1. Genomic Approaches to High Grade Gliomas
I SEVE BALLESTEROS FOUNDATION
TRANSLATIONAL NEURONCOLOGY SUMMIT
Will Parsons, M.D., Ph.D.
Madrid, Spain
29 October 2010

2. Overview Background and overview of GBM and genome studies
Lessons learned from completed analysis of GBM
The role of IDH genes in malignant gliomas

3. Overview Background and overview of GBM and genome studies
Lessons learned from completed analysis of GBM
The role of IDH genes in malignant gliomas

4. Objective
To translate our developing understanding of the genetics and genomics of gliomas into improved patient care
Tumor Biology
Clinical Application
Diagnosis &
Classification
Prognosis
Therapeutics

5. Glioblastoma multiforme (GBM, malignant glioma, grade IV astrocytoma)
Most common and lethal primary brain tumor
Occurs in both adults and children
Categorized into two groups (does not currently impact treatment)
Primary (>90%)
Secondary (<10%): have evidence of pre-existing lower-grade glioma
Gleevec (imatinib) ( i-MAT-in-ib)
Herceptin (trastuzumab - tras too' zoo mab),
Irressa (gefitinib) ge-FI-tye-nib), Tarceva (erlotinib)
Imatinib had shown unparalleled results in patients with advanced chronic myelogenous leukemia (remission rates approaching 98%), and the first GIST patients treated with imatinib demonstrated dramatic response rates unseen with other therapeutic modalities. Thousands of patients worldwide with advanced GIST have been treated with imatinib, with the demonstration of significant response rates, prolongation of survival, and improvement in quality of life.
Trastuzumab has had an enormous impact on the clinical management of breast cancer: the survival of Her-2-positive metastatic breast cancer patients has improved significantly and tumor Her-2 status has been built into the decision-making tree for primary breast cancer patients.
gefitinib

7. Example: colorectal cancer
Cancer is a genetic disease
Example: colorectal cancer

8. Somatic (tumor-specific) mutations drive cancers
Normal *

9. Examples of genotype-directed cancer therapies
Gleevec (imatinib)
Chronic myelogenous leukemia (BCR-ABL)
Gastrointestinal Stromal Tumors (c-KIT)
Herceptin (trastuzumab)
Breast Cancer (HER-2)
Iressa (gefitinib) and Tarceva (erlotinib)
NSCLC (EGFR)
Gleevec (imatinib) ( i-MAT-in-ib)
Herceptin (trastuzumab - tras too' zoo mab),
Irressa (gefitinib) ge-FI-tye-nib), Tarceva (erlotinib)
Imatinib had shown unparalleled results in patients with advanced chronic myelogenous leukemia (remission rates approaching 98%), and the first GIST patients treated with imatinib demonstrated dramatic response rates unseen with other therapeutic modalities. Thousands of patients worldwide with advanced GIST have been treated with imatinib, with the demonstration of significant response rates, prolongation of survival, and improvement in quality of life.
Trastuzumab has had an enormous impact on the clinical management of breast cancer: the survival of Her-2-positive metastatic breast cancer patients has improved significantly and tumor Her-2 status has been built into the decision-making tree for primary breast cancer patients.
gefitinib

10. What we know
about cancer
genetics

11. From gene to genome pre-2003 1 gene 2003 100 genes 2005 250 genes 2006
2007
18,000 genes
2008
20,000 genes

12. Bioinformatic analysis of Identification of candidate
Integrated genomic analysis
Copy number
Mutation
Expression
Hybridization to high density
oligonucleotide arrays
Serial analysis of gene
expression using next
generation sequencing
Bioinformatic analysis of
altered genes
Identification of candidate
cancer genes
Identification of
mutated pathways

13. Overview Background and overview of GBM and genome studies
Lessons learned from completed analysis of GBM
The role of IDH genes in malignant gliomas

14. So what have we learned from our genomic analysis of GBM?

15. GBMs contain a complex variety of genetic alterations

16. Alterations per GBM sample

17. Frequently-altered GBM genes

18. Less frequently-altered GBM genes

19. Landscape of solid tumors

20. A small number of core pathways are altered in a high fraction of GBMs

21. Core genetic pathways in GBMs

22. Individualized cancer pathways

23. Important cancer genes remain to be discovered

24. Frequently-altered GBM genes

25. Overview Background and overview of GBM and genome studies
Lessons learned from completed analysis of GBM
The role of IDH genes in malignant gliomas

