KRAS

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KRAS
Her-2/neu
ER/PR
t(1517)
JAK-2
bcr-abl
ONCOTYPE-DX
EGFR
BRAF
Ki-67 (MIB-1)
EML4-ALK
ResponseDX
FLT3
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Molecular Testing Cancer Diagnosis, Treatment,
and Risk
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Genes in the News
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• Basics in molecular testing
• Diagnostic testing
• Tests for treatment decisions
• Risk assessment
• The future of genetic / proteomic testing

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DNA
Cell
Nucleus
Chromosomes
Gene
DNA molecule (chromosome)
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Chemical Bases in DNA
Gene
Chemical bases
DNA molecule (chromosome)
A
T
C
G
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DNA Molecules
Cell
Chromosomes
Nucleus
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Gene Subunits
Gene
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DNA-gtRNA-gtProtein
Cell membrane
Nucleus
DNA
Chain of amino acids
DNA bases
mRNA
Gene
Protein
Ribosome
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Different Genes Different Functions
Pancreas Cell
Bone Cell
Brain Cell
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Gene Mutations and Disease
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Gene Mutations
Mismatch
Deletion
Repetition
Deletion
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Altered DNA-gtAltered Protein
Cell membrane
Nucleus
DNA
Chain of amino acids
DNA bases
mRNA
Gene
Protein
Ribosome
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Hereditary Mutations
Sperm
Egg
Mutation Occurs
Fertilized Egg
Mutation
Brain
Pancreas
Bone
Reproductive
Body Cells of Offspring
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Acquired Mutations
Normal Bone Cell
Mutation Occurs
Altered Gene
Altered Bone Cells
Normal Bone Cells
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Disease Inheritance Is Complex
Gene Changes in Cystic Fibrosis
Mucus Production Gene
Mutation 2
Normal
Mutation 1
Mutation 3
No Symptoms
No Symptoms
Mild Symptoms
Severe Symptoms
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Many Mutations Lead to Cancer
Normal Cell
First Mutation
Second Mutation
Third Mutation
Malignant Cells
Fourth or Later Mutation
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Most Cancer Is NOT Inherited
All Breast Cancer Patients
Known Inherited Factor
Unknown Factor(s)
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Major Limitations of Gene Testing
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Gene Tests Three Common Methods
Mutation Absent
Mutation Present
Chromosome
DNA
Protein
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Gene Testing

• Look at chromosomes
• RT-PCR
• FISH
• IHC
• Measure protein product of genetic mutation
• Proteonomics

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bcr
abl
bcr-abl
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3 MYC
5 MYC
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Diagnosis
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Earliest Attempts

• Phenylketonuria - accurate, treatable disease,
  everyone tested
• Sickle cell trait
• Tay-Sachs

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Blood Based Cancers

• Chronic Myelogenous Leukemia
• Initial Identification of Philadelphia Chromosome
• Then identification of the fusion protein from
  this mutation
• Identification that this protein had TKI activity
  that resulted in abnormal growth of the CML
  clones
• Followed by the engineering of specific molecule
  to bind the active site of the bcr/abl protein
  (Imatinib/Gleevec)
• Confirmation of activity of Imatinib and other
  similar TKIs in achieving complete remissions of
  the disease

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Blood Based Cancers

• Chronic myelogenous leukemia
• JAK-2 myeloproliferative neoplasms
• Acute myeloid leukemia with recurrent genetic
  abnormalities
• Various lymphomas

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Solid Organ Cancers

• Ewing sarcoma
• Liposarcoma
• Rhabdomyosarcoma
• Synovial sarcoma
• Kidney tumors

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Ewing Sarcoma

• Share unique pattern of chromosomal
  translocations
• T(1122)(q24q12) translocation can be detected
  using FISH analysis
• Encodes a protein involved in the control of
  cellular proliferation, development and
  tumorigenesis
• Introduction of EWS-FLI RNA antisense molecules
  or short interfering RNAs (RNAi) into EFT cells
  result in growth inhibition in vitro and in vivo

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Kidney Tumors

• Hereditary kidney cancer syndromes
• Hereditary papillary renal carcinoma
• Autosomal dominant, MET protooncogene on long arm
  chromosome 7
• Hereditary paraganglioma and pheochromocytoma
• Autosomal dominant
• Due to germline mutation in succinate
  dehydrogenase gene (SDH)
• Tuberous Sclerosis Complex
• Mutation in one of two tumor suppressor genes
  (TSC1 or TSC2)
• Von Hippel-Lindau Disease
• Inherited autosomal dominant
• VHL genes product pVHL is a tumor suppressor
  protein
• Hypoxia-inducible factor-1 (HIF-1) and role in
  erythropoeisis

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Treatment Decisions
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Treatment Decisions

• Markers to indicate whether a cancer may respond
  to treatment
• Her-2/neu (herceptin)
• ER / PR (anti-estrogen therapy)
• EGFR
• Her-1 over-expression (colon) or mutations
  (lung) may respond better to certain drugs
• KRAS
• Resistance to EGFR-directed drugs
• EML4-ALK fusion protein in NSCLC
• Crizotinib -- ALKi

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Treatment Decisions

• Markers to indicate whether a cancer may respond
  to treatment
• Do you need more aggressive treatment?
• Oncotype-DX (breast, colon)
• ResponseDX (lung, colon, gastric)
• Lymphoma
• Or even less treatment?

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Treatment Decisions

• In-vitro culture of tumor cells with exposure to
  various chemotherapy drugs

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Risk Assessment

• Oncotype-DX
• Breast - 21 gene panel
• Colon - 12 gene panel
• BRCA

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Genetic Tests Find Mutations, NOT Disease
Chances of Developing Breast Cancer by Age 65
10
100
90
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8
80
7
70
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60
5
50
4
40
3
30
2
20
1
10
0
0
Normal BRCA1
Altered BRCA1
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Risk Assessment

• Oncotype-DX
• Breast - 21 gene panel
• Colon - 12 gene panel
• BRCA
• Lymphoblastic Leukemia / Lymphoma
• t(922) - worse prognosis
• t(1221) - very favorable prognosis

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The Future of Genomic / Proteomic Testing

• The Cancer Genome Atlas Project
• Various other genome / proteomic studies
• Screening and diagnostic tests
• Treatment decisions
• Prognostic markers

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Questions