Table S7. Clinical responses of advanced PDGFRA-mutant GIST patients treated with first-line imatinib.

Abstract Gastrointestinal stromal tumor (GIST) is the most common sarcoma, and 85% of cases harbor mutations in KIT or PDGFRA receptor tyrosine kinases. Imatinib (IM), a type II TKI, can treat many KIT-mutant GIST, but not GIST with the most common PDGFRA mutation, exon 18 D842V. D842V is resistant to all type II TKIs. Avapritinib (AVA), a type I TKI, was developed and is FDA-approved for all PDGFRA exon 18 mutant GIST but is costly and has severe cognitive side effects in some patients. AVA is also not widely available outside the United States, leaving many exon 18 mutant GIST patients without treatment options. However, limited clinical evidence reports the usage of IM to treat non-D842V exon 18 mutations. As IM is a more tolerable, cost-effective, and accessible drug than AVA, utilizing IM therapy in certain cases would provide treatment for those who cannot access or tolerate AVA. As it is not feasible to model every observed mutation, we utilized in vitro models to predict exon 18 mutations that could be treated with IM. Through collaboration and AACR GENIE, we curated a cohort of 1000+ PDGFRA-mutant GIST. 66% had D842V while the remaining had non-D842V point mutations and complex in/dels. Strikingly, 78% of mutations involved the D842 residue, which plays a key role in the autoinhibition of PDGFRA, and mutations like D842V disrupt this. As nearly every single amino acid substitution at the 842-residue was observed in our cohort, we hypothesized that the characteristics of the 842-position amino acid determine IM sensitivity and will predict treatment responses for any exon 18 mutation. To test our hypothesis, we used Ba/F3 and CHO cells to express every possible D842X and D842_D846delinsX mutation. This 4-residue deletion was the most common in/del in the cohort; therefore, we chose to profile this mutation backbone as well. IM sensitivity was determined by calculating an IC50 value using immunoblotting for phosphorylated and total PDGFRA. We observed similar trends in IM sensitivity depending on the class of amino acid at the 842-position, with little difference between D842X and D842_D846delinsX mutant kinases. Seven out of eight hydrophobic residues conferred IM resistance while amino acids from other classes (polar, +/- charged, special case) conferred IM sensitivity/intermediate sensitivity. Notably, alanine conferred IM sensitivity, different than the other hydrophobic substitutions and in silico modeling revealed how the side chain structure at the 842-position affects IM binding/activity. Lastly, we determined that our results are concordant with first-line IM response data, as patients with predicted IM-sensitive mutations experienced a longer median progression-free survival than those with predicted or known IM-resistant mutations (30 vs 4 months, p <0.0001). Our work highlights an approach to optimize clinical guidelines for the TKI treatment for PDGFRA-mutant GIST based on specific patient mutations. Citation Format: Homma M. Khosroyani, Alina Teuber, Ajia Town, Lillian Klug, Denisse Evans, Jerry Call, Sara Rothschild, Neeta Somaiah, Prapassorn Thirasastr, Ping Chi, Marion Liu, Peter Hohenberger, Piotr Rutkowski, Patrick Schoffski, Abbas Agaimy, Mehdi Brahmi, Carol Beadling, Sebastian Bauer, Johanna Falkenhorst, Michael C. Heinrich. Using in vitro models to predict imatinib responses in PDGFRA-mutant gastrointestinal stromal tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 8.

