New oncogene target for breast cancer: LMTK3

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Published: 22 Jun 2011
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Prof Justin Stebbing - Imperial College London, UK

Prof Justin Stebbing discusses his research which identified a new protein involved in the development of drug resistance in breast cancer. It is hoped that this can ultimately be used as a target for new treatments. In the study, researchers from Imperial College London found that blocking a protein called LMTK3 in human cancer cells that were resistant to tamoxifen made the cells more responsive.


Prof Stebbing explains how this protein was identified and talks about the other research he was presenting at the ASCO meeting. This research included the results of a study investigating the links between weight gain and poor response to chemotherapy, a paper on circulating tumour cells in prostate cancer and a presentation looking at polymorphism in the IGFR1 gene as a predictive factor for patient outcome.



ASCO 2011 Annual Meeting, 3—7 June 2011, Chicago

New oncogene target for breast cancer: LMTK3

Professor Justin Stebbing – Imperial College, London, UK


Congratulations on a cracking good paper in Nature and Medicine, come on, tell us about this gene.

We basically discovered a new oncogene in oestrogen receptor positive breast cancer that may have quite broad applicability to other cancers. The genesis of this came from both a clinical and an observational perspective; the simple clinical problem is that the majority of women with breast cancer have oestrogen receptor positive disease. Depending on the data you read, between 30-50% of those relapse and there’s no specific therapy to target what we call endocrine resistance, compared to, say, triple negative breast cancer where there are a lot of presentations here about the PARP inhibitors or HER2 positive disease where there are drugs in development such as TDM1 or neratinib and so on and so forth. So we thought this was a particularly interesting group of individuals where we don’t fully understand the mechanisms. 

The second observation was if you look at animals, when they develop breast cancer, such as dogs or chimpanzees, it tends to be oestrogen receptor negative; humans seem uniquely susceptible to oestrogen receptor positive breast cancer. So we performed a kinome screen where we knocked out every single kinome in the human genome in a series of breast cancer cells and we knocked out all 700 kinase genes using SRNA-based technology.  


Sequentially, one by one. Now, normally when people look at a read-out from that they look at cell proliferation; what we looked at was the genomic oestrogen response, so this was a lot of work. We looked at PCR of levels of, say, PS2, GREB1, PGR, oestrogen responsive genes. We found that some genes upregulated the oestrogen receptor, some that are known such as MAP kinase and AKT, and those are well known but we found a host of other genes that upregulated the oestrogen receptor that were unknown and the known ones served as a control. We then took a step back and we said, are any of those new to humans that don’t really exist in animals or exist in a pre-kinase form? And we found one of them called LMTK3 which has adaptively evolved, has been subjected to Darwinian positive selection between chimpanzees and humans such that whenever a nucleotide changes it changes the amino acid and that’s very rare in human biology or evolutionary biology in general. I often think of cancer, if you like, as an attempt at speciation and genomic instability, but that’s a slightly different issue.

We then found that very high levels of this gene confer the worst prognosis, we used the Nottingham dataset of 613 patients; it conferred tamoxifen resistance. Then we looked at mutations in it and we found intronic mutations also conferred a worse prognosis but chimpanzees didn’t have those intronic mutations. We then needed to work out how this worked inside the cells, so we found it directly phosphorylated the oestrogen receptor, we found it activated protein kinase C which activated AKT and phosphorylated AKT leads to recruitment of FOXO3a forkhead transcription factor to the ESR1, that’s the oestrogen receptor alpha promoter. So you’ve got a double direct and indirect effect leading to oestrogenic activation. So we’ve got a new kinase which looks like a druggable target, we need to work out the 3D structure but it shouldn’t be underestimated how difficult it is to make a specific kinase inhibitor.

That works.

That works. So we see a lot of presentations about TKIs and other kinase inhibitors but a lot of the effects here, for example at ASCO, are undoubtedly off-target effects. That creates a real problem for drug development because if you’re saying that compound validation relies on targets and then you’re saying you need off-target effects, how do you actually develop a really good specific selective drug, but again maybe that’s another issue. 

Well done, I can’t say any  more than that. Tell me about what you’re presenting at ASCO, not an off-target TKI?

No, I was presenting three things. The first presentation was a very simple observation that about two years ago, it’s a well-known fact that… Sorry, I’ll take a step back. During adjuvant chemotherapy for breast cancer, about 25% of women gain about 10kg in weight and you can’t explain that by steroid use as an antiemetic, comfort eating or people sitting inside.

Gin and tonic?

Exactly. Now that weight gain, as well as being associated with worse cardiovascular complications, orthopaedic problems and body image perception leads to an earlier recurrence of breast cancer. So if you’re being clever you might say, well Justin, that’s just because of increased aromatisation from fat tissue, but the effect is much stronger in oestrogen receptor negative women. So about a year ago we published the first known mechanism of this weight gain which is perturbation of gluconeogenesis via increased alanine and lactate production. We then decided to validate that by looking at patients with metabolic syndrome where they have a constellation of, like I’m getting, increased circumference, high cholesterol, slightly high blood pressure, high LDL, low HDL, slightly high glucose. And we asked a very simple question – do they respond more poorly to chemotherapy? And the answer seems to be yes. Again, that’s not an observation you can explain; fatter people, if you like, have poorer responses to chemotherapy, so that’s the next leg of the study. 

