Oops, you're using an old version of your browser so some of the features on this page may not be displaying properly.

MINIMAL Requirements: Google Chrome 24+Mozilla Firefox 20+Internet Explorer 11Opera 15–18Apple Safari 7SeaMonkey 2.15-2.23

KIT and PDGFRA Wild-type Gastrointestinal Stromal Tumours (GISTs): ESMO Biomarker Factsheet

ESMO Factsheets on Biomarkers

Approximately 15% of GISTs do not have detectable mutations in the receptor tyrosine kinase genes, KIT or PDGFRA, and are generally termed ‘wild-type’ (wt) GISTs[1-3]. These are the primary form of GIST found in children. The wt GISTs harbour other genomic aberrations, including mutations in BRAFNF1, NTRK and subunits of the succinate dehydrogenase (SDH) complex[1, 2, 4-6]. The wt GISTs are rare, which has made it difficult to determine their clinical and genetic features[1, 3]. Analysis of a large cohort of patients with wt GIST (n=95) identified three molecular subtypes—two types of SDH-deficient GIST (SDH-mutant and SDH-epimutant) and SDH-competent GIST (characterised largely by BRAF, NF1 or more rare gene mutations). This classification identifies two distinct diagnostic groups with implications for prognosis and clinical management: SDH-competent GISTs (sharing tumour and demographic features with KIT/PDGFRA-mutated GISTs) and SDH-deficient GISTs (frequently associated with syndromic GIST and harbouring molecular lesions of SDH subunits)[3].

SDH-deficient wt GIST

SDH deficiency is the most frequent molecular alteration in wt GIST[3, 7, 8]. SDH is a mitochondrial enzyme complex comprised of four subunits—SDHA, SDHB, SDHC, and SDHD—whose genes map to 5p15.33, 1p36.13, 1q23.3, and 11q23.1, respectively[4]. Located in the inner mitochondrial membrane, the SDH complex plays a role in the electron transport chain and Krebs cycle, catalysing the oxidation of succinate to fumarate[1, 4]. Deficiency of SDH complex leads to accumulation of succinate, resulting in hypoxia-inducible factor (HIF)1-α stabilisation and constitutive activation of hypoxic signalling and tumorigenesis[1, 4]. In parallel, succinate accumulation also inhibits key enzymes that regulate the epigenome leading to hypermethylation of DNA and histones[9, 10].

Deficiency of SDH in GIST can arise either from mutation in one of the genes encoding the SDH subunits, SDHASDHBSDHC or SDHD (collectively referred to as SDHx mutations) or through epigenetic silencing of SDHC (inactivation through promoter hypermethylation)[3, 7, 10]. A large proportion of GIST SDHx-mutations are present in the germline, which has implications for genetic counselling and testing of first-degree relatives of these patients[3, 11].

SDH-deficient GISTs are diagnosed predominantly in female paediatric or young adult patients, and are characterised by unique clinical, morphological and genetic features[1, 3, 4, 12]. These tumours are predominantly gastric in location, with epithelioid histology and multilobulated/multinodular growth pattern and frequently metastasise to lymph nodes, liver or peritoneal cavity, although generally exhibiting an indolent long-term clinical course[1, 3, 12, 13]. Conventional risk stratification parameters appear not to predict metastatic progression of SDH-deficient GISTs as even small, mitotically inactive SDH-deficient GISTs may metastasise, and when metastases do occur they may be strikingly indolent, sometimes remaining stable for years or decades[1, 4, 14]SDHA mutated-GIST have been associated with a more indolent course of disease compared with KIT/PDGFRA mutated GIST and wt SDH-competent GIST[13].

SDH-deficient GISTs are characterised by a pattern of global, genome-wide DNA hypermethylation[3, 10], and frequently overexpress insulin-like growth factor 1 receptor (IGF1R)[15, 16].

SDH-deficient GISTs can be sporadic, with no other clinical manifestations, but more frequently present as one of two classes of syndromic GISTs, Carney triad and Carney- Stratakis syndrome[11, 17, 18]. Carney-Stratakis syndrome, an inherited predisposition syndrome to multiple gastric GISTs and paragangliomas, is caused by SDHx germline mutations[1, 3, 6, 14]. Surveillance for paragangliomas and other tumours is indicated for patients with inherited SDH-deficient GISTs[4]. Carney-triad, a non-heritable syndrome characterised by multiple gastric GISTs, paragangliomas and pulmonary chondromas, is generally associated with epigenetic SDH inactivation through SDHC hypermethylation[10, 19], and has been rarely associated with germline SDH mutations[20].

