Phosphatidylinositol-3-OH Kinase or RAS Pathway Mutations in Human Breast Cancer Cell Lines

DOI: 10.1158/1541-7786.MCR-06-0263 Published February 2007

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FIGURE 1.
Identification of the PTEN 802insTAGG/834delCTTC mutation in cell line CAMA-1 by PCR amplification and sequencing of genomic DNA (bottom electropherogram). The wild-type PTEN gene sequence is shown for comparison (top electropherogram).
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FIGURE 2.
Analysis of PTEN transcriptional silencing through promoter methylation by cell culture in the presence (+) or absence (−) of 5-azacytidine. Reverse transcription-PCR amplification products are shown from seven mutant and three wild-type PTEN breast cancer cell lines, using primers specific for PTEN (top fragments) and the HPRT housekeeper (bottom fragments). These cell lines included the three cell lines without detectable PTEN expression, but there was no indication of PTEN promoter methylation.

Table 1.

Mutations Identified in the PTEN, PIK3CA, RAS, and BRAF Genes in Human Breast Cancer Cell Lines

Breast Cancer Cell Line	Affected Gene	Gene Sequence	Transcript Sequence	Predicted Protein Effect*	Oncogenic
HCC1937^†	PTEN	HD Ex. 1-9^‡	Not detectable	No expression	Yes
MDA-MB-468^†	PTEN	IVS4+1G>T^‡	c.del210_253 (Ex. 4)	A72fsX5	Yes
BT549^†	PTEN	821delG^‡	821delG	V275X	Yes
EVSA-T	PTEN	951delACTT^‡	951delACTT	T319X	Yes
CAMA-1	PTEN	274G>C^§	274G>C	D92H	Yes
				802insTAGG/	Not detectable	No expression	Yes
				834delCTTC^§
ZR-75-1^†	PTEN	323T>G^‡	323T>G	L108R	Likely
MDA-MB-415^†	PTEN	407G>A^‡	407G>A	C136Y	Yes
MDA-MB-453	PTEN	919G>A	919G>A	E307K	Likely
BT474^†	PIK3CA	333G>C	NA	K111N	Yes
BT20^†	PIK3CA	1616C>G	NA	P539R	Yes
BT483^†	PIK3CA	1624G>A	NA	E542K	Yes
MCF-7^†	PIK3CA	1633G>A	NA	E545K	Yes
MDA-MB-361^†	PIK3CA	1633G>A	NA	E545K	Yes
MDA-MB-361	PIK3CA	1700A>G	NA	K567R	Likely
BT20^†	PIK3CA	3140A>G	NA	H1047R	Yes
MDA-MB-453^†	PIK3CA	3140A>G	NA	H1047R	Yes
OCUB-F	PIK3CA	3140A>G^‡	NA	H1047R	Yes
SK-BR-5	PIK3CA	3140A>G	NA	H1047R	Yes
SUM102PT^†	PIK3CA	3140A>G	NA	H1047R	Yes
SUM185PE^†	PIK3CA	3140A>G^‡	NA	H1047R	Yes
SUM190PT^†	PIK3CA	3140A>G	NA	H1047R	Yes
T47D^†	PIK3CA	3140A>G	NA	H1047R	Yes
UACC893^†	PIK3CA	3140A>G	NA	H1047R	Yes
SUM159PT^†	PIK3CA	3140A>T	NA	H1047L	Yes
MDA-MB-134VI^†	KRAS	34G>C	NA	G12R	Yes
SK-BR-7	KRAS	34G>T	NA	G12C	Yes
SUM229PE	KRAS	35G>A	NA	G12D	Yes
MPE600	KRAS	35G>T	NA	G12V	Yes
MDA-MB-231^†	KRAS	38G>A	NA	G13D	Yes
Hs578T^†	HRAS	35G>A	NA	G12D	Yes
SUM159PT	HRAS	35G>A	NA	G12D	Yes
SK-BR-7	NRAS	182A>G	NA	Q61R	Yes
ZR-75-30^†	BRAF	977T>C	NA	I326T	Unknown
MDA-MB-231	BRAF	1391G>T	NA	G464V	Yes
DU4475	BRAF	1799T>A	NA	V600E	Yes
MDA-MB-435s	BRAF	1799T>A	NA	V600E	Yes

Abbreviations: HD, homozygous deletion; Ex., exon; IVS, intervening sequence; del, deletion; ins, insertion; NA, not analyzed.
↵* Frameshift mutations are indicated by the first changed codon and the number of newly encoded codons, including premature termination codon X.
↵† Cell lines were reported to be mutated in references (17, 26, 37, 45-49).
↵‡ Mutations were homozygous based on sequence analysis and confirmed with polymorphic markers.
↵§ Mutations are heterozygous but are located on different alleles.

Table 2.

Mutational Activation of the PI3K and RAS Pathways Is Mutually Exclusive in Human Breast Cancer Cell Lines

NOTE: Overview of mutations that were identified in 40 human breast cancer cell lines. The mutations are detailed in Table 1.
Abbreviation: NA, not analyzed.