Epigenetic landscape of gastrointestinal stromal tumors: Mechanistic insights and therapeutic opportunities

Table 1 Diagnostic applications of DNA methylation in gastrointestinal stromal tumors[70-72,74-78]

Ref.	Cohort/samples	Targets	Methodology	Key findings
Casey et al[71]	59 GISTs (multi-institutional) + blood/saliva	SDHC promoter	Bisulfite sequencing	Epimutation found in approximately 94% of SDHx-WT cases, including Carney triad; mosaicism in peripheral tissues supports post-zygotic origin
Janeway et al[74]	Pediatric and WT GIST (approximately 100)	SDH subunits (SDHB, SDHC epimutations)	IHC + genetic/epigenetic testing	Established SDH-deficient GIST in children/WT adults; SDHB loss by IHC plus SDHC methylation testing defines subset
Haller et al[75]	Carney triad GISTs	SDHC promoter	Methylation assays	Recurrent SDHC hypermethylation identified as defining event in Carney triad, absent in Carney-Stratakis
Angelini et al[76]	63 tumors (KIT/PDGFRA-mutant vs SDH-deficient)	Genome-wide	450K arrays	C promoter hypermethylation represents a characteristic alteration in Carney triad but is not detected in Carney-Stratakis
Killian et al[70]	SDH-deficient vs syndromic GIST	Genome-wide	450K arrays	SDH-deficient GISTs characterized by a hypermethylator profile, with succinate accumulation blocking TET enzyme activity
Miettinen et al[72]	66/756 gastric GIST SDH-deficient	SDH status	IHC + molecular	Defined clinicopathologic spectrum of SDH-deficient GIST; IHC loss of SDHB as front-line marker
Saito et al[77]	35 GISTs	CpG island panel (p15, p16, p73, MGMT, hMLH1, MINT1/2/31)	MSP	94% tumors showed aberrant methylation; proposed CIMP-like category in GIST
Giger et al[78]	Plasma/tissue paired samples	SEPT9 (plasma methylation)	ddPCR	Circulating methylated SEPT9 showed feasibility as a liquid biopsy biomarker (AUC: 0.74-0.79)

GIST: Gastrointestinal stromal tumors; WT: Wild-type; SDH: Succinate dehydrogenase; SDHB: Succinate dehydrogenase subunit B; MGMT: O-6-methylguanine-DNA methyltransferase; IHC: Immunohistochemistry; MSP: Methylation-specific polymerase chain reaction; ddPCR: Droplet digital polymerase chain reaction; TET: Ten-eleven translocation; AUC: Area under the curve; CIMP: CpG island methylator phenotype.

Table 2 Prognostic biomarkers of DNA methylation in gastrointestinal stromal tumors[32,41,73,75,79-82]

Ref.	Cohort/samples	Targets	Methodology	Key findings
Geddert et al[32]	200 GISTs	CD133 promoter	MSP + IHC	Hypermethylation associated with reduced CD133 expression; paradoxically, CD133 expression predicted shorter DFS
Haller et al[75]	150 GISTs	SPP1 (osteopontin)	Locus-specific assays	Hypomethylation predicted poor DFS across size, site, and mitotic index
House et al[79]	38 gastric GISTs	E-cadherin (CDH1)	MSP + protein	Methylation correlated with loss of E-cadherin and independently predicted recurrence/mortality
Ricci et al[80]	Gastric GISTs	p16INK4a promoter	MSP + IHC	Hypermethylation linked to protein loss and poor outcome
Lou et al[81]	115 cases	REC8, PAX3, p16	MCAM + validation	≥ 1 gene methylated correlated with poor survival; site-specific patterns identified
Niinuma et al[41]	91 cases	MEG3	Methylation + transcript	Hypermethylation correlated with poor prognosis; restoration activated interferon responses
Ohshima et al[73]	KIT exon 11 Δ557-558	Genome-wide	WGS + methylome	Hypomethylation signature linked to CNV burden and p53 pathway inactivation; aggressive behavior
Kleijn et al[82]	28 patients	Genome-wide	EPIC methylome + CNV	CNV burden and DMRs associated with progression; added to risk models

GIST: Gastrointestinal stromal tumors; CD: Cluster of differentiation; IHC: Immunohistochemistry; MSP: Methylation-specific polymerase chain reaction; DFS: Disease-free survival; CNV: Copy number variation; WGS: Whole-genome sequencing; DMR: Differentially methylated region; EPIC: Illumina EPIC methylation array.

Table 3 Predictive biomarkers of DNA methylation in gastrointestinal stromal tumors[42,78,83-85]

Ref.	Cohort/samples	Targets	Methodology	Key findings
Giger et al[78]	SDH-deficient cohorts	MGMT promoter	MSP	MGMT methylation enriched in SDH-deficient GIST; suggested biomarker for temozolomide sensitivity
Ricci et al[83]	74 cases	MGMT promoter	MSP	Confirmed MGMT methylation in SDH-deficient/WT tumors (67% vs 15%); advocated alkylator trials with stratification
Italiano et al[84]	Imatinib-resistant cases	IGF2/IGF1R deregulation	Epigenetic expression analysis	Epigenetic activation of IGF axis implicated in imatinib resistance
Urbini et al[85]	Quadruple WT vs SDH-deficient	FGF4	Genomic vs methylation	In SDH-deficient, FGF4 induced by methylation; in WT, due to duplication. Suggested FGFR inhibitors
Xu et al[42]	53 cases (tissue)	METTL3-MRP1 (RNA methylation)	m6A + functional assays	High METTL3 expression linked to shorter PFS in resistant patients; RNA methylation mechanism of imatinib resistance

