Oncogenic Mutation Screening in Solitary Fibrous Tumors
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Transcript of Oncogenic Mutation Screening in Solitary Fibrous Tumors
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 # Sites Alleles
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 # Sites Alleles
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 105 48.5% 53, 16-89
Meningeal 24 38.9% 45, 16-89
Pleural 22 36.4% 63, 35-81
Intra-abdominal
27 51.9% 53, 27-71
Extremity 15 70.0% 57, 31-69
Trunk 10 53.3% 51, 29-78
Head and neck
7 57.1% 56, 39-72
Patient Demographics
Variable Run 1 Run 2 Total
Number of cases (each in duplicate)
31 96 127
Total number of polymorphism sites tested
175 (41 genes) 174 (41 genes) 174/175
% Successful reads 96.5% 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% 0.3% 0.3%
General Quality Control Indicators
Run 1 Run 2 Total
Number SNPs detected (% of all useable reads)
12 (0.23%)
21 (0.15%)
33 (0.17%)
Site
ALK T3733G (p.F1245V) - 1 1BRAF T1799A* (p.V600E) 2 1 3KRAS G35A (p.G12D)** 1 10 11KRAS G34A (p.G12S)** - 1 1KRAS C181A (p.Q61K) - 1 1MET C2962T (p.R988C) 1 1 2MET C3029T (p.T1010I) - 3 3NRAS G35A (p.G12D)** 7 3 10NRAS 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)
Mutation Tumor status Primary Site Site this metastasis
Outcome
SFT118 (hypercellular)
MET C3029T (p.T1010I)*
Metastasis (10 yr)
Intra-abdominal
Peritoneum DoD 18 yr
SFT118 (hypercellular)
MET C3029T (p.T1010I)*
Metastasis(14 yr)
Intra-abdominal
Peritoneum DoD 18 yr
SFT055 (hypocellular)
MET C3029T (p.T1010I)*
Primary Intra-abdominal
Dead other causes 30 months
SFT048 (hypercellular)
MET C2962T (p.R988C)*
Primary Intra-abdominal
Metastasized at 40 mo.DoD 8.5 yr
SFT092 (hypocellular)
MET C2962T (p.R988C)*
Primary Pleura LTFU 1 month
SFT067 (hypercellular)
ALK T3733G (p.F1245V)
Primary Intra-abdominal
NED 69 mo
SFT112 (hypercellular)
KRAS C181A (p.Q61K)
Metastasis (13 yr)
Intra-abdominal
Peritoneum Dod 16 yrs
MET C3029T (p.T1010I) and C2962T (p.R988C)
Also designated as T992I and R970CJuxtamembrane 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 predominantInsufficient 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
Thank You.