The DU4475 Breast Cancer Cell Line

If ever there was a breast cancer cell line that highlighted the inportance of taking every cell line and indeed every patient as an individual, regardless of the tissue of origin of the cancer, it is the DU4475 cell line.  This cell line was established from a metastatic skin nodule of a 62 year old Caucasian patient previously diagnosed with breast carcinoma.  Thus, this cell line is considered to be a metastatic breast cancer cell line.  The STR profile for this cell line along with other genomic data sets pertinent to the line can be found here at Cellosaurus, or here at COSMIC, or here at DepMap portal.  Interestingly, DepMap Portal lists this cell line as a ER negative, HER2 negative sub-lineage, and belonging to the Luminal HER2 amplified molecular subtype.  As you will see below, these designations are not helpful when it comes to understanding the driving oncogenes and drug sensitivities of this cell line.

Oncogene Signature: The first thing that jumps out from the Oncogene Signature is the classic V600E point mutation in the BRAF oncogene.  This gene was a strong hit in the functional screen and thus is clearly the driving oncogene in this cell line.  It is also of interest that these cells have a fairly common point mutation in the APC gene, though this gene was not a hit in the screen.  These are highly unusual oncogenes in breast cancer, and it may be of interest that the line was derived from a skin nodule.  Beyond these two genomic alterations that are commonly found in melanoma and colon cancer,  it is noteworthy that AKT3 is highly overexpressed in these cells, though not a screen hit.  None of the other candidate oncogenes that have genomic alterations in this cell line were close to being considered essential in the CRISPR screen.

Gene	CRISPR score	Demeter score	Log fold change	DNA amp	mutation	occ. In Cosmic
BRAF	-1.727350736		0.582018108	0.3687	p.V600E	15808
TRAF5	-0.208639383		2.565234805	1.0121
AKT3	-0.174822526		3.920049258	1.0399
ELF3	-0.168265832		-5.907015815	1.0121
SMYD3	-0.153635556		3.645100089	1.0399
H3F3A	-0.095713946		1.555768669	1.0009
IKBKE	-0.023055685		1.004282124	1.0121
PARP1	0.233990615		1.62738237	1.0009
APC	0.266543708		-0.912353408	-1.134	p.E1577*	22

Signature of best druggable targets in this cell line:  There are several very interesting features of the druggable signature for this breast cancer cell line (or is it?) some, but not all of which are related to having mutant BRAF as the driving oncogene.  First, it is immediately obvious that these cells are exquisitely sensitive to several BRAF targeted drugs, particularly PLX-4720 which is now better known as vemurafinib.  Thus, mutant BRAF is a classic functional druggable oncogene.  It is also interesting that the cells are also highly sensitive to two drugs that target MAP2K1 and MAP2K2 but that neither of these genes were screen hits.  There are several lines of evidence to indicate that these drug sensitivities are correct and are related to the mutant BRAF oncogene.  First, as can be seen from the LFC column, both genes are expressed in this cell line at about the same level.  Now, referring to the KEGG pathway for these cells shown below, one can see that these proteins have redundant function and lie between BRAF and ERK in the MAPK pathway.  Thus, whereas the screens are able to reduce the expression of only one gene at a time, some drugs are able to target both family members effectively.  Thus,  one would predict, given the other evidence, that the cells would be highly sensitive to this drug, which blocks immediate downstream signaling from the mutant BRAF.  In addition to the drug sensitive targets related to the mutant BRAF oncogene, there are several genes in the apoptosis pathway that were hits in the screen, namely BCL2L1 and MCL1, and accordingly, these cells are sensitive to several drugs that target these genes.  Thus, in this cell line, there is once again, ample potential to combine oncogene or oncogene pathway targeted drugs with BH3 mimetic drugs, which based on past experience, would be predicted to induce synergistic cell death following low doses of drug.

