Wild-type Gastrointestinal Stromal Tumors Research Articles

Current Drug Resistance Mechanisms and Treatment Options in Gastrointestinal Stromal Tumors: Summary and Update.

Gastrointestinal stromal tumor (GIST) is characterized by well-defined oncogenes. Despite the significant improvement in treatment outcomes with adjuvant imatinib therapy for patients, drug resistance remains a major challenge for GIST therapy. This review focuses on the mechanisms contributing to drug resistance phenotype in GIST, such as primary imatinib-resistant mutants, secondary mutations, non-covalent binding of TKI to its target, tumor heterogeneity, re-activation of pro-survival/proliferation pathways through non-KIT/PDGFRA kinases, and loss of therapeutic targets in wild-type GIST. Corresponding suggestions are proposed to overcome drug-resistance phenotype of GIST. This review also summarizes the suitability of currently approved TKIs on different KIT/PDGFRA mutations and updates related clinical trials. Recent potent drugs and emerging strategies against advanced GISTs in clinical trials are presented. Additionally, metabolic intervention offers a new avenue for clinical management in GIST. A landscape of metabolism in GIST and metabolic changes under imatinib treatment are summarized based on currently published data. The OXPHOS pathway is a promising therapeutic target in combination with TKI against sensitive KIT/PDGFRA mutants. Comprehensive understanding of the above resistance mechanisms, experimental drugs/strategies and metabolic changes is critical to implement the proper therapy strategy and improve the clinical therapy outcomes for GIST.

Exploration of the immunologic characteristics of KIT/PDGFRA wild-type gastrointestinal stromal tumor and potential application of neoantigen vaccination.

Exploration of the immunologic characteristics of KIT/PDGFRA wild-type gastrointestinal stromal tumor and potential application of neoantigen vaccination.

Gastrointestinal Stromal Tumors (GISTs) in Pediatric Patients: A Case Report and Literature Review.

Gastrointestinal stromal tumors (GISTs) are rare mesenchymal neoplasms that primarily affect adults, with pediatric cases constituting only 0.5-2.7% of the total. Pediatric GISTs present unique clinical, genetic, and pathological features that distinguish them from adult cases. This literature review aims to elucidate these differences, emphasizing diagnostic and therapeutic challenges. We discuss the resistance of pediatric GISTs to conventional chemotherapy and highlight the importance of surgical intervention, especially in emergency situations involving intra-abdominal bleeding. The review also explores the molecular characteristics of pediatric GISTs, including rare mutations such as quadruple-negative wild-type GIST with an FGF3 gene gain mutation. To illustrate these points, we conclude with a case from our clinic involving a 15-year-old female with multiple CD117-positive gastric GISTs and a quadruple-negative wild-type genetic profile who required urgent surgical intervention following a failed tumor embolization. This case underscores the critical need for early diagnosis and individualized therapeutic strategies combining oncologic and surgical care to improve outcomes in pediatric GIST patients.

Molecular Profiling of KIT/PDGFRA-Mutant and Wild-Type Gastrointestinal Stromal Tumors (GISTs) with Clinicopathological Correlation: An 18-Year Experience at a Tertiary Center in Kuwait.

In gastrointestinal stromal tumors (GISTs), identifying prototypical mutations in the KIT/PDGFRA oncogenes, or in rare alternate genes, is essential for prognostication and predicting response to tyrosine kinase inhibitors. Conversely, wild-type GISTs (WT-GIST), which lack known mutations, have limited treatment options. Data on the mutational landscape of GISTs and their impact on disease progression are very limited in Kuwait. Using a targeted next-generation sequencing panel, we investigated the spectrum and frequency of KIT, PDGFRA, and RAS-pathway-related mutations in 95 out of 200 GISTs diagnosed at Kuwait Cancer Center from 2005 to 2023 and assessed their correlation with clinicopathological parameters. Among the 200 tumors (median age 55 years; 15-91), 54% originated in the stomach, 33% in the small bowel, 7% in the colorectum, 1.5% in the peritoneum, and 4.5% had an unknown primary site. Of the 95 molecularly profiled cases, 88% had a mutation: KIT (61%), PDGFRA (25%), NF1 (2%), and one NTRK1 rearrangement. Ten WT-GISTs were identified (stomach = 6, small bowel = 2, and colorectum = 2). WT-GISTs tended to be smaller (median 4.0 cm; 0.5-8.0) (p = 0.018), with mitosis ≤5/5 mm2, and were of lower risk (p = 0.019). KIT mutations were an adverse indicator of disease progression (p = 0.049), while wild-type status did not significantly impact progression (p = 0.934). The genetic landscape in this cohort mirrors that of global studies, but regional collaborations are needed to correlate outcomes with genetic variants.

