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. Author manuscript; available in PMC: 2012 Aug 1.
Published in final edited form as: Cancer Genet. 2011 Aug;204(8):447–457. doi: 10.1016/j.cancergen.2011.07.009

Table I.

Validated chimeric protein fusions and gene truncations in MCF7 and HCC1954 breast cancer cell lines.

Cell line Genomic changes Chromosome locations Genes affected Effect on coding Somatic changes reported in cancers Validation method
MCF7 Inter-chromosomal translocation t(17;20)(q23.2;q13.13) BCAS3 and BCAS4 chimeric protein Fusion is recurrently present in MCF7 breast and HCT116 colon cancer cell lines. cDNA, genomic and published [9, 20, 28, 32, 53]
MCF7 Inter-chromosomal translocation t(17;3)(q22;p14.1) RAD51C.2 and ATXN7 chimeric protein Decreased expression of RAD51C found in majority of breast cancer cell lines. FISH, cDNA, genomic and published [28, 32]
MCF7 Intra-chromosomal inversion t(20;20)(q13.13;q13.13) SULF2 and ARFGEF2 chimeric protein SULF2 is a known tumor suppressor. SULF2 siRNA silencing is tumorigenic in vivo. cDNA, genomic and published [9, 28, 32]
MCF7 Inter-chromosomal translocation t(3;20)(p14.1;q13.13) SULF2 and PRICKLE2 chimeric protein see above SULF2 function and phenotype Genomic and published [9, 28, 32]
MCF7 Intra-chromosomal indel t(19;19)(p13.11;p13.11) MYO9B and FCHO1 chimeric protein MYO9B mutations associate with different inflammatory or autoimmune diseases. Genomic and published [9, 32]
MCF7 Intra-chromosomal indel t(17;17)(q22;q23.1) BC017255 and TMEM49 chimeric protein High-level amplification at TMEM49 induces high expression of miR-21, which targets PTEN and results in an aggressive breast cancer phenotype. [54] Genomic and published [9]
MCF7 Intra-chromosomal inversion t(17;17)(q23.1;q23.1) RPS6KB1 and TMEM49 chimeric protein See above TMEM49 function and phenotype. RPS6KB1 is amplified and overexpressed in 10–30% of primary breast cancers and cell lines. RPS6KB1 is regulated by the mTOR pathway which regulates cell cycle, growth and survival. [55] Genomic and published [9, 32]
MCF7 Intra-chromosomal inversion t(5;5)(q12.1;q12.1) DEPDC1B and ELOVL7 chimeric protein ELOVL7 is over expressed in bladder, breast, colorectal, esophageal, gastric, and prostate cancers. High-fat diet promotes growth of in vivo tumors of ELOVL7-expressed prostate cancer. [56] cDNA, genomic and published [9, 28, 32]
MCF7 Inter-chromosomal translocation t(3;17)(p14.2;q22) TEX14 and PTPRG chimeric protein PTPRG is a known tumor suppressor in kidney, lung and breast cancers. PTPRG has been shown to inhibit MCF7 anchorage-independent growth and reduce estrogenic response cell proliferation. [57] Genomic and published [9, 32]
MCF7 Inter-chromosomal translocation t(17;20)(q24.3;q13.32) ABCA5 and PPP4R1L chimeric protein Induction of ABCA5 correlates with differentiation state of human colon tumor. Genomic and published [9]
MCF7 Intra-chromosomal inversion t(X;X)(p22.2;p22.2) CXorf15 and SYAP1 chimeric protein no known cancer phenotype Genomic and published [9, 32]
MCF7 Inter-chromosomal translocation t(3;17)(p14.1;q23.2) BRIP1 truncation BRIP1 truncations confer a two-fold increased risk of developing breast cancer. Truncation mutants block double stranded break repair. Genomic and published [9]
HCC1954 Inter-chromosomal translocation t(5;8)(q23.1;q13.13) EIF3E truncation Truncation is tumorigenic in vivo. Decreased expression found in one third of all human breast carcinomas. cDNA, genomic and published [12, 33]
HCC1954 Inter-chromosomal translocation t(5;8)(q35.3;q24.21) NSD1 truncation Fusion protein in acute myeloid leukemia. FISH, cDNA, genomic and published [33]
HCC1954 Inter-chromosomal translocation t(5;8)(p15.33;q24.21) CLPTM1L and PVT1 truncation Amplification of PVT1 linked to pathophysiology of ovarian and breast cancers. Genomic and published [33]
HCC1954 Inter-chromosomal translocation t(5;8)(p15.35.2;q24.21) UIMC1 or RAP80 truncation Recurrent RAP80 missense mutations identified in breast cancer patients. [45, 46] Genomic