Supplementary Figure 1: Tissue of Origin analysis on 152 cell lines. (a) Heatmap representation of the 30 Tissue scores for the 152 cell lines.
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1 Supplementary Figure 1: Tissue of Origin analysis on 152 cell lines. (a) Heatmap representation of the 30 Tissue scores for the 152 cell lines. The scores summarize the global expression of the tissue specific genes for each one of the 30 tissues analyzed. (b) Plot representation of the weighed expression of the colon genes versus skin genes. Circle highlights COLO741 cells showing high skin score. (c) Log2 expression of the skin-specific tyrosinase (TYR) gene in 152 cell lines. Circle highlights COLO741 cells showing an outlier expression profile for the TYR gene. (d) Plot representation of the weighed expression of the colon genes versus small intestine genes. Circle highlights Hutu80 cells displaying high small intestine score.
2 Supplementary Figure 2. Cetuximab response curves in 150 CRC cell lines. 150 cell lines of colorectal origin were treated with increasing concentrations of cetuximab for 4 days and cell viability was assessed by measuring ATP content. Data are expressed as percent viability compared with medium-only treated cells. Based on their response cells can be classified in sensitive (red lines); partially sensitive (green lines) and resistant (blue lines) to cetuximab treatment.
3 Supplementary Figure 3. Cetuximab effect on CRC cell lines. (a) Cell viability of each CRC cell line at clinical relevant concentration of 10µg/ml of cetuximab after 4 days of treatment (indicated by yellow dots) closely parallel AUC values. (b-e) Analysis of cell viability after 4-5 days of cetuximab treatment indicates net loss of cells compared to the number of cells at time 0, in three representative sensitive cell models, even at clinical relevant dose of 10 µg/ml of cetuximab (b-d); while cetuximab exerts mainly a cytostatic effect (reduction of growth rate) on the intermediate cell lines LIM1215 (e). Data are expressed as percent viability compared to the number of cells at day 0.
4 Supplementary Figure 4: Expression based classification of Assignment of CRC cell lines. to intrinsic subtypes according to five expression-based CRC classifiers. (a) CRCassigner (CRCA) is the reference classifier. Enrichment matrix (Bonferroni-corrected hypergeometric p- values) comparing members of CRCA subtype versus others expression-based CRC classifiers. Orange highlighting indicates enrichment p-values< 0.05, green highlighting indicates depletion p-values< (b) Graphic representation of the consensus across the intrinsic subtypes identified in cell lines by CRCassigner (CRCA) by Sadanandam et al. and other four different classification systems. The number of cell lines significantly assigned to each subtype (FDR<0.2) is reported.
5 Supplementary Figure 5. Characterization of oncogenic TPM3-NTRK1 gene fusion in KM12 cells. (a) RNA seq analysis identified gene fusion event between exon 7 of the TPM3 gene and the exon10 of NTRK1 gene in the KM12 CRC cell line. (b) PCR on the cdna of KM12 cell lines confirmed the TPM3-NTRK1 gene rearrangements. KM12SM cells, a derivate of the KM12 cells, were used as positive control. (c) Break apart FISH analysis of TPM3-NTRK1 in KM12 cells shows clear separation of green (5 ) and red (3 ) signals corresponding to the NTRK1 gene. Scale bars, 10µm. (d) Western blot analysis confirmed overexpression of the TRKA protein (codified by NTRK1 gene) in KM12 cells, at a molecular weight compatible with TPM3-NTRK1 translocation. (e) RNAi knockdown of NTRK1 inhibits cell proliferation of KM12 cells harboring thetpm3-ntrk1 fusion gene. KM12 cells were analyzed by ATP lite proliferation assay 5 days after transfection with NTRK1-specific pooled sirnas, scrambled sirna, or transfection reagent (mock). Data are expressed as average ± s.d. of three independent experiments. si-rna mediated downregulation of NTRK1 levels were verified by western blot. (f) KM12 cells, resistant to the EGFR inhibitor cetuximab, are sensitive to the TRK inhibitor CEP701. Cell viability was assessed by measuring ATP content after 5 days of treatment. Data are expressed as average ± s.d. of three independent experiments. (g) CEP701 treatment downregulates MAPK and PI3K pathways in KM12 cells harboring NTRK1 genetic rearrangment. KM12 cells were treated with 1µM CEP701 for 12h, after which whole-cell extracts were subjected to western blot analysis.
6 Supplementary Figure 6. Oncogenic addiction to FGFR2 genetic amplification. (a) gdna RTPCR identified FGFR2 gene copy number increase in the NCIH716 CRC cell line. (b) Western blot analysis confirmed overexpression of FGFR2 protein in the NCIH716 cells. (c) RNAi knockdown of FGFR2 inhibits NCIH716 cell proliferation overexpressing the tyrosine kinase receptor. Cells were analyzed by ATP lite proliferation assay 5 days after transfection with FGFR2-specific pooled sirnas, scrambled sirna, or transfection reagent (mock). Data are expressed as average ± s.d. of three independent experiments. si-rna mediated downregulation of FGFR2 levels were verified by western blot analysis. (d) NCIH716 cell lines, resistant to EGFR inhibitor cetuximab, are sensitive to FGFR inhibitor AZD4547. Cell viability was assessed by measuring ATP content after 5 days of treatment. Data are expressed as average ± s.d. of three independent experiments. (e) AZD4547 treatment downregulates MAPK and PI3K pathways in NCIH716 cells harboring FGFR2 gene copy number increase. NCIH716 cells were treated with 0.5µM AZD4547 for 12h, after which whole-cell extracts were subjected to western blot analysis.