Abstract 1767: Molecular subclassification of gastrointestinal stromal tumors by genomic backgrounds

Abstract Gastrointestinal stromal tumors (GISTs) are the most common gastrointestinal mesenchymal tumors. While about 10% of GISTs are known to be developed from the KIT or PDGFRA gain-of-function mutations, the rest, which is the majority of GISTs, is so-called as wild-type GISTs. There are attempts to make subclassification of wild-type GISTs in syndromic or non-syndromic group as promising for understanding of heterogeneity or treatment strategy. Genomic states of succinate dehydrogenase B (SDHB) and neurofibromatosis type 1 (NF1) have been raised as candidates for subclassification of wild-type GISTs. In this presentation, we will discuss our recent three cases of wild-type GISTs, carrying germline pathogenic variants in SDHB or NF1. Two cases with SDHB germline pathogenic variants showed stomach GISTs with good clinical course, the maintained performance status and long survival nevertheless of the recurrence. The other case with an NF1 germline pathogenic variant showed multiple GISTs in small intestine which was controlled surgically and the late onset of other clinical symptoms of NF1. These cases might clinically suggest potential prognostic and predictive markers in genomic alterations of SDHB or NF1 for the cases with wild-type GISTs. Citation Format: Hideki Yamamoto, Eiji Nakada, Seiji Kawano, Fumino Kato, Chika Fukano, Mashu Futagawa, Yusaku Urakawa, Risa Ohsumi, Sayaka Ueno, Hiroyuki Yanai, Akira Hirasawa. Molecular subclassification of gastrointestinal stromal tumors by genomic backgrounds [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1767.

Abstract 3142: NN3201, a novel c-Kit targeting ADC, exhibits robust preclinical anti-tumor efficacy in SCLC and GIST models

Abstract c-Kit (CD117) is a type III receptor tyrosine kinase (RTK), which is known to be activated upon binding to its cognate ligand stem cell factor (SCF) to induce critical signaling pathways involved in cell proliferation, survival, and differentiation. Indicative of poor prognosis, overexpression and activating mutations of c-Kit have been implicated in a variety of human cancers including small cell lung cancer (SCLC), gastrointestinal stromal tumors (GIST), and acute myelogenous leukemia (AML). While imatinib, a small molecule c-Kit inhibitor, has been a beneficial treatment for GIST, resistance eventually develops to the drug, moreover, shows limited efficacy in c-Kit overexpressing tumors such as SCLC. Herein, we developed NN3201, a novel c-Kit targeting antibody-drug conjugate (ADC), comprised of fully human 2G4 antibody with a picomolar binding affinity to c-Kit and cytotoxic monomethyl auristatin E (MMAE) as the payload. NN3201 displayed potent in vitro cytotoxicity in various wild-type and mutant c-Kit positive SCLC and GIST cell lines with IC50 in the nanomolar range. In addition, NN3201 was rapidly internalized and inhibited c-Kit-mediated signaling., NN3201 treatment resulted in the increased proportions of the sub G1 and G2/M in the c-Kit positive cancer cell lines, indicating that release of MMAE induced cell cycle arrest. Moreover, bystander effect was confirmed by co-culturing c-Kit high and negative cell lines. Most importantly, in mouse xenograft models, NN3201 showed a remarkable tumor growth inhibition of several wild type, mutant c-Kit positive, and imatinib resistant SCLC and GIST cell lines. Enhanced anti-tumor activity and delayed tumor growth were observed in an SOC-treated (etoposide and carboplatin) SCLC xenograft model, by NN3201 in comparison to second line SOC (topotecan or irinotecan). In the GLP study, repeated intravenous administration of NN3201 was well tolerated at all doses (0.5, 1, 2 mg/kg Q3Wx3) without unscheduled death. Dose-dependent, yet transient, cytotoxicity of NN3201 was observed in the bone marrow. We confirmed HNSTD (Highest Non-Severely Toxic Dose) of NN3201 to be 2 mg/kg through exploratory and GLP repeat dose toxicity studies as no serious irreversible toxicity was observed. Accumulating data suggest that NN3201 is a promising therapeutic alternative for the treatment of SCLC and GIST regardless of wild-type or activating mutations in c-Kit. Citation Format: Chansik Kim, Jin Gu Cho, TaeMin Wi, Jiwoo Moon, Han-Jik Ko, Jina Lee, Jin Woo Park, Yeonjy Lee, Sanghee Kim, Jin-Ock Kim, Jaeyoung Song, Sun-Hwa Lee, Sang Gyu Park. NN3201, a novel c-Kit targeting ADC, exhibits robust preclinical anti-tumor efficacy in SCLC and GIST models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3142.

