The LRG research team continues to investigate a number of key areas. These include research into ways to overcome drug resistance, improve initial response to treatment, clinical trial support, high throughput screening and establishing the basis for moving individual drugs into clinical trials.

Overcoming drug resistance

The general mechanisms of resistance to Gleevec have been fairly well understood since about 2003. During this meeting, further insights were provided about drug resistance to HSPHSP90 inhibitors and additional insights into Wild -type/pediatric GIST signaling with respect to IGF1R. The IGF1R data provides further scientific support for targeting IGF1R in a subset of GIST patients.

New strategies identified by the research team to overcome Gleevec resistance have now entered clinical trials including the phase II STA-9090 trial (HSPHSP90 inhibitor) and a wide array of PI3K inhibitors (phase I) and IGF1R inhibitors (most in phase I). The phase I trials are not specific to GIST. A phase I trial combining an HDAC inhibitor and imatinib is also close to opening.

Additional resistant GIST cell lines have been developed, including a cell line from Dr. Jonathan Fletcher with loss of PTEN, which is a protein normally responsible for blocking the ability of PI3K to accelerate GIST cell growth and survival. These cells should be useful in understanding the details of how PI3K works in GIST cells and also useful in understanding the most effective ways to target PI3K therapeutically.

Dr. Fletcher reported on both first and second generation HSPHSP90 inhibitors. Reports from the IPI-504 phase III trial indicated high toxicity and treatment- related deaths in medically fragile patients with prior liver resection. First generation ansamycin HSPHSP90 inhibitors such as 17-AAG and IPI-504 are derived from natural compounds and seem to have some liver toxicity (some more than others). Second generation compounds are synthetic and so far have not been shown to have the same liver toxicity. The selective and highly potent second generation HSP90 inhibitor, STA-9090 has entered phase II trials for GIST. A total of four sites are expected to open. Dr. Fletcher also described new laboratory studies in which GIST therapeutic response to HSP90 inhibitors was maximized by concurrent inhibition of other crucial growth and survival pathways in the GIST cells.

Improving initial response

Several research groups presented data on different ways to improve the initial response to Gleevec. The hope is that if you can increase the number/type of tumor cells killed, then there is a smaller pool for resistant cells to grow from.

One of the central challenges to improving response seems to stem from the fact that tumor cells that are proliferating seem to be easier to kill than those that are not proliferating. The later state is called quiescence. In many cases Gleevec does not kill tumor cells but causes them to become quiescent and thus, harder to kill. Several researches presented data on different methods of attack against these quiescent tumor cells.

Dr. Brian Rubin presented data on autophagy as a consequence of Gleevec therapy and potential methods to overcome it. Autophagy is a cellular process that can lead to cell death, but can also lead to cell survival when the cell is under stress. During autophagy, stressed cells stop proliferating and can adapt their metabolism to stressful states, such as decreased nutrients, allowing cells to evade cell death. Gleevec appears to induce autophagy in some GIST tumor cells and the autophagy prevents tumor cell death. Giving Gleevec and interrupting the autophagy process at the same time may result in much greater tumor cell kill rates. Dr. Rubin is also collaborating with the Mayo Clinic in characterizing ICC stem cells and has significantly expanded his mouse models.

Dr. Anette Duensing has previously shown that Gleevec induces quiescence in GIST tumor cells. Her studies are now focused on whether it is possible to revert those quiescent GIST cells into a state in which they can more easily be killed. Novel approaches such as this one are needed to shift the cellular responses to Gleevec toward apoptosis instead of cell cycle arrest to make Gleevec-based therapies more effective with a goal towards a cure.

Recently, working with other members of the LRG research team, including Dr. Sebastian Bauer, Dr. Duensing has shown that bortezomib, an approved proteasome inhibitor, has activity against Gleevec-sensitive and Gleevec-resistant GIST tumor cells. Dr. Duensing and her team identified two modes of action for bortezomib, including stabilization of histone H2AX as well as downregulation of KIT. These results provide a rationale for clinical trials to test the efficacy of bortezomib in GIST patients. During the meeting, Dr. Duensing provided additional insights into the mechanisms and possible new targets in quiescent GIST cells.

