Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (human) | MCF10A-5E | Janes et al., 2010 | RRID:CVCL_0598 | |
| Cell line (human) | HEK293T LX | ClonTech Laboratories | Cat # 632180 | |
| Cell line (mouse) | NIH3T3 | ATCC | Cat # CRL-1658 | |
| Cell line (mouse) | SYF mouse embryonic fibroblasts (MEFs) | ATCC | Cat # CRL-2459 | |
| Cell line (Escherichia coli) | Stellar chemically competent cells | ClonTech Laboratories | Cat # 636763 | |
| Recombinant DNA reagent | pCMV-dR8.91 lentivirus packaging plasmid | Gift from Prof. Didier Trono, EPFL | Addgene # 12263 | |
| Recombinant DNA reagent | pMD2.G lenti helper plasmid | Gift from Prof. Didier Trono, EPFL | Addgene # 12259 | |
| Recombinant DNA reagent | pHR EGFR-FusionRed | Yang et al., 2021 | Addgene # 179263 | |
| Recombinant DNA reagent | pHR EGFR-CD3ζ1-FusionRed | This paper | N/A | EGFR-ITAM construct |
| Recombinant DNA reagent | pHR EGFR-CD3ζ2-FusionRed | This paper | N/A | EGFR-ITAM construct |
| Recombinant DNA reagent | pHR EGFR-CD3ζ3-FusionRed | This paper | N/A | EGFR-ITAM construct |
| Recombinant DNA reagent | pHR EGFR-CD3γ-FusionRed | This paper | N/A | EGFR-ITAM construct |
| Recombinant DNA reagent | pHR EGFR-CD3δ-FusionRed | This paper | N/A | EGFR-ITAM construct |
| Recombinant DNA reagent | pHR EGFR-CD3ε-FusionRed | This paper | Addgene # 188626 | EGFR-ITAM construct |
| Recombinant DNA reagent | pHR EGFR- CD3ε-mNeonGreen | This paper | N/A | EGFR-ITAM construct |
| Recombinant DNA reagent | pHR iRFP-ZtSH2 | This paper | Addgene # 188627 | ZtSH2 biosensor |
| Recombinant DNA reagent | pHR mScarlet-ZtSH2 | This paper | N/A | ZtSH2 biosensor |
| Recombinant DNA reagent | pHR EGFR(R84K)-CD3ε-FusionRed | This paper | N/A | GBM-mutant EGFR construct (Figure 3) |
| Recombinant DNA reagent | pHR EGFR(A265V)-CD3ε-FusionRed | This paper | N/A | GBM-mutant EGFR construct (Figure 3) |
| Recombinant DNA reagent | pHR ErbB2-FusionRed | This paper | N/A | ITAM-less ErbB2 construct (Figure 4) |
| Recombinant DNA reagent | pHR ErbB2- CD3ε-FusionRed | This paper | Addgene # 188628 | ITAM-tagged ErbB2 (Figure 4) |
| Recombinant DNA reagent | pHR EGFR-Citrine | This paper | N/A | Fluorescent EGFR construct (Figure 4) |
| Recombinant DNA reagent | pHR Clover-VISH2 | This paper | Addgene # 188629 | tSH2 biosensor (Figure 5) |
| Recombinant DNA reagent | pHR EGFR-CD3ε-TagBFP | This paper | N/A | ITAM-tagged EGFR (Figure 5) |
| Recombinant DNA reagent | pHR EGFR-SLP76-TagBFP | This paper | Addgene # 188630 | ITAM-tagged EGFR (Figure 5) |
| Recombinant DNA reagent | pHR Grb2-TagBFP | This paper | Addgene # 188631 | Grb2-based biosensor (Figure 1) |
| Recombinant DNA reagent | pHR FGFR1-CD3ε-FusionRed | This paper | Addgene # 188632 | ITAM-tagged FGFR1 (Figure 4) |
| Recombinant DNA reagent | pHR FGFR1-FusionRed | This paper | N/A | ITAM-less FGFR1 (Figure 4) |
| Recombinant DNA reagent | pHR PDGFRβ-CD3ε-FusionRed | This paper | N/A | ITAM-tagged PDGFR (Figure 4) |
| Recombinant DNA reagent | pHR PDGFRβ-FusionRed | This paper | N/A | ITAM-less PDGFR (Figure 4) |
| Recombinant DNA reagent | pHR VEGFR3-CD3ε-FusionRed | This paper | N/A | ITAM-tagged VEGFR (Figure 4) |
| Recombinant DNA reagent | pHR VEGFR3-FusionRed | This paper | N/A | ITAM-less VEGFR (Figure 4) |
| Recombinant DNA reagent | pHR ErkKTR-TagBFP | 9 | N/A | |
| Recombinant DNA reagent | pX330 EGFR-sgRNA | This paper, using a plasmid from Feng Zhang, MIT | Addgene # 188633 | EGFR-targeting gRNA (Figure 6) |
| Recombinant DNA reagent | pUC19 EGFRup-CD3ε-mNeonGreen-EGFRdown | This paper | Addgene # 188634 | CRISPR plasmid for EGFR modification (Figure 6) |
| Sequence-based reagent | PEF122 forward primer | This paper | 5′- TTCTTTTGCAGCAACAGCAAGAGGGCCCTCCC-3′ | Used to verify CRISPR tagging; see ‘Methods’ |
| Sequence-based reagent | PEF123 reverse primer | This paper | 5’- TCCGTTTCTTCTTTGCCCAGGAAGGGACAGAGTGGCTTATCC-3’ | Used to verify CRISPR tagging; see ‘Methods’ |
| Antibody | Anti-EGFR antibody (rabbit monoclonal) | Cell Signaling Technology | Cat # 4267 | Used at 1:1000 for western blotting |
| Antibody | Anti-pEGFR antibody (rabbit monoclonal) | Cell Signaling Technology | Cat # 3777 | Used at 1:1000 for western blotting |