Mutation analysis of our PDGFRA-mutant GIST cohort reveals clustering around the exon 18, 842-codon position. A, The protein domains of PDGFRA (AL, activation loop; AP, ATP-binding domain; EC, extracellular domain) and the exon distribution of unique primary mutations seen in PDGFRA-mutant GIST (n = 1,379 cases). B, Breakdown of mutations seen in exon 18 PDGFRA-mutant GIST cases (n = 1,122/1,379). The gray-colored proportion in the chart indicates mutations with five or fewer reported cases (n = 90/1,122). C, Number of cases with exon 18 in/del mutations and the net number of deleted residues in the final protein sequence, along with the breakdown of the type of mutations observed with a 4-residue deletion. Red “X” denotes the number of amino acids inserted (X = 1, XX = 2). D, Proportion of cases with mutations that directly alter the 842 residue. E, Distribution of the amino acid occupying the 842-position in exon 18–mutant cases (n = 1,122). Colors in the legend correspond to the amino acid class of the 842-position residue (hydrophobic, polar uncharged, special case, positively charged, and negatively charged). [Portions of A were Created in BioRender. Khosroyani, H. (2026) https://BioRender.com/l88qy7p.]

Abstract The most common platelet-derived growth factor receptor α (PDGFRA) alteration in gastrointestinal stromal tumors (GIST) is the exon 18 activation loop mutation D842V, which is resistant to imatinib and other type II tyrosine kinase inhibitors (TKI) but sensitive to type I TKI avapritinib. Avapritinib is FDA-approved for first-line treatment of all PDGFRA exon 18–mutant GIST cases but is only available for D842V-mutant cases outside the United States. Non-D842V exon 18–mutant GIST cases are understudied and lack evidence-based treatment guidelines. However, there are a few previous reports describing non-D842V exon 18–mutant patients with GIST who responded well to imatinib therapy. Given that imatinib is more tolerable, globally accessible, and significantly less expensive than avapritinib, we sought to define which patients could be treated with imatinib rather than avapritinib. We assembled a cohort of more than 1,000 PDGFRA exon 18–mutant GIST cases and identified that 78% of these mutations involved a key autoinhibitory aspartic acid residue at position 842. Using cell-based models, we demonstrated that imatinib sensitivity was dependent on the amino acid class of the 842-position residue, with all hydrophobic amino acids except alanine conferring resistance. In contrast, all 842-position mutations were avapritinib-sensitive. Structural modeling supported our biochemical results and revealed how 842-position mutations induce changes that can interfere with imatinib binding. Lastly, our biochemical data were validated using imatinib response data for first-line metastatic disease; patients with predicted exon 18–sensitive mutations had longer progression-free survival than patients with predicted imatinib-resistant mutations. These results provide key evidence that should be used to guide therapy selection for PDGFRA-mutant GIST. Significance: Biochemical and structural modeling of PDGFRA exon 18 842-position mutations allows for the prediction of clinical TKI responses. These data can be used to generate new treatment guidelines for PDGFRA exon 18–mutant GISTs and select optimal therapies for patients.

Table S5. Avapritinib IC50 values and 95% confidence intervals (CIs) of PDGFRA mutations modeled in Ba/F3 and CHO cells.

Table S2. List of primer sequences used to PCR amplify and sequence PDGFRA cDNA.

Table S4. Imatinib IC50 values and 95% confidence intervals (CIs) of PDGFRA mutations modeled in Ba/F3 and CHO cells.

Binding modes of imatinib and avapritinib to PDGFRA-WT, along with activation loop visualization of PDGFRA D842X mutations modeled in silico. All visualizations shown were done in PyMOL, and all structures shown are aligned with apo PDGFRA-WT (PDB: 8PQJ). A, Visualization of apo PDGFRA-WT (PDB: 8PQJ), with the DFG motif in the out conformation and W559 protruding into the back pocket of the protein kinase domain. B, Visualization of the DFG-out motif within the PDGFRA activation loop and imatinib occupying the hydrophobic back pocket of PDGFRA-WT (WT; PDB: 6JOL). C, Visualization of the DFG-in motif within the PDGFRA activation loop bound to avapritinib (PDB: 8PQH), showing how avapritinib occupies the solvent front and Gα pocket but not the hydrophobic back pocket. In silico modeling based on the PDGFRA-T674I crystal structure bound to avapritinib (PDB: 8PQH) with the activation loop (AL) of (D) WT D842, (E) D842V, (F) D842I, (G) D842A, and (H) D842G. In E and F, the green shading indicates that side chains protrude not only into the hydrophobic back pocket and stabilize the active conformation but also fit in a binding pocket formed by the αC-helix and the JMD, whereas in G and H, the red shading indicates that the alanine side chain or no side chain in case of glycine do not protrude into the same pocket between the αC-helix and the JMD and subsequently less likely stabilizing the activation loop in an active conformation.