MRP1: Multidrug resistance protein 1; GIST: Gastrointestinal stromal tumors; WT: Wild-type; SDH: Succinate dehydrogenase; MGMT: O-6-methylguanine-DNA methyltransferase; IGF2: Insulin-like growth factor 2; IGF1R: Insulin-like growth factor 1 receptor; FGF: Fibroblast growth factor; m6A: N6-methyladenosine; MSP: Methylation-specific polymerase chain reaction; PFS: Progression-free survival; FGFR: Fibroblast growth factor receptor.

Table 4 Histone modifications as diagnostic, prognostic, and predictive tools in gastrointestinal stromal tumors[41,50,52,54-56,60-62,64]

Ref.	Patient cohort/clinical role	Methodology	Key findings
Jin et al[60]	119 primary GISTs/diagnostic	IHC, digital quantification	PHH3 counts correlated strongly with mitotic index and NIH risk category improved reproducibility compared with conventional mitotic figures
Huang et al[56]	134 patients (discovery: 18 tumors from 14 patients; prevalence validation: 125 tumors from 120 patients; 89 high-risk/metastatic, 34 low/intermediate-risk)/prognostic	Exome + targeted resequencing (KIT/PDGFRA/SETD2); H3K36me3 IHC; 450K methylation array; RNA-sequencing	SETD2 mutations in 11.2% (10/89) of high-risk and 0% (0/34) of low/intermediate-risk GISTs gastric SETD2-mutant tumors show hypomethylated heterochromatin and reduced H3K36me3; associated with shorter relapse-free survival
Shen et al[54]	48 GISTs, paired tumor vs adjacent tissue/diagnostic/prognostic	IHC, ChIP-qPCR	KDM6A and SPARCL1 correlated with mitotic index, risk classification, and metastatic recurrence. Diagnostic ROC analysis: AUC: 0.698 (KDM6A), 0.834 (SPARCL1), 0.858 (EZH2). Low KDM6A linked to higher metastasis rates and reduced survival
Ji et al[55]	46 GIST tumors with matched adjacent tissue; stratified by NIH risk (low/intermediate/high)/diagnostic/prognostic	IHC, molecular assays	Tumors showed SMYD2 and EZH2 upregulation with H3K27me3 increase and TET1 downregulation; high-risk cases enriched for this profile
Niinuma et al[41]	131 primary GISTs, validation in 44 tumors/prognostic	Methylation assays, ChIP	MEG3 hypermethylation associated with higher recurrence risk (HR = 2.3; 95%CI: 1.2-4.6) altered H3K4me3 linked to poor recurrence-free survival
Qiu et al[52]	26 paired GIST tumors vs adjacent tissues/prognostic	IHC, tissue analysis	miR-409-5p expression is decreased in GIST tumors compared to adjacent normal tissues. Lower miR-409-5p levels correlate with higher GIST risk grade
Gao et al[64]	67 WT GIST patients/prognostic	IHC, tissue studies	SDHB deficiency: Higher ZNF148 expression, significantly shorter PFS (median approximately 104 months vs not reached). High ZNF148-pS306: Inferior PFS. SDHB deficiency = independent predictor of shorter PFS
Wang et al[50]	9 GISTs (3 low-, 3 moderate-, 3 high-risk)/prognostic	Mass spectrometry	Identified 2904 acetyl sites on 1319 proteins (quantified 2548 sites on 1169 proteins) vs low risk, 42 sites (38 proteins) up and 48 sites (44 proteins) down in high/moderate risk. Largest shifts: Ki67 K1063Ac (increase), FCHSD2 K24Ac (decrease)
Yen et al[61]	Public microarray datasets (including GIST samples with exon 11 mutations) compared to other sarcoma subtypes; validation on patient-derived GIST tissues/translational	Connectivity map + tissue validation	ETV1, along with KIT, DOG1, and PKCθ, was significantly overexpressed in GIST patient samples compared to multiple sarcoma subtypes; phenothiazines (trifluoperazine, thioridazine) emerged as candidate ETV1-targeting agents with potential for biomarker-guided drug repositioning
Zeng et al[62]	Twelve matched pairs of GIST resections from the same patients, taken pre-imatinib and after adjuvant imatinib with subsequent relapse/predictive	IHC, paired tissue analysis	IHC on paired samples revealed that BCL6 expression was consistently elevated after imatinib treatment in the 12 patient pairs, linking its upregulation with resistance and recurrence, and suggesting a rationale for combining BCL6 inhibition with imatinib therapy

GIST: Gastrointestinal stromal tumors; WT: Wild-type; NIH: National Institutes of Health; IHC: Immunohistochemistry; ChIP: Chromatin immunoprecipitation; qPCR: Quantitative polymerase chain reaction; ROC: Receiver operating characteristic; AUC: Area under the curve; HR: Hazard ratio; CI: Confidence interval; SDHB: Succinate dehydrogenase subunit B; PFS: Progression-free survival; PKC: Protein kinase C.