| Antibody | Anti-β-actin antibody (mouse monoclonal) | Cell Signaling Technology | Cat # 3700 | Used at 1:1000 for western blotting |
| Antibody | Anti-pAkt antibody (rabbit polyclonal) | Cell Signaling Technology | Cat # 9271 | Used at 1:1000 for western blotting |
| Antibody | Anti-ppErk antibody (rabbit polyclonal) | Cell Signaling Technology | Cat # 9101 | Used at 1:1000 for western blotting |
| Antibody | Anti-EEA1 antibody (mouse monoclonal) | Cell Signaling Technology | Cat # 48453 | Used at 1:100 for immunostaining |
| Antibody | Anti-ZAP70 antibody (rabbit monoclonal) | Cell Signaling Technology | Cat # 3165 | Used at 1:1000 for western blotting |
| Antibody | Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 (goat polyclonal) |
Invitrogen | Cat # A-11001 | Used at 1:500 for immunostaining |
| Antibody | Goat anti-Rabbit IgG (Heavy chain), Superclonal Recombinant Secondary Antibody, Alexa Fluor 647 (goat polyclonal) |
Invitrogen | Cat # A27040 | Used at 1:500 for immunostaining |
| Antibody | Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 (goat polyclonal) |
Invitrogen | Cat # A-21236 | Used at 1:500 for immunostaining |
| Antibody | IRDye 680RD Goat anti-Mouse IgG antibody (goat polyclonal) |
LI-COR | Cat # 926-68070 | Used at 1:10,000 for western blotting |
| Antibody | IRDye 800CW Goat anti-Rabbit IgG antibody (goat polyclonal) |
LI-COR | Cat # 926-32211 | Used at 1:10,000 for western blotting |
| Peptide, recombinant protein | Bovine serum albumin | Sigma-Aldrich | Cat # 12659 | |
| Peptide, recombinant protein | Fibronectin | Corning | Cat # CB-40008A | Cell adhesion coating |
| Peptide, recombinant protein | ClonAmp HiFi PCR polymerase | ClonTech Laboratories | Cat # 639298 | Polymerase |
| Peptide, recombinant protein | Insulin | Sigma-Aldrich | Cat # I6634 | |
| Peptide, recombinant protein | Cholera toxin | Sigma-Aldrich | Cat # C8052 | |
| Peptide, recombinant protein | L-glutamine | Gibco | Cat # 25030-081 | |
| Peptide, recombinant protein | EGF | R&D Systems | Cat # 236-EG-200 | |
| Peptide, recombinant protein | Epiregulin | R&D Systems | Cat # 1195-EP-025 | |
| Peptide, recombinant protein | Epigen | R&D Systems | Cat # 6629-EP-025 | |
| Peptide, recombinant protein | FGF4 | R&D Systems | Cat # 235-F4-025 | |
| Peptide, recombinant protein | PDGF-BB | Millipore Sigma | Cat # P3201 | |
| Peptide, recombinant protein | VEGF-C | R&D Systems | Cat # 9199-VC-025 | |
| Chemical compound, drug | Gefitinib | Cell Signaling Technology | Cat # 4765 | |
| Chemical compound, drug | Hydrocortisone | Sigma-Aldrich | Cat # H0888 | |
| Chemical compound, drug | Penicillin/ streptomycin | Gibco | Cat # 15140–122 | |
| Chemical compound, drug | TrypLE Express | Gibco | Cat # 12605-028 | |
| Chemical compound, drug | FuGENE HD | Promega | Cat # E2311 | |
| Chemical compound, drug | Lipofectamine 3000 | Thermo Fisher Scientific | Cat # L3000015 | |
| Chemical compound, drug | Aminopropyl trimethoxysilane | Sigma-Aldrich | Cat # 281778 | |
| Chemical compound, drug | Glutaraldehyde | Sigma-Aldrich | Cat # 340855 | |
| Chemical compound, drug | 40% acrylamide solution | Bio-Rad | Cat # 1610140 | |
| Chemical compound, drug | 2% bis-acrylamide solution | Bio-Rad | Cat # 161-0142 | |
| Chemical compound, drug | N,N,N’,N’-Tetramethyl ethylenediamine (TEMED) | Sigma-Aldrich | Cat # T9281 | |
| Chemical compound, drug | Ammonium persulfate (APS) | Sigma-Aldrich | Cat # A3678 | |
| Commercial assay or kit | inFusion HD cloning kit | ClonTech Laboratories | Cat # 638911 | Cloning kit |
| Other | DMEM/F12 | Gibco | Cat # 11320033 | Culture media |
| Other | Horse serum | Gibco | Cat # 16050122 | Serum for culture media |
| Other | DMEM | Gibco | Cat # 11995-065 | Culture media |
| Other | Fetal bovine serum | R&D Systems | Cat # S11150 | Serum for culture media |
| Software, algorithm | FIJI | Schindelin et al., 2012 |
http://fiji.sc; RRID:SCR_00228 |
|
| Software, algorithm | Python code for computational model; analysis code for raw data | This paper | https://github.com/toettchlab/Farahani2022/ (copy archived at toettchlab, 2023) | |
| Software, algorithm | R Studio 1.1.456 | RStudio | rstudio.com; RRID:SCR_000432 |