| Antibodies |
|
| Human monoclonal anti-human IL-6 |
Pfizer (MTA) |
PF-04236921 |
| Rat monoclonal anti-mouse IL-6 (clone MP5-20F3) |
BioXcell |
Cat#BE0046; RRID: AB_1107709 |
| Rabbit monoclonal anti-human Vimentin |
Abcam |
Cat#ab16700; RRID: AB_443435 |
| Rat monoclonal anti-mouse PECAM-1 (clone SZ31) |
Dianova |
Cat#DIA-310; RRID: AB_2631039 |
| Goat polyclonal anti-rabbit IgG; FITC conjugated |
BD Biosciences |
Cat#554020; RRID: AB_395212 |
| Goat polyclonal anti-rat IgG; Cy3 conjugated |
Invitrogen |
Cat#A10522; RRID: AB_2534031 |
| Mouse monoclonal anti-mouse p21 (F-5) |
Santa Cruz Biotechnology |
Cat#sc-6246; RRID: AB_628073 |
| Rabbit polyclonal anti-human p53 (FL-393) |
Santa Cruz Biotechnology |
Cat#sc-6243; RRID: AB_653753 |
| Rabbit polyclonal anti-human GAPDH (FL-335) |
Santa Cruz Biotechnology |
Cat#sc-25778; RRID: AB_10167668 |
| Rabbit polyclonal anti-human phospho-S6 (Ser235/236) |
Cell Signaling Technology |
Cat#2211; RRID: AB_331679 |
| Mouse monoclonal anti-human S6 (clone 54D2) |
Cell Signaling Technology |
Cat#2317; RRID: AB_2238583 |
| Rabbit monoclonal anti-human phospho-p65 (Ser 536) (clone 93H1) |
Cell Signaling Technology |
Cat#3033; RRID: AB_331284 |
| Rabbit monoclonal anti-human p65 (clone D14E12) |
Cell Signaling Technology |
Cat#8242; RRID: AB_10859369 |
| Mouse monoclonal anti-β-actin (clone AC-15) |
Sigma-Aldrich |
Cat#A5441; RRID: AB_476744 |
| Donkey anti-goat IgG; HRP conjugated |
Promega |
Cat#V8051; RRID: AB_430838 |
| Goat anti-rabbit IgG (H+L); HRP conjugated |
Promega |
Cat#W4011; RRID: AB_430833 |
| Goat anti-mouse IgG(H+L); HRP conjugated |
Promega |
Cat#W4021; RRID: AB_430834 |
| Goat anti-rat IgG; HRP conjugated |
R and D Systems |
Cat#HAF005; RRID: AB_1512258 |
|
| Chemicals, Peptides, and Recombinant Proteins |
|
| Sunitinib malate |
Pfizer (MTA) |
CAS: 341031-54-7 |
| Axitinib |
Pfizer (MTA) |
CAS: 319460-85-0 |
| Rapamycin |
LC Labs |
Cat#R-5000; CAS: 53123-88-9 |
| Bafilomycin A1 |
Invivogen |
Cat#88899-55-2; CAS: 88899-55-2 |
| 5-dodecanoylaminofluorescein di-β-D-galactopyranoside (C12FDG) |
Setareh Biotech |
Cat#7188; CAS: 138777-25-0 |
|
| Critical Commercial Assays |
|
| Senescence β-galactosidase staining kit |
Cell Signaling Technology |
Cat#9860 |
| Human XL Cytokine Array kit |
R and D Systems |
Cat#ARY022 |
| Mouse Angiogenesis Array kit |
R and D Systems |
Cat#ARY015 |
| Human IL-1α/IL-1F1 DuoSet ELISA |
R and D Systems |
Cat#DY200 |
| Human IL-1β/IL-1F2 DuoSet ELISA |
R and D Systems |
Cat#DY201 |
| Human IL-6 DuoSet ELISA |
R and D Systems |
Cat#DY206 |
| Human CCL2/MCP-1 DuoSet ELISA |
R and D Systems |
Cat#DY279 |
| Mouse IL-6 ELISA MAX Deluxe |
Biolegend |
Cat#431304 |
|
| Deposited Data |
|
| Renal clear cell carcinoma (TCGA; KIRC; Provisional) |
TCGA Research Network; cBioPortal for cancer genomics |
https://cancergenome.nih.gov http://www.cbioportal.org
|
| Expression data from breast cancer tumors treated with a single window of the antiangiogenic agent sunitinib |