Wild-Type Gastrointestinal Stromal Tumors—Molecular Features, Frequency, and Consequences Among the Indian Population

Wild-Type Gastrointestinal Stromal Tumors—Molecular Features, Frequency, and Consequences Among the Indian Population

NTRK2 expression in gastrointestinal stromal tumors with a special emphasis on the clinicopathological and prognostic impacts

Gastrointestinal stromal tumors (GISTs) are typically characterized by activating mutations of the KIT proto-oncogene receptor tyrosine kinase (KIT) or platelet-derived growth factor receptor alpha (PDGFRA). Recently, the neurotrophic tyrosine receptor kinase (NTRK) fusion was reported in a small subset of wild-type GIST. We examined trk IHC and NTRK gene expressions in GIST. Pan-trk immunohistochemistry (IHC) was positive in 25 (all 16 duodenal and 9 out of 16 small intestinal GISTs) of 139 cases, and all pan-trk positive cases showed diffuse and strong expression of c-kit. Interestingly, all of these cases showed only trkB but not trkA/trkC expression. Cap analysis of gene expression (CAGE) analysis identified increased number of genes whose promoters were activated in pan-trk/trkB positive GISTs. Imbalanced expression of NTRK2, which suggests the presence of NTRK2 fusion, was not observed in any of trkB positive GISTs, despite higher mRNA expression. TrkB expression was found in duodenal GISTs and more than half of small intestinal GISTs, and this subset of cases showed poor prognosis. However, there was not clear difference in clinical outcomes according to the trkB expression status in small intestinal GISTs. These findings may provide a possible hypothesis for trkB overexpression contributing to the tumorigenesis and aggressive clinical outcome in GISTs of duodenal origin.

Molecular and clinicopathological features of KIT/PDGFRA wild-type gastrointestinal stromal tumors.

Approximately 10% of gastrointestinal stromal tumors (GISTs) harbor reportedly no KIT and PDGFRA mutations (wild-type GISTs). The clinicopathological features and oncologic outcomes of wild-type GISTs based on molecular profiles are unknown. We recruited 35 wild-type GIST patients from the two registry studies of high-risk GISTs between 2012 and 2015 and primary GISTs between 2003 and 2014. Molecular profiling of wild-type GISTs was performed by targeted next-generation sequencing (NGS) using formalin-fixed paraffin-embedded tumor samples. Among 35 wild-type GISTs, targeted NGS analysis detected NF1, SDH, or BRAF mutation: 16 NF1-GISTs with various NF1 mutations, 12 SDH-GISTs (4 with SDHA mutations, 4 with SDHB mutations, and 4 with SDHB-negative staining), and 5 BRAF-GISTs with the V600E mutation. Two GISTs showed no mutations based on our targeted NGS analysis. Additional gene mutations were infrequent in primary wild-type GISTs and found in TP53, CREBBP, CDKN2A, and CHEK2. Most NF1-GISTs were located in the small intestine (N = 12; 75%) and showed spindle cell features (N = 15; 94%) and multiple tumors (N = 6, 38%) with modest proliferation activities. In contrast, SDH-GISTs were predominantly found in the stomach (N = 11; 92%), exhibiting epithelioid cell (N = 6; 50%) and multiple (N = 6, 50%) features. The overall survival of patients with SDH-GISTs appeared to be better than that of BRAF-GISTs (p = 0.0107) or NF1-GISTs (p = 0.0754), respectively. In conclusion, major molecular changes in wild-type GISTs include NF1, SDH, and BRAF. NF1-GISTs involved multifocal spindle cell tumors in the small intestine. SDH-GISTs occurred in young patients and were multifocal in the stomach and clinically indolent.

Abstract C097: Understanding rare cancers in Hispanic/Latinx populations: Insights from the MyPART natural history study of rare solid tumors

