GIST THERAPY RESISTANCE MECHANISMS
YEAR 1 PROGRESS REPORT

Here is the year one GIST research progress report. The LRG is committed to funding research programs for identification and validation of synergistic targeted therapies that counteract Gleevec-resistance in GIST. Despite remarkable clinical responses to tyrosine kinase inhibition, we are seeing relapses of GIST, even in patients with spectacular initial response to Gleevec. We expect that most GIST patients currently benefiting from Gleevec treatment will eventually develop resistance on the single-regimen therapy.

The ambitious plans and the impressive Year One progress outlined in this report would not be possible in the absence of a closely-knit and highlyinteractive GIST scientist research group. Great pains have been taken to enable collaboration without redundancy, such that the team is emphasized over the individual. This carefully coordinated approach continues to maximize the LRG research productivity. The overall objective in this research is to identify combinations of therapies that can provide synergistic benefit with Gleevec in patients with GIST. The specifics of this progress report represents the input of each LRG research team member.

A series of ten “priority” projects were highlighted for immediate funding. The Year One progress for each of these projects is summarized below. With the exception of project B, all have made outstanding progress and are expected to continue in the same fashion for Year Two.

A. Oncogenic signaling mechanisms as novel therapeutic targets: Substantial progress has been made in identifying “downstream” proteins which play crucial roles in channeling the KIT activation stimulus into the GIST cell which are alternate therapeutic targets in GIST. The Year One research highlighted the crucial rolls of PI3-K and AKT proteins in maintaining cell growth and has begun to catalog comprehensively the cell proteins that bind to the KIT/PDGFRA oncoproteins in GIST.

B. KIT/PDGFRA Wildtype GISTs: These studies have been hampered by the availability of frozen GIST specimens that lack KIT and PDGFRA mutations. The LRG board of directors and research team discussed strategies for obtaining additional frozen GIST specimens that lack KIT and PDGFRA mutations for Year Two. This project is suspended until suitable samples can be obtained.

C. Primary Resistance: Progress has been made in establishing laboratory models for GIST mutations that show primary resistance to Gleevec, and potent alternative KIT kinase inhibitors of such mutants. Future studies will continue to focus on identifying and validating novel KIT kinase inhibitors that are effective against primary KIT/PDGFRA Gleevec-resistant mutations.

D. Stable disease after imatinib: Stable disease, i.e. GIST cells that are suppressed but not killed by Gleevec, remains a major problem for most patients. Year 1 studies show that clinically stable GIST – in patients receiving Gleevec or Sutent – can contain abundant KIT secondary mutations, which are the starting point for progression to eventual outright Gleevec resistance. Future studies of stable GIST will address KIT/PDGFRA mutational heterogeneity, evaluate new therapies that more effectively induce apoptosis (cell death), and identify new therapeutic targets by gene expression profiling and proteomic methods.

E. Secondary resistance mechanisms & clinical evaluation: Great progress has been made in the past year by developing new human GIST and non-GIST cell lines and mouse xenografts of human GISTs that contain various KIT and PDGFRA kinase domain Gleevec and Sutent resistance mutations. These diverse GIST “models” have enabled identification and preclinical validation of novel small molecule kinase inhibitors with expanded efficacy against the Gleevec-resistant KIT and PDGFRA mutations.

F. Kit Degradation: The Year 1 studies have validated the concept that HSP90 and similar proteins are required to protect KIT in GIST cells. HSP90 can be inhibited by various drugs, resulting in substantial destruction of the KIT oncoproteins in all GIST cell lines tested to date, cessation of growth, and induction of death, in the GIST cells. Future studies will focus on identifying HSP90 inhibitors with greater potency and selectivity for KIT/PDGFRA in GIST.

G. Murine Models: The proposed studies are well underway, with Dr. Besmer’s group having shown that the PI3-K pathway is crucial to KIT oncogenic signaling in the murine GISTs, and that therapeutic inhibition of mTOR can reduce the growth of these GISTs. Continuing studies from Drs. Besmerand Rubin will produce mice with Gleevec-resistant inherited mutations, which will be very useful in screening for novel therapies against Gleevec resistant GIST.

H. Resource Development (imatinib sensitive & resistant): Exceptional progress has been made in developing new immortal cell lines. Future efforts will be devoted to expanding the panel of immortal cell lines available for drug testing.

I. Tissue Banks: Excellent progress has been made in establishing a central repository for frozen and paraffinembedded GISTs to enable the collective research efforts in the LRG program. Future efforts will focus on genomic and gene expression annotations for the banked specimens, and histopathologic annotation to assure that GISTs from patients already treated with Gleevec include both clinically stable and progressing specimens.

Pediatric GIST: Dr. Antonescu has identified several genes that are uniquely active in pediatric GISTs, rather than adult GISTs. Future studies will determine whether these genes can be targeted successfully with drugs, producing therapeutic advances for pediatric GIST. This work is particularly crucial because pediatric GIST patients do not respond as well as adult GIST patients to Gleevec.

Gleevec resistance studies are essential to therapeutic progress in GIST. We hope to substantially expand select studies in the following two years. These studies will likely reveal that combinations of GIST therapies are needed to consolidate initial remissions, forestall the emergence of clinical resistance, and enable increased cure rates.