737 Background: The standard of care for patients with moderate or high-risk resectable gastrointestinal stromal tumors (GIST) is surgical resection followed by adjuvant therapy with imatinib. The impact of neoadjuvant imatinib on long-term outcomes is largely unknown. Methods: We interrogated the LifeRaft registry, a large international open cohort of patients with GIST. We included patients who did not have metastatic disease at diagnosis, underwent surgical resection and received neoadjuvant imatinib and had no recorded mutations of Kit exon 13 or PDGFRA exon 18 D842V. Baseline patient characteristics were described and survival probabilities were estimated and plotted using the Kaplan-Meier method. Cox regression was used to estimate the effect of demographic and clinical characteristics on recurrence-free survival (RFS) and overall survival (OS). For RFS, time was calculated from the date of surgery to disease recurrence/death, whichever came first. For OS, time was calculated from the date of surgery to death. Estimated effects of predictors were reported as hazard ratios (HR) along with 95% confidence intervals (CI). All statistical testing was two-sided and assessed for significance at the 5% level using SAS v9.4 (SAS Institute, Cary, NC). Results: Out 2,472 patients with GIST, 137 patients met the inclusion criteria and received neoadjuvant imatinib for a median of 6.8 months. Majority of the patients were aged 40 years or above (129/137, 94.2%) and were males (73/137, 53.3%). The majority of the patients had gastric GIST (72/137, 54.1%), followed by small intestine GIST (34/137, 25.6%) and other (27/137, 20.3%). Most patients had a tumor size of >10 cm (66/137, 52.4%) at the time of diagnosis followed by >5 cm - <=10 cm (42/137, 33.3%) and >2 cm - <=5 cm (18/137, 14.3%). The median RFS for the cohort was 6.1 years. On multivariable analysis, tumor size (HR 1.08, 95% CI 1.05-1.12, p<0.01) and the overall duration of treatment (neoadjuvant and adjuvant) with imatinib therapy (HR 0.98, 95% CI 0.97-0.99, p<0.01) were significantly associated with RFS. A 1-cm increase in tumor size and 1-month increase in total time on imatinib was associated with an 8% increase and 2% decrease in risk of recurrence. The median OS was 14.2 years. Female gender (HR 0.23 95% CI 0.08-0.65, p<0.01) and total length of time on imatinib (HR 0.97 95% CI 0.96-0.99, p<0.01) were found to be significantly associated with OS. Female patients were associated with a 77% decreased risk of death and a 1-month increase in the total time on imatinib was associated with a 3% decrease in the risk of death. Conclusions: We show that most patients receiving neoadjuvant imatinib have gastric GIST with tumor size >10 cm. Smaller tumor size and female gender predicted longer RFS and OS respectively. Longer total duration of imatinib therapy was associated with increased RFS and OS.

