | Cat# CCL-227, RRID:CVCL_0547 |
| Human: HPAF-II (pancreatic adenocarcinoma) | ATCC | Cat# CRL-1997, RRID:CVCL_0313 |
| Human: CFPAC-1 (pancreatic ductal adenocarcinoma, cystic fibrosis) | ATCC | Cat# CRL-1918, RRID:CVCL_1119 |
| Human: SW1990 (pancreatic adenocarcinoma) | ATCC | Cat# CRL-2172, RRID:CVCL_1723 |
| Experimental Models: Organisms/Strains | ||
| Human: hM1A PDAC organoid | (Boj et al., 2015) | (Boj et al., 2015) |
| Human: hT2 PDAC organoid | (Boj et al., 2015) | (Boj et al., 2015) |
| Human: OT227 CRC organoid | (Schütte et al., 2017) | (Schütte et al., 2017) |
| Human: OT228 CRC organoid | (Schütte et al., 2017) | (Schütte et al., 2017) |
| Human: OT302 CRC organoid | (Schütte et al., 2017) | (Schütte et al., 2017) |
| Rat: HPAF II PDAC model | ATCC | ATCC# CRL-1997 |
| Rat: CFPAC-1 PDAC model | ATCC | ATCC# CRL-1918 |
| Rat: SW1990 PDAC model | ATCC | ATCC# CRL-2172 |
| Oligonucleotides | ||
| shRNA targeting sequence: ARAF #1 CCGGCCAGCCAATCAATGTTCGTCTCTCG AGAGACGAACATTGATTGGCTGGTTTTTT |
(Freeman et al., 2013) | TRCN0000000567 |
| shRNA targeting sequence: ARAF #2 CCGGGTAGAGGAGGTAGTGATGGAACTC GAGTTCCATCACTACCTCCTCTACTTTTT |
(Freeman et al., 2013) | TRCN0000000568 |
| shRNA targeting sequence: BRAF #1 CCGGCCGCTGTCAAACATGTGGTTACTCG AGTAACCACATGTTTGACAGCGGTTTTT |
(Freeman et al., 2013) | TRCN0000006290 |
| shRNA targeting sequence: BRAF #2 CCGGGCTGGTTTCCAAACAGAGGATCTCG AGATCCTCTGTTTGGAAACCAGCTTTTT |
(Freeman et al., 2013) | TRCN0000006291 |
| shRNA targeting sequence: CRAF #1 CCGGGCTTCCTTATTCTCACATCAACTC GAGTTGATGTGAGAATAAGGAAGCTTTTT |
(Freeman et al., 2013) | TRCN0000001065 |
| shRNA targeting sequence: CRAF #2 CCGGCGGAGATGTTGCAGTAAAGATCTC GAGATCTTTACTGCAACATCTCCGTTTTT |
(Freeman et al., 2013) | TRCN0000001066 |
| shRNA targeting sequence: KRAS #1 CAGTTGAGACCTTCTAATTGG | (Singh et al., 2009) | TRCN0000010369 |
| Software and Algorithms | ||
| ImageJ version 2.0.0-rc-69/1.52n software | (Schneider et al., 2012) | https://imagej.nih.gov/ij/ |
| DESeq2 package (version 1.22.2) | (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| GSEA (version 3.0) | (Subramanian et al., 2005) | http://www.gsea-msigdb.org/gsea/index.jsp |
| MSigDB (version 6.2) | (Liberzon et al., 2015) | https://www.gsea-msigdb.org/gsea/msigdb/index.jsp |
| Prism software (version 8.0.2) | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| Python (version 3.6.3) | Python Software Foundation | https://www.python.org/ |
| R (version 3.5.1) | R Core Team (2013) | http://www.R-project.org/ |
| Sci-Kit Learn (version 0.20.3) | (Pedregosa et al., 2011) | https://scikit-learn.org |
| SynergyFinder (version 1.6.1) | (lanevski et al., 2017) | https://bioconductor.org/packages/release/bioc/html/synergyfinder.html |