No disclosures
description
Transcript of No disclosures
AN INTEGRATED ANALYSIS OF GENETIC AND EPIGENETIC ALTERATIONS IN GASTROINTESTINAL STROMAL TUMORS
REVEALS DISTINCT CLINICAL PHENOTYPES
Sosipatros A. Boikos, Suzanne George, Katherine A. Janeway, Keith J. Killian, Su Young Kim, Michael P. LaQuaglia, Lauren Long, Paul S. Meltzer, Markku M. Miettinen, Karel Pacak, Alberto Pappo, Margarita Raygada, Joshua Schiffman, Constantine Stratakis, Jonathan Trent, Margaret Von Mehren, Christopher B. Weldon, Jennifer Wright, Lee J. Helman
On behalf of the Consortium for Pediatric & wildtype GIST Research
October 31, 2013Connective Tissue Oncology Society
NO DISCLOSURES
Overview
• Presentation of the most recent genetic and clinical findings of the NIH Pediatric and Wildtype GIST clinic.
Overview
• Presentation of the most recent genetic and clinical findings of the NIH Pediatric and Wildtype GIST clinic.
• Correlation of the genetic and epigenetic findings with the clinical phenotype
Overview
• Presentation of the most recent genetic and clinical findings of the NIH Pediatric and Wildtype GIST clinic.
• Correlation of the genetic and epigenetic findings with the clinical phenotype
• Discussion
Wild-Type GIST
• 85% of GIST occurring in young population is lacking mutations in KIT or PDGFRA
Wild-Type GIST
• 85% of GIST occurring in young population is lacking mutations in KIT or PDGFRA
• Stomach location, epithelioid histology
Wild-Type GIST
• 85% of GIST occurring in young population is lacking mutations in KIT or PDGFRA
• Stomach location, epithelioid histology• May be syndromic (Carney Triad, Stratakis-
Carney Syndrome)
Wild-Type GIST
• 85% of GIST occurring in young population is lacking mutations in KIT or PDGFRA
• Stomach location, epithelioid histology• May be syndromic (Carney Triad, Stratakis-
Carney Syndrome)• Tyrosine kinase inhibition is less effective
compared to KIT or PDGFRA mutant tumors
Wild-Type GIST
• 85% of GIST occurring in young population is lacking mutations in KIT or PDGFRA
• Stomach location, epithelioid histology• May be syndromic (Carney Triad, Stratakis-
Carney Syndrome)• Tyrosine kinase inhibition is less effective
compared to KIT or PDGFRA mutant tumors• Mutations in Succinate Dehydrogenase (SDH)
genes have been found in some but not in all patients
10 WT GIST clinics; 115 patients have been seen till An international clinic twice a year115 patients have been seen in 10 clinics since 2008.