Braga et al., 2017
|
GEO: GSE58837
|
| Gene expression changes during development of sunitinib resistance in renal cell carcinoma patient derived xenografts |
Diaz-Montero et al., 2016
|
GEO: GSE76068
|
| Tumor-independent host gene expression changes induced by tyrosine kinase inhibitors |
Mastri et al., 2018
|
GEO: GSE112466
|
| Gene expression changes in human breast cancer cells (LM2-4) after sunitinib resistance and long-term withdrawal |
This paper |
GEO: GSE122819
|
| Gene expression changes in mouse fibroblasts (3T3) after sunitinib resistance, and short/long-term withdrawal |
This paper |
GEO: GSE122820
|
| Gene expression changes in mouse kidney cancer cells (RENCA) after sunitinib resistance, and short/long-term withdrawal |
This paper |
GEO: GSE122821
|
|
| Experimental Models: Cell Lines |
|
| LM2-4 |
Laboratory of R. Kerbel |
N/A |
| LM2-4 SuR |
This paper |
N/A |
| LM2-4 SuR/LT-W |
This paper |
N/A |
| SN12-PM6 |
Laboratory of R. Kerbel |
N/A |
| SN12-PM6-N |
This paper |
N/A |
| SN12-PM6-N SuR |
This paper |
N/A |
| SN12-PM6-N SuR/LT-W |
This paper |
N/A |
| MeWo |
Laboratory of R. Kerbel |
RRID: CVCL_0445 |
| MeWo SuR |
This paper |
N/A |
| MeWo SuR/LT-W |
This paper |
N/A |
| 4T1 |
Laboratory of A. Gudkov |
RRID: CVCL_0125 |
| 4T1 SuR |
This paper |
N/A |
| 4T1 SuR/LT-W |
This paper |
N/A |
| 4T1 AxR |
This paper |
N/A |
| 4T1 AxR/LT-W |
This paper |
N/A |
| RENCA |
Laboratory of R. Pili |
RRID: CVCL_2174 |
| RENCA SuR |
This paper |
N/A |
| RENCA SuR/LT-W |
This paper |
N/A |
| RENCA AxR |
This paper |
N/A |
| RENCA AxR/LT-W |
This paper |
N/A |
| 3T3 |
Laboratory of I. Gelman |
RRID: CVCL_0594 |
| 3T3 SuR |
This paper |
N/A |
| 3T3 SuR/LT-W |
This paper |
N/A |
| PY4.1 |
Laboratory of D. Dumont |
RRID: CVCL_A336 |
| PY4.1 SuR |
This paper |
N/A |
| PY4.1 SuR/LT-W |
This paper |
N/A |
|
| Experimental Models: Organisms/Strains |
|
| SCID mouse |
Roswell Park Comprehensive Cancer Center; Laboratory animal shared resource (LASR) |
N/A |
| Balb/cAnNCrl mouse |
Charles River Labs |
Strain code: 028; RRID: IMSR_CRL:547 |
|
| Oligonucleotides |
|
| Primers, see Table S2
|
This paper; Integrated DNA Technology (IDT) |
N/A |
|
| Software and Algorithms |
|
| Illumina Genome Studio v2011.1 |
Illumina |
N/A |
| R v.3.3.2 |
The Comprehensive R Archive Network |
N/A |
| RStudio v.1.0.136 |
Integrated Development for R |
N/A |
| Lumi v.3.30.0 |
|
http://bioconductor.org/packages/release/bioc/html/lumi.html
|
| Limma v.3.34.9 |
|
http://bioconductor.org/packages/release/bioc/html/limma.html
|
| GraphPad Prism v6.07 |
GraphPad Software |
N/A |
| JAVA based Morhpeus |
Broad Institute |
https://software.broadinstitute.org/morpheus/
|
| GSEA |
Broad Institute |
http://software.broadinstitute.org/gsea/index.jsp
|
|
| Other |
|
| HumanHT-12v4 Expression BeadChip |
Illumina |
Cat#BD-103-0204 |
| MouseWG-6v2 Expression BeadChip |
Illumina |
Cat#BD-201-0202 |