e23513 Background: Most studies of gastrointestinal stromal tumors (GIST) focus upon patients in a single country. However, differences in patient presentation, treatment, and outcomes may differ between nations. We sought to compare Hispanic patients with localized GIST treated in North and South America. Methods: We performed a retrospective analysis including all Hispanic GIST patients treated at 3 tertiary referral centers in the United States (US), Mexico (MX) and Argentina (AR), as well as those enrolled by 2 patient advocacy groups in US and MX from 2000-2022. Demographic, clinicopathologic and survival data were collected and compared using Pearson’s chi-square or one-way ANOVA test. Disease-specific survival (DSS) was calculated using the Kaplan-Meier method and compared using the log-rank test. Results: Overall, 1,504 Hispanic patients (54.5% female) were analyzed. Median age at diagnosis was significantly lower in US (48 y) than MX/AR (55/57 y, p = 0.001). Presentation stage varied by country. Localized presentation was more frequent in US/MX (77%/88%) than AR (60%, p = 0.001). In 1,208 patients (80.4%) with localized disease, 97.9% underwent surgical resection. Rates of adjuvant imatinib treatment varied from 82.4%/77.0% in US/MX to 35.6% in AR (p < 0.001). Median duration of adjuvant therapy was longer in US (29 mos; range: 16-48) than MX (12 mos; range: 4-36, p < 0.001). With a median follow up of 44 mos (range: 24-78) for patients presenting with localized GIST, the estimated median DSS was 136 mos (95% CI 104-167), being significantly longer in US (267 mos, 95% CI 95-439, p = 0.02). Conclusions: While most studies of disparities focus on differences between races/ethnicities in a single country, we found that disparities also exist within similar ethnic groups across nations. Underappreciated sociopolitical determinants of health likely lead to differences in presentation, management, and long-term outcomes of Hispanic GIST patients in the Americas. Prospective cooperative studies are needed to better define barriers to care in order to improve patient outcomes in Hispanic GIST patients. [Table: see text]

Mutational testing for Gastrointestinal Stromal Tumor (GIST) patients remains underutilized. In this retrospective analysis, the target population (n = 1556) reported: 904 had molecular testing ("Tested") vs. 652 without testing ("Untested"). Overall survival (OS) was 14.7 vs. 12.7 years (p < 0.00001), in metastatic patients 1st line OS was 8.9 vs. 5.9 years in the Tested vs. Untested group (n = 416 vs. n = 254), respectively. From 1st - 3rd-line, no difference has been (self-)reported for progression-free survival (PFS). Dropout to/for further lines of treatment was 15% for patients with a Tested mutation vs. 47% in Untested patients.

Background Due to the low mutational testing rate in patients with Gastrointestinal Stromal Tumors (GIST), The Life Raft Group (LRG), a non-profit organization that provides support, advocacy and conducts research for patients with GIST, analyzed various factors that may have an impact on patients’ ability to receive mutational testing. Methods A survey about mutational testing for patients with GIST or their caregivers, was conducted in June 2020. The survey, sent to 1004 GIST patients and caregivers through email, was promoted through social media with instructions to contact the LRG to participate. The survey was designed by the LRG Patient Registry Department. Members of the LRG, regardless of Patient Registry status, were eligible to participate. Results A total of 295 patients/caregivers participated in this study (response rate: 29.4%). The percentage of patients who indicated they had received mutational testing was much higher in this survey (80%) than in the general GIST community (26.7%). Several reasons were cited for having a test, including: “My doctor ordered/suggested that I have it done” (54%); “The Life Raft Group advised/suggested I have it done” (25%); “I asked my doctor to have it done” (22%); “I had it done as part of a clinical trial” (5%); “I am not sure” (3%) and “Other” (14%). Mutational testing resulted in a treatment change in 25% of cases. Patients were able to select more than one option when completing this question resulting in a percentage greater than 100. Conclusions The LRG membership is voluntary and proactive; patients who join are more likely to participate in surveys and mutational testing, as well as more likely to have a GIST specialist. Mutational testing can influence understanding of a patient’s GIST and the treatment best suited to each case. These are extremely important findings, as it helps ensure that patients are on the proper treatment, which should lead to better outcomes.