Abstract PURPOSE: Rare cancers (<15 cases per 100,000 people/year) are poorly understood, particularly in Hispanic/Latinx populations. The My Pediatric and Adult Rare Tumor (MyPART) network conducts a Natural History Study of Rare Solid Tumors (NHSRT) to better understand rare tumor biology and develop effective therapeutic strategies. We analyzed NHSRT Hispanic/Latinx participants. METHODS: Patients of any age with rare solid tumors are eligible. All participants complete medical and family history forms, patient-reported outcomes (PRO) and provide saliva for DNA. Tumors undergo comprehensive molecular analysis and are discussed in a molecular tumor board. A subset of participants is invited to NIH Clinical Center (NIHCC) to undergo a clinical evaluation, genetic counseling, blood collection, and imaging studies, as indicated. Spanish-speaking participants are offered a medical interpreter. Forms are only available in English. RESULTS: Between January 2019 and December 2020, 16 of 200 participants identified as Hispanic/Latinx. Additionally, two international patients, a 15-year-old from Panama with Medullary Thyroid Carcinoma (MTC) who underwent total thyroidectomy with lymphadenectomy, and a 19-year-old from Mexico with Fibrolamellar Carcinoma (FLC) who underwent left hepatectomy and lymphadenectomy were enrolled later and received surgical treatment at NIHCC, which was not accessible in their home countries. Tumor types were neuroendocrine tumors (NET) (n=7), wild-type gastrointestinal stromal tumors (wt-GIST) (n=4), adrenocortical carcinoma (ACC) (n=1), MTC (n=3), and FLC (n=1). Two participants were relatives of patients with an SDHA mutation. Females accounted for 66% of the cohort; the median age was 35 years (range 15-69), enrolled from five US states and five countries. Nine patients used interpreter services. The median time from diagnosis to enrollment was 5.3 years. Half had metastatic disease at diagnosis. At enrollment, 57% of cases with local disease at diagnosis had progressed to metastasis, and 20% showed no evidence of disease. Twelve patients had successful tumor sequencing, and eight were found to have Pathogenic/Likely Pathogenic (Path/LP) variants. MEN1, SMAD4, and LZTR/RPS6KB2 in NET; SDHC in GIST; CDKN2B loss in ACC; DNAJB1-PRACA fusion in FLC; and RET mutations in MTC. Of 12 participants with germline mutation testing, Path/LP variants were found in 10, including SDHA, SDHC, and MUTYH in GIST patients and their relatives; PMS2 and RET in MTC; MEN1 and PALB2 in NET; SLC26A2, OTOF, XPC, and DNAH8 in ACC. CONCLUSION: Enrollment and comprehensive data collection were feasible, granting access to specialty care unavailable to several participants. Hispanic/Latinx representation was low, indicating recruitment challenges and the need for targeted strategies. Remote enrollment facilitated international participation. Making all forms available in Spanish is a priority. Ongoing analysis with over 500 NHRST participants will yield further insights. Citation Format: Juan C. Fierro Pineda, Shadin Ahmed, Karlyne Reilly, Robin Lockridge, Margarita Raygada, Barbara Thomas, John Glod, Abby Sandler, Brigitte Widemann, Mary Frances Wedekind Malone. Understanding rare cancers in Hispanic/Latinx populations: Insights from the MyPART natural history study of rare solid tumors [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C097.

Embryonic stem cell factor FOXD3 (Genesis) defects in gastrointestinal stromal tumors.

Gastrointestinal stromal tumors (GISTs) are mesenchymal neoplasms, believed to originate from the interstitial cells of Cajal (ICC), often caused by overexpression of tyrosine kinase receptors (TKR) KIT or PDGFRA. Here, we present evidence that the embryonic stem cell factor FOXD3, first identified as 'Genesis' and involved in both gastrointestinal and neural crest cell development, is implicated in GIST pathogenesis; its involvement is investigated both in vitro and in zebrafish and a mouse model of FOXD3 deficiency. Samples from a total of 58 patients with wild-type GISTs were used for molecular analyses, including Sanger sequencing, comparative genomic hybridization, and methylation analysis. Immunohistochemistry and western blot evaluation were used to assess FOXD3 expression. Additionally, we conducted in vitro functional studies in tissue samples and in transfected cells to confirm the pathogenicity of the identified genetic variants. Germline partially inactivating FOXD3 sequence variants (p.R54H and p.Ala88_Gly91del) were found in patients with isolated GISTs. Chromosome 1p loss was the most frequent chromosomal abnormality identified in tumors. In vitro experiments demonstrate the impairment of FOXD3 in the presence of those variants. Animal studies showed disruption of the GI neural network and changes in the number and distribution in the ICC. FOXD3 suppresses KIT expression in human cells; its inactivation led to an increase in ICC in zebrafish, as well as mice, providing evidence for a functional link between FOXD3 defects and KIT overexpression leading to GIST formation.

Multi-omic characterization of gastrointestinal stromal tumor (GIST) in a large real-world patient cohort.