Objectives of the Wildtype Clinic at NIH
•To bring together healthcare providers who have the most experience treating and studying GIST•To obtain clinical history, response to prior treatments, histopathologic results, radiographic assessments and genetic/molecular analyses•Continue long-term follow-up for these patients
Summary of Mutation Analysis of 78 Patients with Wild-Type GIST Fully Analyzed for SDH, BRAF, and NF1 Mutations
78 patients
NF1 (3)
BRAF (3) 78 patients
6 patients Have NF1 or BRAF mutations
SDHA (22)
SDHB (10)
SDHC (11)
SDHD (1)
44 Patients Have Mutations in SDHA, B, C, D
78 patients
None (28)
28 Patients Have No Detectable Mutation To Date
78 patients
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15U USDHA1 52 315 402 487 585 664
FAD binding CAP FAD Helical C
R31X H99Y R171C
R188W
A223fs R352X Splice site
T256I
T273I
S445L
A454E
S505fs
R512X
K598NL511P
A454T
AA 1 28 40 133 176 206 280
SDHB 1 2 3 4 5 6 7 8U U
2Fe-2S 4Fe-4S
c.17_42dupR201fs
W200Cc189F
I127SSplice site
S92TR46Q
R46X
1 2 3 4 5U USDHC
1L 2L 3L 4L 5L 3S 4S
R133X
p54TSplice Site
R15X G75DM1V
H127R
1 2 3 4U USDHD
1S 2S 3S 4S
D118fs
Mutations Distributed across all exons-90% Germline
78 patients
Wildtype GIST can have negative SDHB staining regardless of the status of mutations in SDH genes
Janeway and Kim et al. 2011 PNAS 108:314
NF1 (3) BRAF (3) SDHA (22)SDHB (10) SDHC (11) SDHD (1)
None (28)
78 patients
53 tumors had negative SDHB staining
9 had positive staining
NF1 (3) BRAF (3) SDHA (22)SDHB (10) SDHC (11) SDHD (1)
None (28)
1st CircleMutated Genes:
2nd CircleSDHB staining:
Negative (53)
Positive (9)
78 patients
BRAF (3) SDHA (22)SDHB (10) SDHC (11) SDHD (1)
None (28)
1st CircleMutated Genes:
2nd CircleSDHB staining:
Negative (53)
Positive (9)
• Tumors with SDHA, B, C, D mutations have always negative SDHB staining.
NF1 (3)
78 patients
BRAF (3) SDHA (22)SDHB (10) SDHC (11) SDHD (1)
None (28)
1st CircleMutated Genes:
2nd CircleSDHB staining:
Negative (53)
Positive (9)
• Tumors with SDHA, B, C, D mutations have always negative SDHB staining.
NF1 (3)
78 patients
BRAF (3) SDHA (22)SDHB (10) SDHC (11) SDHD (1)
None (28)
1st CircleMutated Genes:
2nd CircleSDHB staining:
Negative (53)
Positive (9)
• Tumors with SDHA, B, C, D mutations have always negative SDHB staining.
• Tumors with negative SDHB staining and no mutations have probably alterations in SDH pathway.
NF1 (3)
78 patients
BRAF (3) SDHA (22)SDHB (10) SDHC (11) SDHD (1)
None (28)
1st CircleMutated Genes:
2nd CircleSDHB staining:
Negative (53)
Positive (9)
• Tumors with SDHA, B, C, D mutations have always negative SDHB staining.
• Tumors with no mutations and negative SDHB staining have probably alterations in SDH pathway.
• Tumors with BRAF or NF1 mutations had SDHB positivity.
• Tumors with SDHB positivity and no mutations likely have alterations outside the SDH pathway.
NF1 (3)
78 patients
Infinium 450 methylation dataKillian et al. Cancer Discovery 2013
Succinate Dehydrogenase Mutations lead to a hypermethylator phenotype in Gastrointestinal Stromal Tumor
78 patients
NF1 (3)
BRAF (3)
SDHA (22)1st CircleMutated Genes:
Infinium 450 methylation dataKillian et al. Cancer Discovery 2013
Negative SDHB staining by IHC correlates with Hypermethylation in 66 tumors
78 patients
How SDHB loss is causing hypermethylation?