SDH-competent GIST

SDH-competent wt GISTs are primarily comprised of tumours harbouring mutations in components of cell signalling pathways, including BRAF and NF1, that act downstream of the receptor tyrosine kinases[1]. SDH-competent GISTs generally share tumour and patient characteristics with those of KIT/PDGFRA-mutated tumours: they exhibit normal genomic methylation patterns, are generally sporadic, presenting predominantly in older adults, located in either the stomach or small bowel, with spindle cell histology. They rarely metastasise to lymph nodes but generally follow a more aggressive course of disease compared to SDH-deficient tumours[3].

Mutations in the tumour suppressor gene, NF1, cause syndromic neurofibromatosis type I (NF1), and have also been identified in patients with KIT/PDGFRA wt GIST[1, 4, 5]. The NF1 gene encodes neurofibromin, which negatively regulates the RAS–RAF–MEK–ERK signalling pathway downstream of receptor tyrosine kinases such as KIT and PDGFRA[4, 5]. Patients with NF1 appear to be overrepresented among GIST patients and GISTs occur in approximately 5–25% of NF1 patients[1, 21]NF1- associated GISTs are characterised by duodenum and small intestine location, small size, tumour multiplicity, and low mitotic rates[1, 5]. These tumours generally follow an indolent clinical course reflected in low recurrence and metastases rates, although NF1-associated GISTs arising from the duodenum can display an aggressive behaviour, being large mitotically active tumours with pronounced metastatic potential[1, 5, 21].

BRAF is a key intracellular protein kinase also involved in the RAS–RAF–MEK–ERK signalling pathway and is mutated in a wide range of cancers, including malignant melanoma, thyroid cancer and colorectal cancer[22, 23]. Multiple studies have identified BRAF mutations in KIT/PDGFRA wt GISTs, with a prevalence of up to 13%[22, 24-27]. Like other tumour types in which BRAF mutations are common, BRAF mutations in GIST predominantly involve the exon 15 V600E hot spot[1, 22, 24-27]BRAF-mutated GISTs appear to predominantly arise in the small intestine and generally share clinicopathological features characteristic of KIT/PDGFRA-mutated GISTs[22, 25].

Other genomic aberrations affecting oncogenes and tumour suppressors have been identified in SDH-competent wt GISTs including mutations in PIK3CANRASHRASKRAS, and gene fusions including ETV6-NTRK3 and FGFR1-TACC1; however, the numbers of patients with these different mutations remains small, such that genotype-phenotype correlations are not yet possible[4].

Treatment response in KIT/PDGFRA wt GIST

The scarcity of KIT/PDGFRA wt GISTs makes it difficult to identify any relationship between their genotype and response to conventional systemic tyrosine kinase inhibitor therapies, such as imatinib, sunitinib, and regorafenib, used for non-wt GIST[1, 3].

Multiple studies have previously demonstrated that KIT/PDGFRA wt GISTs are characterised overall by poor responses to standard imatinib therapy in both the advanced and adjuvant GIST treatment setting, with a 76% greater risk of death reported for patients with advanced wt GIST compared with those with KIT exon 11 mutations[4, 28-30]IGF1R amplification, observed primarily in SDH-deficient GIST, and signalling pathway mutations downstream of KIT and PDGFRA (like NF1 and BRAF exon 15 V600E mutations) in SDH-competent GIST, may represent alternative mechanisms of imatinib resistance in KIT/PDGFRA wt tumours[1, 16, 25, 31, 32].

SDH-deficient GIST have generally demonstrated poor responses to imatinib. For instance, only one of 49 patients treated with imatinib had a partial response[3]. By contrast, antiangiogenic agents may have some activity: seven of 38 patients with SDH-deficient GISTs showed responses to sunitinib[3] and six patients experienced clinical benefit from regorafenib[33]. A current clinical trial at NCI is investigating guadecitabine in epigenetic SDH-deficient GIST (NCT03165721).

While SDH-competent GISTs are generally considered to be less responsive to the conventional tyrosine kinase inhibitors, identifying tumour mutations might prove useful in determining appropriate treatment[1, 3]. For example, emerging data suggest that BRAF-mutated GIST may respond to BRAF inhibitors such as dabrafenib[34], and MEK inhibitors, such as selumetinib, may have utility in NF1-mutated GIST[3]. Responses to a neurotrophic tropomyosin receptor kinase (NTRK) inhibitor in patients bearing GIST with NTRK fusion have also been reported[35].  