7 Supplementary Figure 7. Oncogenic addiction to overexpressed NTRK2 and RET kinases. (a) RNAi knockdown of NTRK2 inhibits cell proliferation of SNU503 cell line. SNU503 cells were analyzed by ATP lite 5 days after transfection with NTRK2-specific pooled sirnas, or transfection reagent (mock). Data are expressed as average ± s.d. of three independent experiments. si-rna mediated downregulation of NTRK2 levels were verified by cdna RTPCR. (b) SNU503 cells, resistant to the EGFR inhibitor cetuximab, are sensitive to the TRK inhibitor CEP701. Cell viability was assessed by measuring ATP content after 5 days of treatment. Data are expressed as average ± s.d. of three independent experiments. (c) Treatment with TRK inhibitor CEP701 initiates apoptosis in NTRK2-dependent SNU503 CRC cells. Protein lysates were analyzed by western blot after 3 days of treatment with 1µM CEP701. (d) Western blot analysis confirmed overexpression of RET protein in NCIH716 cells. (e) NCIH716 cells, resistant to the EGFR inhibitor cetuximab, are sensitive to the RET inhibitor ponatinib and to the FGFR inhibitor AZD4547. Cell viability was assessed by measuring ATP content after 5 days of treatment. Data are expressed as average ± s.d. of three independent experiments. (f) RNAi knockdown of RET inhibits cell proliferation in the NCIH716 cells. NCIH716 cells were analyzed by ATP lite proliferation assay 5 days after transfection with RET-specific pooled sirnas, scrambled sirna, or transfection reagent (mock). Data are expressed as average ± s.d. of three independent experiments. si-rna mediated downregulation of RET levels were verified by western blot analysis.
8 Supplementary Figure 8. Functional validation of KIT and PDGFRA overexpression. (a) Western blot analysis confirmed overexpression of KIT protein in HCA24 cell lines. (b) RNAi knockdown of KIT inhibits cell proliferation in HCA24 cells. HCA24 cells were analyzed by ATP lite 5 days after transfection with KIT-specific pooled sirnas, scrambled sirna, or transfection reagent (mock). Data are expressed as average ± s.d. of three independent experiments. si-rna mediated downregulation of KIT levels were verified by western blot. (c) RNAi knockdown of KIT initiates apoptosis in KIT-dependent HCA24 CRC cell lines. Protein lysates were analyzed by western blot 3 days after transfection with KIT-specific pooled sirnas, scrambled sirna, or transfection reagent (mock). (d) HCA24 cells, resistant to the EGFR inhibitor cetuximab, are resistant also to the KIT kinase inhibitors nilotinib or imatinib. Cell viability was assessed by measuring ATP content after 5 days of treatment. Data are expressed as average ± s.d. of three independent experiments. (e) Western blot analysis confirmed overexpression of PDGFRA protein in CACO2 cell lines. (f-g) CACO2 cells are not addicted to the PDGFRA overexpression. RNAi knockdown of PDGFRA failed to induce apoptosis. Protein lysates were analyzed by western blot 3 days after transfection with PDGFRA-specific pooled sirnas, scrambled sirna, or transfection reagent (mock). (h) CACO2 cell lines, resistant to the EGFR inhibitor cetuximab, are resistant also to the PDGFRA kinase inhibitors nilotinib or imatinib. Cell viability was assessed by measuring ATP content after 5 days of treatment. Data are expressed as average ± s.d. of three independent experiments.
9 Supplementary Figure 9. Full lengths western blot of Figure 4. (4e) C10 CRC cells overexpress ALK protein. (4f) RNAi knockdown of ALK inhibits cell proliferation of C10 cell line harboring the EML4-ALK fusion gene. (4h) Crizotinib treatment downregulates MAPK and PI3K pathways in C10 cells.
10 Supplementary Figure 10. Full lengths western blot of Supplementary Figure 5. (S5d) KM12 CRC cells overexpress TRKA protein. (S5e) RNAi knockdown of TRKA inhibits cell proliferation of KM12 cell line harboring the TPM3-NTRK1 fusion gene. (S5g) CEP701 treatment downregulates MAPK and PI3K pathways in KM12 cells.
11 Supplementary Figure 11. Full lengths western blot of Supplementary Figure 6. (S6b) NCIH716 CRC cells overexpress FGFR2 protein. (S6c) RNAi knockdown of FGFR2 inhibits cell proliferation of NCIH716 cell line harboring the FGFR2 gene amplification. (S6e) AZD4547 treatment downregulates MAPK and PI3K pathways in NCIH716 cells.
12 Supplementary Figure 12. Full lengths western blot of Supplementary Figure 7. (S7c) Treatment with TRK inhibitor CEP701 initiates apoptosis in NTRK2-dependent SNU503 CRC cells. (S7d) NCIH716 CRC cells overexpress RET protein. (S7f) RNAi knockdown of RET inhibits cell proliferation of NCIH716 cell line harboring the RET overexpression
13 Supplementary Figure 13. Full lengths western blot of Supplementary Figure 8. (S8a) HCA24 CRC cells overexpress KIT protein. (S8b) RNAi knockdown of KIT inhibits cell proliferation of HCA24 cells. (S8c) RNAi knockdown of KIT initiates apoptosis in KIT-dependent HCA24 CRC cells. (S8e) CACO2 CRC cells overexpress PDGFRA protein. (S8bf) RNAi knockdown of PDGFRA does not affect cell proliferation of CACO2 cells. (S8g) RNAi knockdown of PDGFRA does not induce apoptosis in CACO2 CRC cells.
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