11522 Background: Molecular knowledge of GIST is limited due to its rarity, few genes have been identified as relevant determinants of outcomes, tumor evolution and therapeutic targets. Therefore, we aimed to dissect the GIST molecular landscape in the largest series of real-world patients reported to date. Methods: 946 GIST patient samples (536 localized, 369 metastatic, 41 unknown) underwent next-gen sequencing of DNA (592-gene, N = 495; whole exome, N = 451) and RNA (whole transcriptome, N = 592) at Caris Life Sciences (Phoenix, AZ). Gene expression signatures of proliferation (Cristescu, 2021), cell cycle activation (CINSARC; Chibon, 2010), inflammation (T-cell inflamed; Ayers, 2017) and tumor microenvironments (MCP-counter; Becht, 2016) were examined. Statistical significance tested by χ2, Fisher’s exact, or Mann-Whitney U as appropriate. Results: GIST samples were comprised of 80% (N = 758) KITmut, 8.1% (N = 77) PDGFRAmut, and 11.7% (N = 111) KIT/PDGFRA wild-type (WT), with 14.8% (N = 140) samples harboring a secondary KIT variant suggestive of TKI resistance. Overall median TMB was 2 mutations/MB (range 0-13). WT GIST were identified with mutations in NF1 (33.7%), DNA repair genes (16.7%), SDHX (8.2%), BRAF (6.3%), and PTEN (1.9%), along with NTRK3 fusions (3.1%). Primary KIT variants occurred in exons 11 (83.5%), 9 (13.9%), and 13 (2.6%), and secondary KIT variants (14.6% of total KIT mutations) were distributed across the ATP binding pocket (36.8%) and activation loop (63.2%). Primary PDGFRA mutations were in exons 18 (62.4%), 12 (11.0%), 14 (4.6%) and other (16.5%). KIT/PDGFRAmut GIST infrequently harbored RB1, TP53, SETD2, ARID1A, PIK3CA, PTEN, TSC1, BRCA1, or CHEK2 co-mutations (1-5% each) . Copy number amplification (≥6 copies) was overall uncommon (≤2% for all genes). Proliferation and cell cycle activation signatures were higher in KIT exon 11 indels v. missense mut (1.2-fold, p < 0.05) and KIT resistant v. KIT primary (1.2-fold, p < 0.05), but not in KIT exon 11 557/558 v. others, nor between KIT v. PDGFRA v. WT subgroups. Deletion of tumor progression genes MAX (40.0%), CDKN2A (32.3%), and DEPDC5 (33.9%) was associated with increased proliferative gene expression (1.2-, 1.3-, and 1.2-fold, p < 0.05 each), while DMD deletion (52.5%) was not (1.1-fold, p = 0.37). Compared to KITmut and WT GIST, PDGFRAmut had increased abundance of several immune cell populations (range 1.2-3.7-fold, p < 0.05), along with enhanced inflammation signatures (1.1- and 1-2-fold, p < 0.05). Conclusions: This series provides unprecedented resolution of KIT/PDGFRAmut GIST with features of clinical aggressiveness associated with KIT exon 11 indels and resistance mutations, illustrating a specific cytogenetic genotype with more aggressive growth and malignant behavior. Identification of less common molecular alterations that drive kinase activation and impaired DNA damage repair warrant further investigation.

Efficient Identification of Patients With NTRK Fusions Using a Supervised Tumor-Agnostic Approach.

The neurotrophic tropomyosin receptor kinase (NTRK) family gene rearrangements have been recently incorporated as predictive biomarkers in a "tumor-agnostic" manner. However, the identification of these patients is extremely challenging because the overall frequency of NTRK fusions is below 1%. Academic groups and professional organizations have released recommendations on the algorithms to detect NTRK fusions. The European Society for Medical Oncology proposal encourages the use of next-generation sequencing (NGS) if available, or alternatively immunohistochemistry (IHC) could be used for screening with NGS confirmation of all positive IHC results. Other academic groups have included histologic and genomic information in the testing algorithm. To apply some of these triaging strategies for a more efficient identification of NTRK fusions within a single institution, so pathologists can gain practical insight on how to start looking for NTRK fusions. A multiparametric strategy combining histologic (secretory carcinomas of the breast and salivary gland; papillary thyroid carcinomas; infantile fibrosarcoma) and genomic (driver-negative non-small cell lung carcinomas, microsatellite instability-high colorectal adenocarcinomas, and wild-type gastrointestinal stromal tumors) triaging was put forward. Samples from 323 tumors were stained with the VENTANA pan-TRK EPR17341 Assay as a screening method. All positive IHC cases were simultaneously studied by 2 NGS tests, Oncomine Comprehensive Assay v3 and FoundationOne CDx. With this approach, the detection rate of NTRK fusions was 20 times higher (5.57%) by only screening 323 patients than the largest cohort in the literature (0.30%) comprising several hundred thousand patients. Based on our findings, we propose a multiparametric strategy (ie, "supervised tumor-agnostic approach") when pathologists start searching for NTRK fusions.