Molecular testing of KIT/PDGFRA wt GIST

All GIST with no detectable KIT or PDGFRA mutations should be analysed by SDHB immunostaining. If a GIST is SDH-deficient by SDHB-IHC, sequencing of SDHx in the tumour and germline should be performed[3]. If no SDH mutation is identified, then the presence or absence of SDHC promoter methylation should be determined[3]. If an SDHx mutation is found in the germline then genetic counselling is indicated, together with mutation screening of first-degree relatives, and regular screening for paraganglioma, pheochromocytoma, or other tumours[3, 4]. SDHC promoter hypermethylation is generally not germline, therefore genetic counselling for these patients is not required, but do still require screening for paragangliomas, as they are often associated with syndromic GIST[3].

SDHB-competent cases should be analysed by next-generation sequencing assays to identify potential other targetable alterations (BRAF, NF1, NTRK, FGFR1…).


  1. Szucs Z, Thway K, Fisher C, et al. Molecular subtypes of gastrointestinal stromal tumors and their prognostic and therapeutic implications. Future Oncol 2017;13(1):93-107.
  2. von Mehren M, Joensuu H. Gastrointestinal Stromal Tumors. J Clin Oncol 2018;36(2):136-143.
  3. Boikos SA, Pappo AS, Killian JK, et al. Molecular Subtypes of KIT/PDGFRA Wild-Type Gastrointestinal Stromal Tumors: A Report From the National Institutes of Health Gastrointestinal Stromal Tumor Clinic. JAMA Oncol 2016;2(7):922-928. 
  4. Mei L, Smith SC, Faber AC, et al. Gastrointestinal Stromal Tumors: The GIST of Precision Medicine. Trends Cancer 2018;4(1):74-91.
  5. Niinuma T, Suzuki H, Sugai T. Molecular characterization and pathogenesis of gastrointestinal stromal tumor. Transl Gastroenterol Hepatol 2018;3:2.
  6. Ricci R. Syndromic gastrointestinal stromal tumors. Hered Cancer Clin Pract 2016;14:15. 
  7. Miettinen M, Lasota J. Succinate dehydrogenase deficient gastrointestinal stromal tumors (GISTs) - a review. Int J Biochem Cell Biol 2014;53:514-519. 
  8. Pantaleo MA, Astolfi A, Urbini M, et al. Analysis of all subunits, SDHA, SDHB, SDHC, SDHD, of the succinate dehydrogenase complex in KIT/PDGFRA wild-type GIST. Eur J Hum Genet 2014;22(1):32-39. 
  9. Favier J, Amar L, Gimenez-Roqueplo AP. Paraganglioma and phaeochromocytoma: from genetics to personalized medicine. Nat Rev Endocrinol 2015;11(2):101-111. 
  10. Killian JK, Kim SY, Miettinen M, et al. Succinate dehydrogenase mutation underlies global epigenomic divergence in gastrointestinal stromal tumor. Cancer Discov 2013;3(6):648-657.
  11. McWhinney SR, Pasini B, Stratakis CA, et al. Syndrome Consortium. Familial gastrointestinal stromal tumors and germ-line mutations. N Engl J Med 2007;357(10):1054-1056. 
  12. Martin-Broto J, Martinez-Marin V, Serrano C, et al. Gastrointestinal stromal tumors (GISTs): SEAP-SEOM consensus on pathologic and molecular diagnosis. Clin Transl Oncol 2017;19(5):536-545. 
  13. Pantaleo MA, Lolli C, Nannini M, et al. Good survival outcome of metastatic SDH-deficient gastrointestinal stromal tumors harboring SDHA mutations. Genet Med 2015;17(5):391-395. 
  14. Miettinen M, Killian JK, Wang ZF, et al. Immunohistochemical loss of succinate dehydrogenase subunit A (SDHA) in gastrointestinal stromal tumors (GISTs) signals SDHA germline mutation. Am J Surg Pathol 2013;37(2):234-240. 
  15. Chou A, Chen J, Clarkson A, et al. Succinate dehydrogenase-deficient GISTs are characterized by IGF1R overexpression. Mod Pathol 2012;25(9):1307-1313. 
  16. Lasota J, Wang Z, Kim SY, et al. Expression of the receptor for type i insulin-like growth factor (IGF1R) in gastrointestinal stromal tumors: an immunohistochemical study of 1078 cases with diagnostic and therapeutic implications. Am J Surg Pathol 2013;37(1):114-119. 
  17. Carney JA, Sheps SG, Go VL, et al. The triad of gastric leiomyosarcoma, functioning extra-adrenal paraganglioma and pulmonary chondroma. N Engl J Med 1977;296(26):1517-1518. 
