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1 Supplementary Appendix This appendix has been provided by the author to give readers additional information about his work. Supplement to: Croce CM. Oncogenes and cancer. N Engl J Med 2008;358:
2 Supplementary FIGURE 1.
3 Supplementary FIGURE 2.
4 Legends to Figures Supplementary Fig.1 Chromosome translocations observed in Burkitt lymphomas (BL). Upper: chromosomes included in the translocations. Lower: translocated chromosomes. Similar translocations have been observed in a fraction of human B-ALLs. In every case of BL the MYC oncogene is juxtaposed to enhancers present in the human immunoglobulin loci. Supplementary Fig. 2 The t(14;18) reciprocal chromosome translocation characteristic of human follicular lymphoma, one of the most common human lymphomas. The translocation juxtaposes the BCL2 gene to enhancer element of the immunoglobulin heavy chain locus causing deregulation of expression of oncogene BCL2.
5 Supplementary Table 1. Oncogenes Oncogene Chromosome Method of Identification Neoplasm Mechanism of Activation Protein Function Transcription factors v-myc 8q24.1 (MYC) Viral homologue Carcinoma myelocytomatosis Deregulated activity Transcription factor N-MYC 2p24 DNA amplification Neuroblastoma:lung carcinoma Deregulated activity Transcription factor L-MYC 1p32 DNA amplification Carcinoma of lung Deregulated activity Transcription factor v-myb 6q22-24 Viral homologue Myeloblastosis Deregulated activity Transcription factor v-fos Transcription factor 14q21-22 Viral homologue Osteosarcoma Deregulated activity API v-jun Transcription factor P31-32 Viral homologue Sarcoma Deregulated activity API v-ski 1q22-24 Viral homologue Carcinoma Deregulated activity Transcription factor v-rel 2p12-14 Viral homologue Lymphatic leukemia Deregulated activity Mutant NFKappa B v-ets-1 11p23-24 Viral homologue Erythroblastosis Deregulated activity Transcription factor v-ets-2 21q24.3 Viral homologue Erythroblastosis Deregulated activity Transcription factor v-erba1 T3 Transcription 17-p11-21 Viral homologue Erythroblastosis Deregulated activity factor v-erba2 T3 Transcription 3p Viral homologue Erythroblastosis Deregulated activity factor Inhibitors of apoptosis and others BCL2 18q21.3 Chromosomal translocation B-cell lymphomas Deregulated activity Antiapoptotic protein Gene amplification/ increased MDM2 12q14 DNA amplification Sarcomas protein Complexes with p53 Chromatin modifiers ALL1(MLL) 11q23 Chromosome translocation ALL or AML Gene fusion Chromatin modifier (This gene can fuse with >50 genes)
6 Growth factors v-sis 22q Sequence homology Glioma/fibrosarcoma Constitutive production B chain PDGF int2 11q13 Proviral insertion Mammary carcinoma Constitutive production Member of FGF family KS3 11q13.3 DNA transfection Kaposi s sarcoma Constitutive production Member of FGF family HST 11q13.3 DNA transfection Stomach carcinoma Constitutive production Member of FGF family Growth factor receptors Tyrosine kinases:integral membrane proteins EGFR 7P DNA amplification/dna Squamous cell carcinoma Gene amplification/protein/point EFG receptor sequencing Non-small cell lung cancer mutation v-fms 5q33-34 (FMS) Viral homologue Sarcoma Constitutive activation CSF1 receptor v-kit 4q11-21 (KIT) Viral homologue/dna Sarcoma/GIST Constitutive activation/ point Stem cell factor sequencing mutation receptor v-ros 6q22 (ROS) Viral homologue Sarcoma Constitutive