e23519 Background: The Life Raft Group (LRG) identified that succinate dehydrogenase (SDH) deficient GISTs are under-recognized. In the LRG Registry only 30% of KIT/PDGFRA wildtype patients had received the advanced mutational testing (or SDHB staining) required to identify this unique subtype of GIST with a different natural history and response to treatment, and very strong familial associations. We proposed that two changes would significantly increase the diagnosis of SDH-deficient GIST patients: 1. SDHB staining for all GIST patients with a stomach primary tumor at initial biopsy, 2. Initial pathology report should contain strong recommendations for specific mutational testing. Methods: The LRG collaborated with key medical opinion leaders on a diagnostic algorithm that illustrated the need for wider use of targeted diagnostic procedures and submitted the algorithm to the College of American Pathologists (CAP) GIST editorial board. Results: Because SDH-deficient GISTs require germline genetic analysis and, if mutation related, subsequent surveillance for paragangliomas/pheochromocytomas, and cascade genetic testing for family members, it is necessary to screen all gastric GISTs for loss of SDH by immunohistochemistry. This is best accomplished by immunohistochemical staining for SDHB, which is lost in all genetic subtypes of SDH-deficient GISTs. If SDHB is absent, additional staining for SDHA may be performed, as this protein is selectively lost in SDHA-mutant GISTs and this may help focus genetic analysis. All patients with SDH-deficient GIST should be referred to a genetic counselor. The CAP incorporated both SDHB and SDHA testing paradigms into the updated GIST protocols which were published in August 2019. Conclusions: We believe this will result in significantly better diagnosis and treatment for SDH-deficient GIST patients. We encourage other groups that advise on guidelines to develop similar recommendations. This is a great example of a patient advocacy group utilizing real world evidence derived from a patient registry to influence protocols for treatments that affect GIST patients on a large scale.

Targeted treatment has become a major modality in cancer management. Such cancer drugs are generally designed to treat tumors with certain genetic/genomic makeups. Mutational testing prior to prescribing targeted therapy is crucial in identifying who can receive clinical benefit from specific cancer drugs. Over the last two decades, gastrointestinal stromal tumors (GISTs) have evolved from histogenetically obscure to being identified as distinct gastrointestinal mesenchymal tumors with well-defined clinical and molecular characteristics, for which multiple lines of targeted therapies are available. Although the National Comprehensive Cancer Network (NCCN) strongly recommends mutational testing for optimal management of GIST, many GIST patients still have neither a mutation test performed or any mutation-guided cancer management. Here, we review the mutation-guided landscape of GIST, mutational testing methods, and the recent development of new therapies targeting GIST with specific mutations.

Background: Activating mutations of the receptor tyrosine kinase KIT are early events in the development of most gastrointestinal stromal tumors (GISTs). Although GISTs generally remain dependent on oncogenic KIT during tumor progression, KIT mutations alone are insufficient to induce malignant behavior. This is evidenced by KIT-mutant micro-GISTs, which are present in up to one-third of normal individuals, but virtually never progress to malignancy. Methods: We performed whole exome sequencing on 29 tumors obtained from 21 patients with high grade or metastatic KIT-mutant GIST (discovery set). We further validated the frequency and potential prognostic significance of aberrations in CDKN2A/B, RB1, and TP53 in an independent series of 71 patients with primary GIST (validation set). Results: Using whole exome sequencing we found significant enrichment of genomic aberrations in cell cycle-associated genes (Fisher's Exact p = 0.001), most commonly affecting CDKN2A/B, RB1, and TP53 in our discovery set. We found a low mutational tumor burden in these 29 advanced GIST samples, a finding with significant implications for the development of immunotherapy for GIST. In addition, we found mutation of spliceosome genes in a minority of cases, implicating dysregulation of splicing as a potential cancer promoting mechanism in GIST. We next assessed the prognostic significance of CDKN2A, RB1 or TP53 mutation/copy loss in an independent cohort of 71 patients with primary GIST. Genetic events (mutation, deletion, and/or LOH) involving at least one of the three genes examined were found in 17% of the very low-risk, 36% of the low-risk, 42% of the intermediate risk, 67% of the high-risk/low mitotic-count, and in 86% of the high-risk/high mitotic-count group. The presence of cell cycle-related events was associated with a significantly shorter relapse-free survival (median 67 months versus not reached; p < 0.0001) and overall survival (Log Rank, p = 0.042). Conclusion: Our results demonstrate that genomic events targeting cell cycle-related genes are associated with GIST progression to malignant disease. Based on this data, we propose a model for molecular pathogenesis of malignant GIST.