78 patients
Yang M, Pollard PJ Cancer Cell 2013
NF1 (3)
BRAF (3)
SDHA (22)
SDHB (10) SDHC (11) SDHD (1)
None (28)
1st CircleMutated Genes:
2nd CircleSDHB staining:
Negative (53)
Positive (9)
Deviator (66)
Centrist (12)
3rd CircleMethylation
Group A (n=12)
Positive SDHB IHCNormal Methylation pattern
Mutations in NF1, BRAF or other unknown genes
78 patients
Group A
NF1 (3)
BRAF (3)
SDHA (22)
SDHB (10) SDHC (11) SDHD (1)
None (28)
1st CircleMutated Genes:
2nd CircleSDHB staining:
Negative (53)
Positive (9)
Deviator (66)
Centrist (12)
3rd CircleMethylation
Group B (n=22)
Negative SDHB staining by IHCHypermethylation (Deviator)
Not known mutations
78 patientsGroup B
NF1 (3)
BRAF (3)
SDHA (22)
SDHB (10) SDHC (11) SDHD (1)
None (28)
1st CircleMutated Genes:
2nd CircleSDHB staining:
Negative (53)
Positive (9)
Deviator (66)
Centrist (12)
3rd CircleMethylation
Group C (n=44)
Negative SDHB staining by IHCHypermethylation (Deviator)
SDHA, B, C, D mutations
78 patients
Group C
NF1 (3)
BRAF (3)
SDHA (22)
SDHB (10) SDHC (11) SDHD (1)
None (28)
1st CircleMutated Genes:
2nd CircleSDHB staining:
Negative (53)
Positive (9)
Deviator (66)
Centrist (12)
3rd CircleMethylation
Comparison of Group B and C
1. Group B=young age
Age
60
40
20
0B C
Years
2. All patients in Group B are females while in Group C 65% are females.
We have Carney Triad patients (chondroma, paraganglioma) or Carney-Stratakis Syndrome patients (paraganglioma) in both groups B and C.
At the moment we have no statistically significant differences in overall Survival, Recurrence free Survival.
78 patientsGroup B
Group C
NF1 (3)
BRAF (3)
SDHA (22)
SDHB (10) SDHC (11) SDHD (1)
None (28)
1st CircleMutated Genes:
2nd CircleSDHB staining:
Negative (53)
Positive (9)
Deviator (66)
Centrist (12)
3rd CircleMethylation
Conclusions
Group A Group B Group C
Mutated genes NF1, BRAF or other genes
Unknown genes SDH genes
SDHB expression by ICH normal no no
SDH Function Normal Impaired Impaired
Methylation Pattern Centrist Deviator(hypermethylation)
Deviator(hypermethylation)
Gender Both Females Female predominance
Age Young adults, adults Pediatric, young adults
Young adults, adults
Location Gastric, small bowel Gastric Gastric
3 distinct groups of Wildtype GIST
Group A Group B Group C
Mutated genes NF1, BRAF or other genes
Unknown genes SDH genes
SDHB expression by ICH normal no no
SDH Function Normal Impaired Impaired
Methylation Pattern Centrist Deviator(hypermethylation)
Deviator(hypermethylation)
Gender Both Females Female predominance
Age Young adults, adults Pediatric, young adults
Young adults, adults
Location Gastric, small bowel Gastric Gastric
ConclusionsGroup B tumors have loss of SDHB staining without SDH mutations.We assume these 20 tumors have alterations in SDH pathway.
Discussion
Should we redefine Wildtype GIST as tumors having SDHB deficiency by IHC?
Should we use demethylating agents for SDHB deficient GIST?
Acknowledgements
Our patients!
