Oncogenic Mutation Screening in Solitary Fibrous Tumors Elizabeth G. Demicco, Khalida Wani, Kenneth Aldape, Alexander J. Lazar, and Wei-Lien Wang

Solitary Fibrous Tumor (SFT) Background Phenotypic spectrum comprising classic solitary fibrous tumor (hypocellular variant) and hemangiopericytoma (hypercellular variant) Rarely metastasizing– Behavior can be difficult to predict

Limited data on cytogenetic abnormalities. Relatively simple genomic alterations Few recurrent features Limited data on genetic abnormalities PDGFRB mutations, 2/88 pleural SFT No mutations in DDR1 (n=8), ERBB2 (n=10), FGFR1 (n=15), PDGFRB (n=39) TP53 one case, dedifferentiated SFT of nasal cavity Solitary Fibrous Tumor (SFT) Background

Examine a large series of solitary fibrous tumors for common oncogenic mutations. Purpose

Screening Approach to Mutational Analysis (Sequenom MassArray) Detection method for single nucleotide polymorphisms (SNP) Step 1. PCR-based Allele (WT vs. mutant) specific probes Single nucleotide extension across site of SNP Different probe sizes allow for allele differentiation and multiplexed reaction Step 2. MALDI-TOF mass spectrometry Analyze primer extension product Time of flight mass spectrometry differentiates based on probe size

Gene# SitesAlleles AKT1 1 G49A AKT2 1 G49A AKT3 1 G49A BCOR 1 A4220GCT CC2D1A 1 C3036G EPHA3 1 G2283TC FOXL2 1 C402G GRM3 1 G2608A JAK2 1 G1849T MGA 1 C5421A PPP2R1A 1 T769G RET 1 T2753C RPL22 1 A44CGT SFRS9 1 C722A SMO 1 G970A SRC 1 C1591T TGM2 1 T734C CDK4 2 C70T; G71A CSMD1 2 G1225T; C9013T FBXO4 2 T68A; C226A FGFR1 2 C754A; C374T FGFR2 2 T1647GA; C755G GNA11 2 A626TC; C547T GNAQ 2 A627T; A626TCG Gene# SitesAlleles CTNNB1 12 A95CGT; G94CAT, G101ATC; A107CG; T104AGC; T97GCA; T109GCA; C110GTA; T133GCA; C134GTA; A121GCT; C122TAG KIT 12 A2447GTC; G2446CAT; A1924G; T1727C; A1696G; T2466GCA; A2464TCG; C1900T; T1676CAG ; T1679AGC ; T2474C ; T1657A BRAF 12 A1781GT; G1756A; G1391ATC; G1397ATC; G1396CA; G1406ATC; G1405CA; A1801G; T1790GA; G1800ATC; G1800ATC; T1799ACG_F; T1799ACG_R; G1798TA GNAS 2 G602A; C601AT PIK3CA 28 C3137T; T1258C; G328A; G1252A; G1357A; G1624AC; A1625TG; A1634CGT; G1635CT; G1633AC; C2727G; G353A; A3140GT_F; A3140GT_R; C3139T; A2102C; G333C; G3129ATC; A3127G; T1035A; C1616G; C178A; C1636GA; A1637TCG; G263A; C1214T; A3073TG; A3062G; T3061CA IDH1 3 G209A; C394TGA; G395AT IDH2 4 G419TA; A514GT; G515TA; G516T MAP2K7 4 C870T; G485A; T811A; C932T PDGFRA 5 A2525T; G2524TA; C1977A; A1975T ; T1682A FBXW7 6 C1393T; G1394AT; G1436AT; C1513TA; G1514ATC; C1745T RAF1 6 G955T; C1837G; A344G; G1005C; T775G; T1018G FGFR3 7 G1108T; G1138A; G2089T; A1949TC ; C742T ; C746G ; A1118G KRAS 7 G436CA; G28A; G35ACT; G34ACT; G38ACT; G37ACT; C181GAT MET 7 A3335GT; C3334T; T3803C; A1124G ; C2962T ; C3029T ; T3742CG ALK 8 T3521GC; C3522AG; T3520CAG; T3734G; C3735AG; T3733GA; T3512A; G3824AT EGFR 8 G2155TA; A2579T; T2573G; T2582AG; T2158C ; C2369T ; C2561T ; A2438G NRAS 8 G436A; G35ACT; G34ACT; G38ACT; G37ACT; C181GAT; A183TCG; A182GCT