DU4475.Tier1
Drug name	Gene symbol_HGNC	z_score_GDSC1	z_score_GDSC2	DNA_amp	lfc	mutation	COSMIC_hit
Dabrafenib	BRAF	-3.461211	-4.145031	0.3687	0.582018108	p.V600E	1
PLX-4720	BRAF	-3.974495	-3.288462	0.3687	0.582018108	p.V600E	1
Olaparib	PARP1	-0.916673	-1.741401	1.0009	1.62738237	NULL	0
Niraparib	PARP1	0	-1.626684	1.0009	1.62738237	NULL	0
AZ628	BRAF	-2.807417	0	0.3687	0.582018108	p.V600E	1
SB590885	BRAF	-4.41058	0	0.3687	0.582018108	p.V600E	1
DU4475.Tier2
Drug name	Gene symbol_HGNC	z_score_GDSC1	z_score_GDSC2	DNA_amp	mutation	lfc	achilles_score	demeter
WEHI-539	BCL2L1	0	-3.505726	0.0417	NULL	-0.614301461	-1.816590803	NULL
ABT737	BCL2	0	-2.99367	-0.4467	NULL	1.387803208	-0.532011853	NULL
ABT737	BCL2A1	0	-2.99367	0.0131	NULL	6.292885906	-0.996132321	NULL
ABT737	BCL2L1	0	-2.99367	0.0417	NULL	-0.614301461	-1.816590803	NULL
Tozasertib	AURKA	-0.329408	-2.526678	0.0423	NULL	-0.390751163	-1.397145279	NULL
Tozasertib	AURKB	-0.329408	-2.526678	-0.0191	NULL	0.600280425	-1.292795471	NULL
RO-3306	CDK1	-0.421263	-2.218674	0.3609	NULL	0.616276421	-1.782839183	NULL
Entinostat	HDAC3	-1.267387	-2.205466	0.0542	NULL	0.270827125	-1.581762288	NULL
LJI308	RPS6KA1	0	-2.059636	-0.0034	NULL	1.298533522	-0.647991739	NULL
Axitinib	PDGFRA	-0.139564	-1.765024	0.0446	NULL	0	-0.564642508	NULL
JQ1	BRD2	-0.810683	-1.500408	-0.0526	NULL	-0.242788536	-1.130520866	NULL
JQ1	BRD4	-0.810683	-1.500408	-0.0156	NULL	1.289661134	-1.145723129	NULL
Alisertib	AURKA	-2.062328	-0.274104	0.0423	NULL	-0.390751163	-1.397145279	NULL
XMD14-99	CDK7	-2.017441	0	0.0644	NULL	0.006759802	-2.034821471	NULL
AZ628	BRAF	-2.807417	0	0.3687	p.V600E	0.582018108	-1.727350736	NULL
SB590885	BRAF	-4.41058	0	0.3687	p.V600E	0.582018108	-1.727350736	NULL
SL0101	AURKB	-2.53603	0	-0.0191	NULL	0.600280425	-1.292795471	NULL
DU4475.Tier3
Drug Name	Gene SymbolHGNC	z_score_GDSC1	z_score_GDSC2	DNA_amp	lfc	mutation	achilles_score	demeter
SCH772984	MAPK3	0	-3.243074	0.0032	-0.350073519	NULL	-0.122930226	NULL
PD0325901	MAP2K1	-2.352646	-3.128407	-0.0647	0.385986599	NULL	-0.251666558	NULL
PD0325901	MAP2K2	-2.352646	-3.128407	-0.0044	0.354334418	NULL	-0.211672308	NULL
Trametinib	MAP2K1	-2.112662	-2.943476	-0.0647	0.385986599	NULL	-0.251666558	NULL
Trametinib	MAP2K2	-2.112662	-2.943476	-0.0044	0.354334418	NULL	-0.211672308	NULL
Ulixertinib	MAPK3	0	-2.512322	0.0032	-0.350073519	NULL	-0.122930226	NULL
GSK1904529A	IGF1R	-0.48926	-2.473885	0.0279	-1.324925212	NULL	-0.418323741	NULL
GSK1904529A	INSR	-0.48926	-2.473885	-0.0044	1.138324276	NULL	-0.144982834	NULL
LJI308	RPS6KA2	0	-2.059636	-0.0165	-0.925383688	NULL	0.219697705	NULL
LJI308	RPS6KA3	0	-2.059636	0.0217	0.401757493	NULL	0	NULL
XMD14-99	ALK	-2.017441	0	-0.8008	1.40284809	NULL	-0.151042355	NULL
XMD14-99	LTK	-2.017441	0	-0.0736	4.168525979	NULL	0.130334181	NULL
Refametinib	MAP2K1	-2.684568	0	-0.0647	0.385986599	NULL	-0.251666558	NULL
CI-1040	MAP2K1	-3.061957	0	-0.0647	0.385986599	NULL	-0.251666558	NULL
Selumetinib	MAP2K1	-2.350468	0	-0.0647	0.385986599	NULL	-0.251666558	NULL
Refametinib	MAP2K2	-2.684568	0	-0.0044	0.354334418	NULL	-0.211672308	NULL
CI-1040	MAP2K2	-3.061957	0	-0.0044	0.354334418	NULL	-0.211672308	NULL
Selumetinib	MAP2K2	-2.350468	0	-0.0044	0.354334418	NULL	-0.211672308	NULL
SL0101	PIM1	-2.53603	0	-0.0526	0.736328775	NULL	0.137540582	NULL
SL0101	PIM3	-2.53603	0	-0.3425	-0.113170478	NULL	-0.350262639	NULL