26. IDH1 mutations are found in ~10% of GBMs

27. IDH1 mutations

28. Isocitrate + NAD(P)+ ----------> a-ketoglutarate + CO2 + NAD(P)H
Isocitrate dehydrogenases (IDHs)
Isocitrate + NAD(P) > a-ketoglutarate + CO2 + NAD(P)H
NAD(+)
Form homodimer
Regeneration of NADPH
for biosynthetic processes
-Defense against oxidative
damage?
NADP(+)
Form heterotetramer a2bg
Catalyze rate-limiting
step of TCA cycle
IDH3A
Chr 15
IDH3G
Chr X
IDH3B
Chr 20
IDH1
Chr 2
IDH2
Chr 15
Mitochondria
Cytoplasm/peroxisomes

29. IDH1-mutated GBMs have distinctive clinical and genetic characteristics

30. IDH1 mutation and patient age

31. IDH1 mutation and patient survival

32. IDH1-mutated GBMs

33. IDH1 mutations define a specific molecular subgroup of GBMs (secondary GBMs)

35. IDH1 mutations in gliomas target a single amino acid (R132)

36. IDH1 structure
NADP
Isocitrate
Arg 132

37. Equivalent IDH2 mutations are found in some gliomas without IDH1 mutations

39. IDH1/IDH2 mutations are also found in lower grade astrocytomas and oligodendrogliomas

41. Our improving knowledge of cancer genetics needs to be translated into clinical advances for our patients

42. Molecular classification of gliomas
WHO classification, astrocytic tumors
Pilocytic astrocytoma (grade I)
Diffuse astrocytoma (grade II)
Anaplastic astrocytoma (grade III)
Glioblastoma multiforme (grade IV)
Molecular classification
Astrocytoma with recurrent genetic lesions
BRAF gene fusion
IDH1/2 mutation
EGFR mutation/amplification
Other genetic alterations
Astrocytoma, therapy related

43. Targeted inhibition of mutant IDH1/IDH2 may be a therapeutically-useful strategy

44. IDH1/IDH2 mutations were found to abolish the enzymatic activities of the proteins

45. Enzymatic activity of wild-type and mutant IDH1 and IDH2
Cell lysates were extracted from
HOG cells transfected with vectors
encoding the indicated proteins.
Expression of wild-type and
mutant IDH1 and IDH2 was determined
by Western blotting using an anti-flag
antibody.
The activity levels of these proteins
were analyzed by monitoring the
production of NADPH.
Figure 2. Enzymatic Activity of Wild-Type and Mutant IDH1 and IDH2 Proteins. Cell lysates were extracted from a human oligodendroglioma cell line without IDH1 or IDH2 mutations that had been transfected with vectors encoding the indicated proteins. Panel A shows the expression of proteins encoded by wild-type and mutant IDH1 and IDH2, as determined by Western blotting, with the use of an anti-FLAG antibody. Panel B shows the activity levels of these proteins, as analyzed by monitoring the production of NADPH. GAPDH denotes glyceraldehyde 3-phosphate dehydrogenase.
Yan H et al. N Engl J Med 2009;360:

46. IDH1/IDH2 mutations were found to impart a new function on the enzymes

48. Conclusions
Integration of genome-wide analyses is important to obtain global picture of genetic alterations
Cancers display high degree of complexity and heterogeneity
Small number of core pathways are altered in high fraction of human cancers
Mutated genes and pathways provide potential targets for therapeutic and diagnostic intervention

49. Conclusions
Tumor heterogeneity emphasizes the critical importance of continued investment in tumor banking, creation of model systems
Characterization of altered GBM genes
“Mountains” and “hills”
“Drivers” and “passengers”
Functional studies

50. Conclusions
IDH1 and IDH2 mutations are frequent early events in several types of malignant gliomas
IDH-mutated gliomas have characteristic clinical and genetic findings
Identifies IDH1/IDH2 as a previously unsuspected and potentially-useful target for diagnostics and therapeutics
Further functional studies required to clarify role of IDH1/IDH2 mutation in tumorigenesis

51. Conclusions
The identification of characteristic molecular alterations such as IDH1 and IDH2 mutations in gliomas can facilitate molecular classification
To allow prognostication and aid decision-making regarding use of currently-available therapies
To allow rational application of targeted therapies to specific biological groups
Additional analyses of specific subgroups of gliomas (example: pediatric GBM) will be necessary to improve our understanding of these tumors

52. Acknowledgements