Clinical utility of liquid-based comprehensive genomic profiling (CGP) in gastrointestinal stromal tumors (GIST).

11541 Background: GIST is the most common mesenchymal cancer of the digestive tract. Beyond surgery, treatment for GIST focuses largely on tyrosine kinase inhibitors (TKI), whose selection and potential resistance depend on select mutations. We present the molecular landscape of GIST utilizing tissue and liquid biopsies with emphasis on the clinical utility of liquid biopsy in advanced GIST. Methods: Liquid (FoundationOne Liquid CDx [F1LCDx]) and tissue (FoundationOne CDx) CGP was performed by hybrid capture, targeted NGS at Foundation Medicine Inc. Tissue and liquid samples from 2,198 and 147 patients, respectively, were analyzed. A cohort of 27 paired tissue and liquid samples were also evaluated. The levels of circulating tumor DNA (ctDNA) in liquid biopsies was quantified by tumor fraction (TF), with a TF algorithm incorporating aneuploidy, variant allele frequency, and canonical alterations detected on F1LCDx. Results: Tissue CGP (n = 2,198) revealed the following prevalence of primary driver alterations: KIT (77%), PDGFRA (8%), NF1 (6%), SDHA/B/C/D (SDHx, 3%) and BRAF (1%). Rates of molecular markers previously associated with worse prognosis included: CDKN2A (29%), RB1 (9%), TP53 (6%) and SETD2 (4%). 7% of cases had no reportable known pathogenic alterations in canonical GIST genes (wild-type GIST), while 2% of cases had a mutation in more than one driver. In a cohort of 147 liquid biopsies, TF was < 1% in 68.0%, 1-10% in 18.4%, > 10% in 13.6% of samples. In samples with elevated TF ( > 10%), the prevalence of targetable driver alterations in KIT (89%), PDGFRA (4%) , NF1 (4%) and BRAF (4%) was comparable to the tissue prevalence. In liquid, 58% (39/67) of samples with a KIT-driver mutation had a co-occurring imatinib-resistant KIT alteration. In addition, 4/147 patients (3%) were predicted to harbor a germline KIT mutation, including one patient (0.6%) with a potential imatinib-resistant KIT D820G germline mutation and another with clinical suspicion of germline KIT L576P mutation due to the presence of multiple primary GISTs, hyperplasia of myenteric plexus and dysplastic skin nevi. In paired tissue/liquid samples, liquid detected 2/2 driver mutations found in tissue when liquid TF was > 10%, and 5/6 in specimens with TF > 1%. In the overall cohort, the relative prevalence of KIT exon 9 and 11 driver alterations was comparable in tissue vs liquid, while imatinib-resistance KIT exon 13 and 17 mutations were enriched in liquid samples. Conclusions: Known driver and TKI-resistant mutations of both somatic and potential germline origin are identified in peripheral blood ctDNA of GIST patients. Liquid biopsy shows high concordance to tissue in identifying driver mutations in the presence of elevated TF and may exhibit TKI-resistant specific alterations. This study indicates that liquid biopsy may be useful in the molecular classification of GIST during the medical management of advanced GIST patients.

Longitudinal follow-up and outcomes of pediatric and adult patients with SDH-deficient GIST.

