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"Suzanne George, MD is Assistant Professor of Medicine, Harvard Medical School, and Clinical Director, Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Boston. In her capacity as medical oncologist, she is part of a multidisciplinary team that treats and provides consultation to sarcoma patients throughout the New England area, as well as elsewhere in United States and abroad. She is also extremely active in clinical research — developing and executing clinical trials focused on new avenues of therapy for GIST and other soft tissue sarcomas." 

GSI posed questions about the evolution and management of GIST resistance mutations to Suzanne George, MD, Assistant Professor of Medicine, Harvard Medical School, and Clinical Director, Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Boston.

1. What role do mutations in KIT and PDGFRα proteins have in GIST?

KIT and PDGFRα belong to the family of proteins called Class III receptor tyrosine kinases, which act as cellular “on/off” switches, promoting cell growth and survival when in the “on” state. Under normal conditions this activity is tightly regulated, so that KIT and PDGFRα are only active when bound to specific signaling molecules (ligands), such as hormones or growth factors. However, the KIT or PDGFRa proteins found in GISTs are often defective, containing mutations that favor the “on” state and result in deregulated cell growth and tumor formation.

2. How do these mutations affect GIST treatments?

Standard kinase inhibitor drugs for GIST (imatinib, sunitinib, regorafenib) bind to KIT and PDGFRα proteins in a manner that stabilizes the “off” state, silencing the abnormal growth signals. However, research has shown that a few specific mutations can alter the structure of KIT or PDGFRα in ways that are incompatible with the binding of a given drug. When the drug’s ability to bind to its target protein is impaired, signaling proceeds unchecked and tumor growth occurs.
Such “resistance mutations” are uncommon in treatment-naïve primary GISTs -- although one primary mutation, PDGFRα D842V, does notably confer resistance to standard kinase inhibitors. In the majority of cases, though, resistance mutations emerge only after prolonged drug exposure. Some resistance mutations can be addressed by switching to a different kinase inhibitor, but mutations in a critical region of the KIT and PDGFRα protein structure called the activation loop (A loop) have shown a high degree of resistance to all GIST treatments to date.

3. What is the activation loop (or A loop)? Why are mutations located in the A loop referred to as “Exon 17” for KIT and “Exon 18” for PDGFRa, and what is their clinical significance?

The DNA of a gene is very long, and specific locations along that stretch are indicated by a system of numbered “exons.” Exons are analogous to the mile markers along a highway that tell you where you are. They indicate which segment of the gene or its related part of the protein is being discussed. The individual structural components of a protein correlate to specific exon segments (Figure 1).

Figure 1: The molecular architectures of KIT protein and KIT gene. A gene is divided into functional segments called exons. The individual structural components of a protein correlate to specific exon segments. Exon 17 encodes the activation loop in the kinase domain of KIT. The activation loop is a structural feature that guides the “on/off” state of the kinase.

Instructions for the A loop – the flexible region in protein kinases that governs their “on/off” switch – are encoded via exon 17 of KIT and exon 18 of PDGFRa. When the A-loop is switched “on” (open conformation) the result is an active kinase. When the A loop is switched “off “ (closed conformation) the kinase is incapable of signaling and remains in an inactive state.

The structural status of the A loop is critical for the binding of kinase inhibitors such as imatinib and sunitinib, and mutations distorting it can cause drug resistance. Resistance mutations in KIT exon 17 have been identified at positions 816, 820, 822 and 823. The The PDGFRα exon 18, D842V, mutation structurally analogous to the D816V mutation in KIT.

4. Drugs that inhibit KIT and PDGFRα have been categorized as Type 1 or Type 2 kinase inhibitors based on their binding characteristics. How do mutations in KIT Exon 17 and PDGFRα D842 affect a Type 1 inhibitors vs Type 2 inhibitors?

Type 2 kinase inhibitors like imatinib fit neatly into “binding pockets” that are created when the A loop adopts a closed conformation (Figure 2). However, they are incapable of binding to KIT mutants with the A loop in an open conformation. GIST primary mutations such as those in KIT exon 11, while activating, do not limit the A loop to an open conformation. Therefore, Type 2 inhibitors can effectively bind to and inhibit oncogenic KIT activated by exon 11 mutations. In contrast, exon 17/18 mutations stabilize the A loop in an open conformation, which obstructs binding of Type 2 inhibitors (Figure 3A).
Type 1 inhibitors bind to and inhibit kinases more potently when the A loop is in the open conformation (Figure 3B). The investigational drug BLU-285 is an example of a selective Type 1 kinase inhibitor that binds potently to KIT and PDGFRα having exon 17/18 activating mutations.

Figure 2:

Figure 2 shows KIT bound to imatinib (yellow) with the A loop in a closed conformation (purple). When in this conformation, imatinib fits nicely into the binding pocket of KIT. Exon 17/18 mutations in KIT or PDGFRα stabilize the A-loop in an open conformation (green), which obstructs binding of imatinib and other type 2 inhibitors.

Figure 3:



Figure 3. Panel A shows a closer view of the clash that occurs between the type 2 inhibitor imatinib and the kinase when the A-loop is in the open conformation (green). This clash prevents effective binding of imatinib to the kinase when the A-loop is in this open conformation. Panel B shows the binding of a type 1 inhibitor to the kinase. In this case the type 1 inhibitor clashes with the A-loop in the closed (purple) conformation and effective binding is prevented.