activation? MET 7p31 DNA transfection MNNG-treated human HGF/SF receptor osteocarcinoma cell line DNA rearrangement/ ligandindependent constitutive activation (fusion proteins) NGF receptor TRK 1a32-41 DNA transfection Colon/thyroid carcinomas DNA rearrangement/ligandindependent constitutive activation (fusion proteins) NEU 17q Point mutation/dna Neuroblastoma/breast Gene amplification/point mutation? amplification carcinoma/nsclc RET 10q11.2 DNA transfection Carcinomas of thyroid Men 2A. DNA rearrangement/point mutation GFNG/NTT/ART/PSP Men 2B (ligand-indepen- dent constitutive receptor
7 activation/ fusion proteins) Receptors lacking protein kinase activity mas 6q24-27 DNA transfection Epidermoid carcinoma Rearrangement of 5 non-coding Angiotensin receptor region Signal transducers Cytoplasmic tyrosine kinases SRC Viral homologue Colon carcinoma Constitutive activation Protein tyrosine kinase v-yes 18q21-3 (YES) Viral homologue Sarcoma Constitutive activation Protein tyrosine kinase v-fgr 1p (FES) Viral homologue Sarcoma Constitutive activation Protein tyrosine kinase v-fes 15q25-26 (FES) Viral homologue Sarcoma Constitutive activation Protein tyrosine kinase ABL 9q34.1 Chromosome translocation CML DNA rearrangement (constitutive Protein tyrosine activation/fusion proteins) kinase Membrane-associated G proteins H-RAS 11p15.5 Viral homologue/dna Colon, lung, pancreas Point mutation GTPase transfection carcinomas K-RAS 12p Viral homologue/dna AML, thyroid carcinoma, Point mutation GTPase transfection melanoma/colon/lung N-RAS 1p11-13 DNA transfection Carcinoma, melanoma Point mutation GTPase BRAF 6 DNA sequencing Melanoma, thyroid, colon, Point mutation Ser/Thr kinase ovary gsp 20 DNA sequencing Adenomas of thyroid Point mutation Gs alpha gip 3 DNA sequencing Ovary, adrenal carcinoma Point mutation Gi alpha
8 GTPase excange factor (GEF) Dbl Xq27 DNA transfection Diffuse B-cell lymphoma DNA rearrangement GEF for Rho and Cdc42Hs Vav 19p13.2 DNA transfection Hematopoietic cells DNA rearrangement GEF for Ras? Serine/threonine kinases : cytoplasmic v-mos 8q11 (MOS) Viral homologue Sarcoma Constitutive activation Protein kinase (ser/thr) v-raf 3p25 (Raf-1) Viral homologue Sarcoma Constitutive activation Protein kinase (ser/thr) pim-i 6p21 (PIM-) Insertional mutagenesis T-cell lymphoma Constitutive activation Protein kinase (ser/thr) Cytoplasmic regulators v-crk 17q13 (CRK) Viral homologue Constitutive tyrosine phosphorylation SH-2/SH-3 adaptor of cellular substrates (eg, paxillin) ALL acute lymphoblastic leukemia ; AML= acute myeloid leukemia ; CML=chronic myelogenous leukemia ; GTPase- guanosine triphosphatase ; PDGF=plateletderived growth factor. Supplementary Table 2. Consistent Chromosome Translocations in Human Cancers Affected Gene Rearrangements Disease Protein Type Oncogenes juxtaposed with IG loci c-myc t(8:14) (q24:q32) BurKITt s lymphoma;bl- HLH domain ALL t(2:8) (p12:q24)
9 t(8:22) (q24:q11) BCL1 (Cyclin D1) t(11:14) (q13:q32) B-cell chronic lymphocyte PRADI-GI Cyclin D1 leukemia BCL-2 t(14:18) (q32:q21) Follicular lymphoma Inner mitochondrial membrane BCL-3 t(14:19) (q32:q13.1) Chronic B-cell leukemia CDC10 motif IL-3 t(5:14) (q31:q32) Acute pre-b-cell leukemia Growth factor Oncogenes juxtaposed with TRC loci c-myc t(8:14) (q24:q11) Acute T-cell leukemia HLH domain LYLA t(7:19) (q35:p13) Acute T-cell leukemia HLH domain TAL1/SCL/TCL-5 t(1:14) (q32:q11) Acute T-cell leukemia HLH domain TAL-2 t(7:9) (q35:q34) Acute T-cell leukemia HLH domain Rhombotin 1/Ttg-1 t(11:14) (p15:q11) Acute T-cell leukemia LIM domain Rhombotin 2/Ttg-2 t(11:14) (p13:q11) Acute T-cell leukemia LIM domain t(7:11) (q35:p13) HOX 11 t(10:14) (q24:q11) Acute T-cell leukemia Homeodomain t(7:10) (q35:q24) TAN-1 t(7:9) (q34:q34.3) Acute T-cell leukemia Notch homologue TCL-1 T(14;14) q11;q32.1) T-cell prolymphocytic or t(7q35-14q32.1) leukemia