11542 Background: Gastrointestinal stromal tumor (GIST) are gastrointestinal non-epithelial neoplasms most commonly driven by somatic mutations in KIT or PDGFRA. Approximately ten percent of GIST are due to germline mutations in SDHx or epigenetic loss of expression of SDHC. While KIT and PDGFRa driven GIST respond to treatment with tyrosine kinase inhibitors, effective systemic therapies for SDH-deficient GIST have not yet been identified. SDH-deficient GIST are indolent tumors that typically progress slowly over time. A better understanding of the natural history of patients with these neoplasms is critical to identify effective treatments and improve patient care. A cohort of patients with SDH-deficient GIST is followed at the NIH Clinical Center and through the NIH Pediatric and Wild-type GIST Clinic. The aim of this study is to characterize the long-term outcome of this cohort of patients. Methods: Data from patients with SDH-deficient GIST enrolled in a study Natural History and Biospecimen Acquisition for Children and Adults with Rare Solid Tumors (NCT03739827) from January 2019 through January 2023 at the NIH were evaluated. In addition to review of medical records and imaging, when available, tumors were characterized by sequencing of SDH genes. Germline analysis of SDH genes was offered to consenting patients and families. Results: Clinical information and specimens were collected from 77 GIST patients (median age at diagnosis 21.5, [range 7-57] years; 72.7% (56) female, 21.3% (21) male) were classified by molecular subtypes: 33.8% SDHC epimutation, 28.6% SDHA, 22.1% SDHB, 14.3% SDHC and 1.3% SDHD. Median age at presentation of SDHC epimutation was younger (14.5 years, range: 8-56) when compared to SDHA (27.5 years, range: 7-55), SDHB (22 years, range: 8-54), SDHC (18 years, range: 10-57) and SDHD (39 years, N = 1). Most commonly, patients had at least one surgery (55.8%) while a lower proportion had four or more (7.8%). Primary tumors occurred in the stomach with 26% having metastases at presentation the most common location being the liver (10.4%). Overall, 64.9% of patients were treated with imatinib, 39% were treated with sunitinib and 15.6% received other additional systemic therapies. Within the cohort there were 13% of patients with paragangliomas and 6.5% with chondromas while only 9.1% had a family history of GIST. Conclusions: Longitudinal follow-up of an SDH-deficient GIST patient cohort will allow for better understanding of the natural history including treatment history and survival of patients with this rare disease and will help to optimize strategies for treatment and follow-up of these patients.

Anaplastic lymphoma kinase expression in PDGFRA-mutated gastrointestinal stromal tumors probably correlates with poor prognosis

BackgroundAnaplastic lymphoma kinase (ALK) overexpression and gene alterations have been detected in several mesenchymal tumors, with significant implications for diagnosis, therapy and prognosis. However, few studies have investigated the correlation between ALK expression status and clinicopathological characteristics in patients with gastrointestinal stromal tumors (GISTs).MethodsA total of 506 GIST patients were enrolled. Sanger sequencing was employed to detect c-KIT and PDGFRA gene mutations. The tissue microarray (TMA) technique and immunohistochemistry were employed to identify the ALK (clone: 1A4 and D5F3) expression status in the tumor tissues. The ALK gene variants of IHC-positive cases were analyzed by fluorescence in situ hybridization (FISH) and next-generation sequencing (NGS). The clinicopathological data were analyzed using SPSS Statistics 26.0.ResultsAmong the 506 GIST patients, the c-KIT mutation accounted for 84.2% (426/506), followed by PDGFRA mutation (10.3%, 52/506), while the wild-type accounted for the least (5.5%, 28/506). ALK-positive expression was detected in PDGFRA-mutant GISTs (7.7%, 4/52) but negative for c-KIT-mutant or wild-type GISTs by IHC. Four ALK IHC-positive patients were all male. The tumors all occurred outside the stomach. The predominant patterns of growth were epithelioid (2/4), spindle (1/4), and mixed type (1/4). They were all identified as high-risk classification according to the National Institutes of Health (NIH) classification. Aberrant ALK mutations were not identified by DNA-based NGS except in one of the 4 cases with amplification by FISH.ConclusionOur study revealed 7.7% (4/52) of ALK expression in PDGFRA-mutant GISTs, indicating that molecular tests were required to rule out the possibility of PDGFRA-mutant GISTs when encountering ALK-positive mesenchymal tumors with CD117-negative or weakly positive in immunohistochemical staining.

Natural history and treatment efficacy in an ambispective case series of NTRK-rearranged mesenchymal tumors

Apart for infantile fibrosarcoma (IFS), very little is known about NTRK-rearranged mesenchymal tumors (NMTs). The objective of this study is to describe the distribution, characteristics, natural history, and prognosis of NMT. This study was carried out as a translational research program, retrospectively from a cohort of 500 soft tissue sarcoma (STS; excluding IFS) and prospectively both in routine practice and from the RNASARC molecular screening program (N= 188; NCT03375437). Using RNA-sequencing, NTRK fusion was detected in 16 patient tumors diagnosed as STS: 8 samples of sarcoma with simple genomics (4 NTRK-rearranged spindle cell neoplasm, 3 ALK/ROS wild-type inflammatory myofibroblastic tumor, and 1 quadruple Wild-type gastrointestinal stromal tumor) and 8 samples of sarcomas with complex genomics (dedifferentiated liposarcoma, intimal sarcoma, leiomyosarcoma, undifferentiated pleomorphic sarcoma, high-grade uterine sarcoma, malignant peripheral nerve sheath tumor). Among the eight patients with simple genomics, four were treated with tyrosine receptor kinase inhibitor (TRKi) at different stages of the disease and all benefited from the treatment, including one complete response. Among the eight other patients, six evolved with metastatic spreading and the median metastatic survival was 21.9 months, as classically reported in these tumor types. Two of them received a first-generation TRKi without objective response. Our study confirms low frequency and histotype diversity of NTRK fusion in STS. While the activity of TRKi in simple genomics NMT is confirmed, our clinical data encourage subsequent studies focusing on the biological relevance of NTRK fusions in sarcomas with complex genomics together with the efficacy of TRKi in this population.