Dr. Lee Helman labLauren LongYeung ChohArnaldez FernandaErin GombosChristine HeskeAmy McCalla-MartinAnna NkrumahWan Xiaolin
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15U USDHA1 52 315 402 487 585 664
FAD binding CAP FAD Helical C
R31X H99Y R171C
R188W
A223fs R352X Splice site
T256I
T273I
S445L
A454E
S505fs
R512X
K598N
A454T
SDHA
SDHB
SDHC
SDHD
FAD Binding Domain
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15U USDHA1 52 315 402 487 585 664
FAD binding CAP FAD Helical C
R31X H99Y R171C
R188W
A223Fs R352X Splice site
T256I
T273I
S445L
A454E
S505fs
R512X
K598N
A454T
SDHA
SDHB
SDHC
SDHD
K589N
L511P
H99AA454L
R188W
T256I
A454EA454T
R171C
T273I
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15U USDHA1 52 315 402 487 585 664
FAD binding CAP FAD Helical C
R31X H99Y R171C
R188W
A223fs R352X Splice site
T256I
T273I
S445LA454E
S505fs
R512X
K598N
A454T
SDHA
SDHB
SDHC
SDHD
K589N
L511P
H99AA445L
R188W
T256I
A454EA454T
R171C
T273I
FAD domain mutations
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15U USDHA1 52 315 402 487 585 664
FAD binding CAP FAD Helical C
R31X H99Y R171C
R188W
A223fs R352X Splice site
T256I
T273I
S445LA454E
S505fs
R512X
K598N
A454T
SDHA
SDHB
SDHC
SDHD
K589N
L511P
H99AA445L
R188W
T256I
A454EA454T
R171C
T273I
FAD domain mutations
Protein-truncating mutations
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15U USDHA1 52 315 402 487 585 664
FAD binding CAP FAD Helical C
R31X H99Y R171C
R188W
A223fs R352X Splice site
T256I
T273I
S445LA454E
S505fs
R512X
K598N
A454T
SDHA
SDHB
SDHC
SDHD
K589N
L511P
H99AA445L
R188W
T256I
A454EA454T
R171C
T273I
FAD domain mutations
Protein-truncating mutations
Mutations disrupting the FAD domain
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15U USDHA1 52 315 402 487 585 664
FAD binding CAP FAD Helical C
R31X H99Y R171C
R188W
c.666delT R352X Splice site
T256I
T273I
S445L
A454E
S505fs
R512X
K598N
A454T
SDHA
SDHB
SDHC
SDHD
K589N
L511P
H99AA454L
R188W
T256I
A454EA454T
R171C
T273I
Correlation of Metastasis and site of mutation
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15U USDHA1 52 315 402 487 585 664
FAD binding CAP FAD Helical C
R31X H99Y R171C
R188W
c.666delT R352X Splice site
T256I
T273I
S445L
A454E
S505fs
R512X
K598N
A454T
SDHA
SDHB
SDHC
SDHD
K589N
L511P
H99AA454L
R188W
T256I
A454EA454T
R171C
T273I
Correlation of Metastasis and site of mutation
Similar analysis on SDHB, C and D subunits is ongoing
AA
61 85 89 114 119 145 150 158
AA 1 28 40 133 176 206 280
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15U USDHA
1 2 3 4U U
SDHB
1 2 3 4 5U USDHC
1 2 3 4 5 6 7 8U U
SDHD
1 52 315 402 487 585 664
FAD binding CAP FAD Helical C
1S 2S 3S 4S
AA
33 44 63 91 95 104 110 139 144 160
1L 2L 3L 4L 5L 3S 4S
2Fe-2S 4Fe-4S
R31X H99Y
c.17_42dup
R171C
R188W
A223fs R352X Splice site
T256I
T273I
S445L
A454E
S505fs
R512X
K598NL511P
A454T
R201fsW200C
c189F
I127SSplice site
S92TR46Q
D118fs
R46X
R133X
p54TSplice Site
R15X G75DM1V
H127R
Female Gender
Age
at d
iagn
osis
Group CSDHx mutations
Hypermethylator phenotype
Group BNo mutations
Hypermethylator phenotype
Wildtype GIST Phenotype
Paragangliomas
Chondromas
Carney Triad
Female Gender
Age
at d
iagn
osis
Group CSDHx mutations
Hypermethylator phenotype
Group BNo mutations
Hypermethylator phenotype
Almost all patients in group B are younger and female in comparison with group C
Paragangliomas
Chondromas
Carney Triad
Age
60
40
20
0B C
Years
Female Gender
Age
at d
iagn
osis
Group CSDHx mutations
Hypermethylator phenotype
Group BNo mutations
Hypermethylator phenotype
We have Carney Triad patients (paraganglioma) or Carney-Stratakis Syndrome (chondroma, paraganglioma) in both groups B and C
ParagangliomasChondromasCarney Triad