10 or inv14(q11;q32.1) Hematopotetic tumor Gene fusion c-abl (9q34) t(9:22) (q34:q11) Chronic myelogenous Tyrosine kinase activated by leukemia and acute leukemia BCR BCR (22q11) PBX-1 (1q23) t(1:19) (q23:p13.3) Acute pre-b-cell leukemia Homeodomain E2A(19p13.3) HLH PML(15q21) t(15:27) (q21:q11- Acute promyelocytic Zn finger 22) leukemia RAR(17q21) CAN(6-23) t(6:9) (P23:q34) Acute myeloid leukemia No homology DEK(9q34) REL ins(2:12) (p ) Non-Hodgkin s lymphoma NF-κB family ALL1(MLL)* 11q23 ALL and AML Chromatin modifier Solid tumors Gene Fusions in sarcomas FLI1,EWS t(11:22) (q24:q12) Ewing s sarcoma Ets transcription factor family ERG,EWS t(21:22) (q22:q12) Ewing s sarcoma Ets transcription factor
11 family ATV1,EWS t(7:21) (q22:q12) Ewing s sarcoma Ets transcription factor family ATF1,EWS t(12:22) (q13:q12) Soft-tissue clear cell sarcoma Transcription factor CHN,EWS t(9:22) (q22 31:q12) Myxoid chondrosarcoma Steroid receptor family WT1,EWS t(11:22) (p13:q12) Desmoplastic small round Wilms tumor gene cell tumor SSX1,SSX2,SYT t(x18) (p11.2:q11.2) Synovial sarcoma HLH domain PAX3,FKHR t(2:13) (q37:q14) Alveolar Homeobox homologue PAX7,FKHR t(1:13) (q36:q14) Rhabdomyosarcoma Homeobox homologue CHOP,TLS t(12:16) (q13:p11) Myxoid liposarcoma Transcription factor var,hmg1-c t(var:12) (var:q13- Lipomas HMG DNA-binding protein 15) HMG2-C? t(12:14) (q13:q15) Leiomyomas HMG DNA-binding protein Gene fusions in thyroid carcinomas RET/ptc1 inv(10) (q11.2:q2.1) Papillary thyroid carcinomas Tyrosine kinase activated by H4 RET/ptc2 t(1:17) (q11.2:q23) Papillary thyroid carcinomas Tyrosine kinase activated by RIa(PKA)
12 RET/ptc3 inv(10) (q11.2) Papillary thyroid carcinomas Tyrosine kinase activated by ELE1 TRK inv(1) (q31:q22-23) Papillary thyroid carcinomas Tyrosine kinase activated by TPM3 TRK-T1(T2) inv(1) (q31:q25) Papillary thyroid carcinomas Tyrosine kinase activated by TPR TRK-T3 t(1q31:3) Papillary thyroid carcinomas Tyrosine kinase activated by TFG Gene fusions in prostate cancer TMPR552 ERG or t(21q22;21q22.3 or Prostate carcinoma Ets transcription factor ETV1 7p21.2 family activated by TMPR552 Deregulation of oncogenes Parathyroid tumors PTH deregulates PRAD1 inv(11)(p15q:q13) Parathyroid adenoma PRADI/Cyclin D1 (Cyclin D1) *ALL1 can fuse with more than 50 different genes. More frequently it fuses with AF4 in ALL and AF9 in AML
13 Supplementary Table 3. Oncogene Amplification in Human Cancers Tumor Type Gene Amplified Percent of Tumors Neuroblastoma MYCN ~20 Small cell lung cancer MYC ~15 Glioblastoma ERBB1 (EGFR) ~30 Breast cancer MYC ~20 EGFR2 ~20 FGFR1 ~10 FGFR2 ~10 CCND1 (Cyclin D1) Esophageal cancer MYC ~35 CCND1 (Cyclin D1) 25 Gastric cancer KRAS 10 CCNE (Cyclin E) 15 Hepatocellular cancer CCND1 (Cyclin D1) ~15
14 Sarcoma MDM CDK4 ~10 Cervical cancer MYC Ovarian cancer MYC ERBB2 (EGFR2) AKT2 ~10 Head and neck cancer MYC ~10 ERB B2 (EGFR2) 10 CCND (Cyclin D1) ~50 Colorectal cancer MYB HRAS 29 KRAS 22
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