Dr. Sebastian Bauer presented data on other pathways involved in quiescence. In addition, Dr. Bauer is taking the lead in starting a new GIST trial in Germany very soon for Gleevec combined with the LBH589, a HDAC inhibitor made by Novartis. This trial is the result of previous work done by the LRG team, including Dr. Bauer and Dr. Maria Debiec- Rychter, which showed that LBH589 and other HDAC inhibitors had a significant effect on GIST cells.

On behalf of Dr. Besmer, Dr. Antonescu reported on signaling pathways activated by imatinib. He also reported progress in developing mouse models with double mutations. A careful characterization of these mice is in progress.

Drug screening

Further progress was made for in vitro and in vivo drug screening of mutant KIT oncoproteins including:

• KIT inhibitors
• HSP90 inhibitors
• Combination therapies

Dr. Maria Debiec-Rychter reported on screening with drug combinations in several xenograft models (human tumors from patients implanted into mice).

Clinical support

Dr. Chris Corless presented on behalf of himself and Dr. Mike Heinrich, an update on the Z9001 imatinib adjuvant trials. The Heinrich/Corless labs have provided mutational analysis for the correlative studies of this trial. Some of this data was presented at the 2010 GI ASCO meeting and will be summarized in another article in this issue of the newsletter (see 2010 GI ASCO).

The Heinrich/Corless team also reported that 40-50 percent of adult wildtype GISTs have high levels of IGF1R expression. Additional analyses of IGF1R related proteins are in progress. The Heinrich/Corless labs have also screened new potent KIT inhibitors, some of which target KIT in a different manner than previous KIT inhibitors. Dr. Heinrich and Dr. Corless are also collaborating with a research group from Bologna and at the University of British Columbia on different projects.

New targets

Dr. Cristina Antonescu presented data on a new protein that is overexpressed in GIST. Inhibition of this protein resulted in a decrease in GIST tumor cell proliferation as well as an increase in apoptosis. In addition, this protein is expressed in certain ICC cells, but not in other ICC cells. This may help pinpoint the cells of origin of GIST tumors. This protein represents a new potential target in GIST tumor cells.

High throughput screening

A number of teams are using various high throughput screening techniques to identify new targets in GIST. Dr. Matt van de Rijn is collaborating with three groups on tissue micro-array projects using 3-SEQ technology. These include the LRG tissue bank project, a project with Brazil (Bacchi) and a project with Norway. The LRG project and the Norway project both have clinical outcome data. Dr. van de Rijn presented some data on the expression of four different proteins in GIST.

Dr. Sebastian Bauer presented proteomic screening data comparing several GIST cell lines. Dr. Anette Duensing, in collaboration with Dr. Brian Rubin, is working on a kinome screen for GIST 882 and GIST-T1 cell lines. The primary and secondary screens for the GIST882 cell line are complete and targets are now being validated, focusing on the 10 most prominent hits. The GIST-T1 screen will be done +/- imatinib.

Dr. Jonathan Fletcher has several highthroughput studies in progress. These include shRNA knockdown of single genes in a GIST-T1 cell line. In this study, individual genes are silenced in individual cells to find the most important genes/targets in GIST. This is in collaboration with the Broad Institute.

In perhaps the most ambitious GIST research project ever, Dr. Fletcher – in conjunction with Dr. George Demetri and Dr. Edward Fox at Dana-Farber Cancer Institute – is also sequencing the entire GIST genome. It was only a few years ago (2003), that the human genome was first sequenced. The human genome project took 13 years, cost several billion dollars and collaborators weren’t labs, they were countries. While the cost of sequencing a genome has come down dramatically, it still costs several hundred thousand dollars. This work is currently underfunded, although considered to be very high priority because it offers hope of identifying additional mutated proteins (analogous to KIT and PDGFRA) that can be targeted by biologically rationale therapies in GIST.