Tumor Characteristics 122 tumors (105 patients) 72 Primary 9 Local recurrence 41 Metastasis 13 Patients with multiple tumors tested 6 primary and metastasis(es) 5 multiple metastases 2 local recurrence(s) +/- metastasis

Site Number of Patients Gender (% F) Age at first diagnosis, years (median, range) All %53, Meningeal2438.9%45, Pleural2236.4%63, Intra- abdominal %53, Extremity1570.0%57, Trunk1053.3%51, Head and neck 757.1%56, Patient Demographics

VariableRun 1Run 2Total Number of cases (each in duplicate) Total number of polymorphism sites tested 175 (41 genes)174 (41 genes)174/175 % Successful reads96.5%91.9%93.0% Duplicate concordance success rate (out of all possible reads) 94.4% 86.5%88.4% Duplicate failure rate due to no result one or both duplicates (out of all possible reads) 5.3%13.2%11.3% Duplicate discordance rate (WT/mut read) (out of all possible reads) 0.3% General Quality Control Indicators

Run 1Run 2Total Number SNPs detected (% of all useable reads) 12 (0.23%) 21 (0.15%) 33 (0.17%) Site ALK T3733G (p.F1245V)-11 BRAF T1799A* (p.V600E)213 KRAS G35A (p.G12D)**11011 KRAS G34A (p.G12S)**-11 KRAS C181A (p.Q61K)-11 MET C2962T (p.R988C)112 MET C3029T (p.T1010I)-33 NRAS G35A (p.G12D)**7310 NRAS G38A (p.G13D)**1-1 * Mutation identified on forward probe, WT on reverse ** Problems with probes later reported – Determined to be WT by CAST-PCR Potential Mutations Identified by Sequenom

Characteristics of Tumors with Identified SNPs * Presence of SNP did not correlate with c-MET expression by IHC Patient (phenotypic variant) MutationTumor statusPrimary SiteSite this metastasis Outcome SFT118 (hypercellular) MET C3029T (p.T1010I)* Metastasis (10 yr) Intra- abdominal PeritoneumDoD 18 yr SFT118 (hypercellular) MET C3029T (p.T1010I)* Metastasis (14 yr) Intra- abdominal PeritoneumDoD 18 yr SFT055 (hypocellular) MET C3029T (p.T1010I)* PrimaryIntra- abdominal Dead other causes 30 months SFT048 (hypercellular) MET C2962T (p.R988C)* PrimaryIntra- abdominal Metastasized at 40 mo. DoD 8.5 yr SFT092 (hypocellular) MET C2962T (p.R988C)* PrimaryPleuraLTFU 1 month SFT067 (hypercellular) ALK T3733G (p.F1245V) PrimaryIntra- abdominal NED 69 mo SFT112 (hypercellular) KRAS C181A (p.Q61K) Metastasis (13 yr) Intra- abdominal PeritoneumDod 16 yrs

MET C3029T (p.T1010I) and C2962T (p.R988C) Also designated as T992I and R970C Juxtamembrane domain Initially reported as rare somatic oncogenic mutations Identified in a wide range of tumors Frequency in involved cancers ~1-10% Later proposed to represent germline polymorphisms Seen in ~1% of individuals without cancer (1/96) Germline in several patients with cancer No evidence of transformation in cell models T1010I as cooperative germline oncogenic mutation? Identified in ~4.5% familial CRC Mutation proposed to indirectly activate c-MET via inhibition of inhibitor Not initiator, may promote progression

ALK T3733G (p.F1245V) Kinase-activating mutation Rare mutation Reported in neuroblastoma

KRAS C181A (p.Q61K) Activating mutation reported rarely in colonic and lung adenocarcinoma, misc. other carcinomas various sites Much more rare than the equivalent NRAS mutation

Summary We performed screening SNP analysis in a large series of SFT Confirmed that SFT have low frequency of mutations in oncogenes commonly reported in other malignancies 7/122 cases (5.7%) Abdominal location predominant Insufficient data on relevance to status, prognosis

Conclusions Mutations in commonly identified oncogenes do not appear to function in pathogenesis of SFT. Alternative mechanisms? Mutations in uncommon genes Imprinting miRNA regulation Studies are ongoing

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