[This corrects the article DOI: 10.1186/s13569-019-0114-5.].

e21625 Background: Created in 2001, The Lift Raft Group GIST Patient Registry has always put the patient at the heart of its work. Those contributing data are not merely study participants but people in need of help. In 2017, the newest evolution of the Registry debuts- GIST/PRIME, an interactive desktop/mobile application that serves both the patient and doctor to track treatment efficacy and disease progression over time rather than the traditional single survey input. Methods: The Registry operates on an SQL cloud based platform under an IRB informed consent process. Incoming members provide their full disease history. Examples of data collected include: Demographic, primary tumor site, date(s) of diagnosis, initiation of treatment, dosage, and response to treatment. Outcomes are based upon response to drug therapy. Research analysis is supported by the platform’s filterable, queryable and auto-calculating fields as well as unique features such as treatment lines which chart therapy history to investigate potential correlation between mutational status, drug treatment and order of drug taken. Results: The traditional registry structure only provides a one-way benefit- from patient to registry. GIST/PRIME seeks to remedy this by providing a clear set of benefits and user-friendly features back to patients: The Dashboard displays Registry demographics and how the patient relates others within the system. Based on entered data, this dashboard can also calculate Risk of Recurrence and provide education on treatment and mutational types; Input and editing of Diagnosis, Evaluation and Treatment; push notifications; The GISTORY- An exportable, printable document that provides a comprehensive summary of a patient’s GIST medical history, helping facilitate efficient communication between patient and doctor. Conclusions: The idea of reframing a patient registry as a tool which can provide as much benefit to its members as it does to the researchers who analyze its data is overdue. By committing to a patient-centered structure and style, registry members are more deeply engaged over time, providing richer data that is not limited to a single drug or place of treatment.

BACKGROUND:Gastrointestinal stromal tumors (GIST), one of the most common mesenchymal tumors of the gastrointestinal tract, prior to routine immunohistochemical staining and the introduction of tyrosine kinase inhibitors, were often mistaken for neoplasms of smooth muscle origin such as leiomyomas, leiomyosarcomas or leiomyoblastomas. Since the advent of imatinib, GIST has been further delineated into adult- (KIT or PDGFRα mutations) and pediatric- (typified by wild-type GIST/succinate dehydrogenase deficiencies) types. Using varying gender ratios at age of diagnosis we sought to elucidate prognostic factors for each sub-type and their impact on overall survival.METHODS:This is a long-term retrospective analysis of a large observational study of an international open cohort of patients from a GIST research and patient advocacy's lifetime registry. Demographic and disease-specific data were voluntarily supplied by its members from May 2000-October 2010; the primary outcome was overall survival. Associations between survival and prognostic factors were evaluated by univariate Cox proportional hazard analyses, with backward selection at P < 0.05 used to identify independent factors.RESULTS:Inflections in gender ratios by age at diagnosis in years delineated two distinct groups: above and below age 35 at diagnosis. Closer analysis confirmed the above 35 age group as previously reported for adult-type GIST, typified by mixed primary tumor sites and gender, KIT or PDGFRα mutations, and shorter survival times. The pediatric group (< age 18 at diagnosis) was also as previously reported with predominantly stomach tumors, females, wild-type GIST or SDH mutations, and extended survival. "Young adults" however formed a third group aged 18-35 at diagnosis, and were a clear mix of these two previously reported distinct sub-types.CONCLUSIONS:Pediatric- and adult-type GIST have been previously characterized in clinical settings and these observations confirm significant prognostic factors for each from a diverse real-world cohort. Additionally, these findings suggest that extra diligence be taken with "young adults" (aged 18-35 at diagnosis) as pediatric-type GIST may present well beyond adolescence, particularly as these distinct sub-types have different causes, and consequently respond differently to treatments.