5. How common are KIT Exon 17 and PDGFRα D842V mutations? Does the frequency change over the course of the disease? 

KIT exon 17 mutations are rare at the time of diagnosis, appearing in only 1% of treatment-naïve GISTs. However, 23% of patients who have progressed on imatinib and over 90% of those who have progressed on both imatinib and sunitinib demonstrate mutations in KIT exon 17 (Figure 4). These secondary KIT exon 17 mutations confer resistance to both imatinib and sunitinib. In advanced GIST, approximately 5% of tumors have a PDGFRα D842V mutation. PDGFRα D842V is a primary mutation and is not felt to change over time nor is it found to emerge as a cause of secondary resistance to current TKIs used to treat GIST.

Figure 4:

6. How can I determine whether my GIST contains mutations in KIT or PDGFRα? 

Mutational tests for GIST are widely available through academic and commercial laboratories. Testing is often done for KIT mutations initially. If no mutations are detected in KIT, then testing for mutations in PDGFRα is performed. Speak with your physician to learn more about GIST mutational testing. Itis important to note that current testing is very good at identifying primary mutations in GIST. Because secondary mutations can vary from tumor to tumor within an individual person, routine mutational testing may not be able to accurately identify resistance mutations in every person, including exon 17.

7. What are the current recommendations for mutational testing? How do the results inform treatment decisions?

According to the National Comprehensive Care Network guidelines (NCCN Soft Tissue Sarcoma Guidelines v1 2015), testing for mutations in KIT and PDGFRα is strongly recommended as part of the workup for newly diagnosed patients. Testing should be performed particularly when treatment with kinase inhibitors is planned, since the presence or absence of mutations in specific regions of the KIT or PDGFRα genes can predict whether or not a patient will respond to particular agents. The results may inform the following treatment decisions:

  • Knowing if you have a primary mutation in KIT exon 9 vs KIT exon 11 can help your physician select an appropriate dose of imatinib, since patients with KIT exon 9 mutations are more likely to respond to 800 mg imatinib than the standard 400 mg dose in the setting of metastatic disease.
  • Knowing if you have a PDGFRα mutation can help your physician make decisions about therapy, since tumors with the PDGFRα D842V mutation do not respond to imatinib, whereas most other mutations in the PDGFRα gene are associated with a response to imatinib.

Note: While testing for KIT exon 17 mutations is also available at some academic and commercial laboratories, the guidelines do not recommend testing at GIST progression -- as currently there are no treatment decisions that would be affected by the resulting information.

8. What is circulating tumor DNA? Can it be used to find acquired resistance mutations?

Analysis of circulating free tumor DNA, or ctDNA, is an exploratory test being studied in GIST and other cancers. Currently it is not available for routine care.

Over time, DNA from tumor cells is shed into the bloodstream. After performing a simple blood draw, this circulating DNA can be analyzed or “sequenced” to identify what molecular alterations exist in the cancerous cells. In contrast to a biopsy, which only reflects molecular changes that have occurred in the biopsied region, ctDNA can reveal changes that have occurred at multiple tumor sites. (Mutations are not uniform and can vary from tumor to tumor within a single individual.) The hope is that this approach will provide a cumulative picture of the patient’s cancer and ultimately guide selection of the best therapeutic option.

Performing a blood draw before and after drug treatment can inform the physician of molecular changes that have occurred over the course of therapy. In particular, if a patient’s tumor is no longer responding to a given drug, newly identified mutations in the ctDNA may help to explain therapeutic failure. In the future, monitoring the status of ctDNA may permit physicians to select or change therapeutic interventions based on the molecular status of the patient’s tumor in real time. Technology is still being developed to identify the best way to determine ctDNA in patients with GIST, because of this, ctDNA is not routinely available, but is included in many new GIST research trials.

9. What are possible strategies for the treatment of resistant GIST containing a KIT Exon 17 or PDGFRα D842V mutation?

Of the currently approved therapies for GIST, regorafenib is the only agent that has shown some effectiveness against KIT exon 17 mutations. In standard of care practice, regorafenib would typically be recommended after progression on imatinib and sunitinib, independent of tumor genotype. Regorafenib is the only FDA-approved drug for the treatment of GIST following progression on imatinib and sunitinib.

There are several studies in development with the goal of treating patients with GIST following progression on standard therapy (imatinib, sunitinib, and regorafenib). Many people in this situation will indeed have KIT exon 17 mutations in addition to the primary KIT mutation and will likely have other resistance mutations as well. Most of the active studies for GIST patients in this situation can be found on

BLU-285 is a small molecule that is being developed with very specific activity against both KIT exon 17 mutations and PDGFRα D842V mutations. This compound is being studied in a first-in-human clinical trial at several centers in the US, as well as in Europe. (See Identifier: NCT02508532.) The compound is unique in that it is highly specific for these mutations, which are resistant to other therapies. Additional novel compounds being developed for resistant GIST include PLX9486, another small molecule with broad activity against both primary and secondary KIT mutations in GIST. At this writing, PLX9486 in GIST is not currently recruiting participants. (Further information can be found at Identifier: NCT02401815.) DCC-2618 is yet another novel compound being studied in advanced GIST after failure on at least imatinib. This compound is felt to inhibit multiple primary and secondary KIT mutations in GIST. (More information on the first-in-human trial of DCC-2618 can be found at Identifier NCT02571036.)

Crenolanib is a very potent inhibitor of PDGFRα D842V mutations that is also being evaluated in advanced GIST. The first trial using crenolanib in GIST patients with this unique mutation is currently closed, and detailed results have yet to be reported. (More information is available at Identifier: NCT01243346.)

It is important to talk to your doctor when considering clinical trial participation. There are multiple new compounds and combinations of compounds in development for patients with GIST, and the options available for clinical trial participation are always being updated.

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