And they certainly do worse, all the meta-analysis from Dana-Farber and all say the same thing.

Exactly, and that validates the new approaches, so using things like metformin or metabolism inducers or inhibitors to treat breast cancer. So we’ll see what happens there. Going back to the original MD Anderson paper on pathologic complete responses in diabetics who take metformin during neoadjuvant chemo.

And that’s very interesting and very exciting too.

Then the next thing I presented was a paper on circulating tumour cells in prostate cancer where I like the Einstein quote when he said not everything that counts can be counted and not everything that can be counted counts. 

And that’s CTC in prostate cancer? You can count them but they don’t count?

Exactly, or they can be counted but they don’t count. What we’re observing is they are a quicker and more rapid predictor of outcome than PSA.

Outcome post-treatment?

During and post. They seem to be both a prognostic and a predictive biomarker, so people with high numbers do worse. They’re also predictive, so if you can take them from high numbers to low numbers it’s like you started with low numbers in the first place and maybe if you don’t reduce them you should switch therapies. They seem to have stood the test of time but they’re blooming expensive, they really are. When we are talking about repeat biopsies, though, which are labour intensive, expensive as well and can lead to side effects, circulating tumour cells seem an easier way to do a real-time image. But we don’t even know if they’re living or dead or whether they represent cells en route to metastasis.

Which is Larry Norton’s idea.

We don’t really know what they are, they’re circulating epithelial cells, we shouldn’t have them, but the truth is we don’t fully understand what they are in my opinion.

Third presentation?

Third presentation was with the LMTK3, which is the new oncogene we’ve identified in breast and maybe colon cancer, we found that single nucleotide polymorphisms predicted outcome and so we looked at a more common gene that’s well-studied, the IGFR1 insulin growth factor receptor number 1, and we found again, in a large cohort, that using the same dataset that single nucleotide polymorphisms predicted outcome. SNPs are entering real-time but the one proviso I would say about them is that the most interesting SNPs tend to be intronic and so what one is postulating is you’re altering transcription and then translation, leading to different recruitment of transcription factors to promoters and enhancers. The problem is that for most of them we lack the mechanism of how they do that and so what I want to see is more mechanistic work on SNPs so you’ve got this SNP, how is it conferring a worse prognosis. Because they’re intronic, it’s a very difficult area to study and you’re not seeing really anything on that subject yet. So it’s watch this space.

Next year.


What about this year at ASCO, any highlights that have hit you in the eye?

From a breast perspective I have to say I think you have to be absolutely honest about it and say things have been disappointing. If you were to say anything else I think that would be wrong. The exemestane study, while interesting, is small – 38 events, but the things that really grabbed me is the BRAF inhibitors in melanoma. When you’re seeing hazard ratios of 0.2, 0.3, we used to see hazard ratios in things that work of 0.7, 0.8, 0.9, you’re seeing hazard ratios of 0.2, 0.3. Compare that to ipilimumab with a hazard ratio of 0.72, you see a staggering effect, regardless of whether they get squamous cancers and they rebound rapidly off treatment. So we’ll need to know how to sequence them, whether you can combine them, how long people need to be on them for, that’s number one. What I think is interesting, if you like, as a jobbing oncologist, although some people might not call me that, what I think is interesting is that it’s great to come to ASCO and go to other sessions not in your area. So Onyx’s drug, carfilzomib, in myeloma  looks staggering and fourth line response rates of nearly 25%, a lot of those complete responses with no neuropathy, that looks like a real drug. And then a lot of other things, you have to say, are a bit me too. So you might argue Avastin in ovarian cancer, there probably is an effect on PFS, there probably is an effect on OS, will the FDA approve it? I don’t really care, it’s an expensive drug, we need to keep an eye on that. 

And it’s given by injection, which is not the most patient-friendly thing for a long-term maintenance.

Exactly. And then you compare that, say, to prostate cancer where you’re now seeing abiraterone, we’re waiting to see the results of AFFIRM for MDV3100, a direct androgen receptor blocker where you’ve got a good marriage of basic science and clinical work where you’re seeing direct AR blockade in tissues, tissues reacting by upregulating testosterone levels, could that be harmful? We’re going to see in sequential bone marrow biopsies. But those are oral therapies, so abiraterone and MDV3100, they’re oral therapies and they are much easier. But, again, abiraterone $5,000 a month, they’re on it for fourteen months, who’s going to pay for it?

And provenge is worse, $30,000 which I think is the most expensive at the moment?

No, it’s $94,000 for a year. 

I don’t even want to think about it. 

And the benefits seem, to me, modest but where do you draw the line?

I can’t see the National institute of Clinical Excellence in the United Kingdom rushing to approve it, put it that way.

No, they’re not going to.

Justin, that was terrific, a tour de force, and I’m really, really chuffed that you could spare the time to come in because I know you’re busy and I know you’ve got lots of other…

No, no, thanks for having me.