CT-based assessment of sarcopenia for differentiating wild-type from mutant-type gastrointestinal stromal tumor

Non-invasive prediction for KIT/PDGFRA status in GIST is a challenging problem. This study aims to evaluate whether CT based sarcopenia could differentiate KIT/PDGFRA wild-type gastrointestinal stromal tumor (wt-GIST) from the mutant-type GIST (mu-GIST), and to evaluate genetic features of GIST. A total of 174 patients with GIST (wt-GIST = 52) were retrospectively identified between January 2011 to October 2019. A sarcopenia nomogram was constructed by multivariate logistic regression. The performance of the nomogram was evaluated by discrimination, calibration curve, and decision curve. Genomic data was obtained from our own specimens and also from the open databases cBioPortal. Data was analyzed by R version 3.6.1 and clusterProfiler (http://cbioportal.org/msk-impact). There were significantly higher incidence (75.0% vs. 48.4%) and more severe sarcopenia in patients with wt-GIST than in patients with mu-GIST. Multivariate logistic regression analysis showed that sarcopenia score (fitted based on age, gender and skeletal muscle index), and muscle fat index were independent predictors for higher risk of wt-GIST (P < 0.05 for both the training and validation cohorts). Our sarcopenia nomogram achieved a promising efficiency with an AUC of 0.879 for the training cohort, and 0.9099 for the validation cohort with a satisfying consistency in the calibration curve. Favorable clinical usefulness was observed using decision curve analysis. The additional gene sequencing analysis based on both our data and the external data demonstrated aberrant signal pathways being closely associated with sarcopenia in the wt-GIST. Our study supported the use of CT-based assessment of sarcopenia in differentiating the wt-GIST from the mu-GIST preoperatively.

Genetic mutations in the molecular pathogenesis of gastrointestinal stromal tumor

Gastrointestinal stromal tumors are mesenchymal tumors which predominantly originate from the interstitial cells of Cajal in the intestinal lining. Around ~85% of malignant GISTs possess activating mutations in the tyrosine kinase receptors KIT or PDGFRA. The driver mutations in genes other than KIT or PDGFRA account for around 15% GISTs and belong to highly heterogeneous groups called wild-type GISTs. Around 20–40% of WT-GISTS are deficient for the succinate dehydrogenase complex (SDHA, SDHB, SDHC, SDHD). Mutations in SDH cause the accumulation of oncometabolite succinate that increases the level of HIF1α which enhances the transcription of several genes including IGF1, IGF2, and VEGF inducing the proliferation of the cancer cells. The remaining WT-GISTS are associated with mutations in BRAF, loss-of-function of NF1, hyperactivation FGFR, inactivation of tumor suppressor genes (p53 and dystrophin), and mutations in DNA damage response genes such as RAD51 and BRCA2 which results in the activation of the PI3K/mTOR or RAS/RAF/MAPK signaling cascade. Therefore, understanding the mutational status and molecular characterization of GIST plays a very crucial role in the overall management of GIST.

Current Molecular Profile of Gastrointestinal Stromal Tumors and Systemic Therapeutic Implications.

Gastrointestinal stromal tumors (GISTs) are malignant mesenchymal tumors arising from the intestinal pacemaker cells of Cajal. They compose a heterogenous group of tumors due to a variety of molecular alterations. The most common gain-of-function mutations in GISTs are either in the KIT (60-70%) or platelet-derived growth factor receptor alpha (PDGFRA) genes (10-15%), which are mutually exclusive. However, a smaller subset, lacking KIT and PDGFRA mutations, is considered wild-type GISTs and presents distinct molecular findings with the activation of different proliferative pathways, structural chromosomal and epigenetic changes, such as inactivation of the NF1 gene, mutations in the succinate dehydrogenase (SDH), BRAF, and RAS genes, and also NTRK fusions. Currently, a molecular evaluation of GISTs is imperative in many scenarios, aiding in treatment decisions from the (neo)adjuvant to the metastatic setting. Here, we review the most recent data on the molecular profile of GISTs and highlight therapeutic implications according to distinct GIST molecular subtypes.