  18. Carney JA, Stratakis CA. Familial paraganglioma and gastric stromal sarcoma: a new syndrome distinct from the Carney triad. Am J Med Genet 2002;108(2):132-139. 
  19. Haller F, Moskalev EA, Faucz FR, et al. Aberrant DNA hypermethylation of SDHC: a novel mechanism of tumor development in Carney triad. Endocr Relat Cancer 2014;21(4):567-577. 
  20. Boikos SA, Xekouki P, Fumagalli E, et al. Carney triad can be (rarely) associated with germline succinate dehydrogenase defects. Eur J Hum Genet 2016;24(4):569-573. 
  21. Miettinen M, Fetsch JF, Sobin LH, et al. Gastrointestinal stromal tumors in patients with neurofibromatosis 1: a clinicopathologic and molecular genetic study of 45 cases. Am J Surg Pathol 2006;30(1):90-96. 
  22. Hostein I, Faur N, Primois C, et al. BRAF mutation status in gastrointestinal stromal tumors. Am J Clin Pathol 2010;133(1):141-148. 
  23. Italiano A, Hostein I, Soubeyran I, et al. KRAS and BRAF mutational status in primary colorectal tumors and related metastatic sites: biological and clinical implications. Ann Surg Oncol 2010;17(5):1429-1434. 
  24. Agaimy A, Terracciano LM, Dirnhofer S, et al. V600E BRAF mutations are alternative early molecular events in a subset of KIT/PDGFRA wild-type gastrointestinal stromal tumours. J Clin Pathol 2009;62(7):613-616. 
  25. Agaram NP, Wong GC, Guo T, et al. Novel V600E BRAF mutations in imatinib-naive and imatinib-resistant gastrointestinal stromal tumors. Genes Chromosomes Cancer 2008;47(10):853-859. 
  26. Huss S, Pasternack H, Ihle MA, et al. Clinicopathological and molecular features of a large cohort of gastrointestinal stromal tumors (GISTs) and review of the literature: BRAF mutations in KIT/PDGFRA wild-type GISTs are rare events. Hum Pathol 2017;62:206-14. 
  27. Rossi S, Gasparotto D, Miceli R, et al. KIT, PDGFRA, and BRAF mutational spectrum impacts on the natural history of imatinib-naive localized GIST: a population-based study. Am J Surg Pathol 2015;39(7):922-930. 
  28. Corless CL, Ballman KV, Antonescu CR, et al. Pathologic and molecular features correlate with long-term outcome after adjuvant therapy of resected primary GI stromal tumor: the ACOSOG Z9001 trial. J Clin Oncol 2014;32(15):1563-1570.
  29. Debiec-Rychter M, Sciot R, Le Cesne A, et al. KIT mutations and dose selection for imatinib in patients with advanced gastrointestinal stromal tumours. Eur J Cancer 2006;42(8):1093-1103. 
  30. Joensuu H, Eriksson M, Sundby Hall K, et al. One vs three years of adjuvant imatinib for operable gastrointestinal stromal tumor: a randomized trial. JAMA 2012;307(12):1265-1272. 
  31. Gramza AW, Corless CL, Heinrich MC. Resistance to Tyrosine Kinase Inhibitors in Gastrointestinal Stromal Tumors. Clin Cancer Res 2009;15(24):7510-7518. 
  32. Heinrich MC, Corless CL, Blanke CD, et al. Molecular correlates of imatinib resistance in gastrointestinal stromal tumors. J Clin Oncol 2006;24(29):4764-4774. 
  33. Ben-Ami E, Barysauskas CM, von Mehren M, et al. Long-term follow-up results of the multicenter phase II trial of regorafenib in patients with metastatic and/or unresectable GI stromal tumor after failure of standard tyrosine kinase inhibitor therapy. Ann Oncol 2016;27(9):1794-1799. 
  34. Falchook GS, Trent JC, Heinrich MC, et al. BRAF mutant gastrointestinal stromal tumor: first report of regression with BRAF inhibitor dabrafenib (GSK2118436) and whole exomic sequencing for analysis of acquired resistance. Oncotarget 2013;4(2):310-315. 
  35. Drilon A, Laetsch TW, Kummar S, et al. Efficacy of larotrectinib in TRK fusion-positive cancers in adults and children. N Engl J Med 2018; 378(8):731-739. 
Last update: 05 Jul 2018

This site uses cookies. Some of these cookies are essential, while others help us improve your experience by providing insights into how the site is being used.

For more detailed information on the cookies we use, please check our Privacy Policy.

Customise settings
  • Necessary cookies enable core functionality. The website cannot function properly without these cookies, and you can only disable them by changing your browser preferences.