Download Advances in Colorectal Cancer Biomarker Discovery

Advances in Colorectal
Cancer Biomarker
Discovery
Stan Hamilton, MD
Head, Pathology and Laboratory Medicine
Major Uses of Biomarkers
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Risk assessment
Exposure Assessment
Screening
Surveillance
Diagnosis
Prognosis
Prediction
Monitoring
Five Types of Biomarker Studies
• Exploratory (correlative) studies
using clinically annotated
biospecimens and research assays
• “Retrospective-prospective” studies
using clinically annotated
biospecimens, known clinical
outcomes, and analytically validated
assays
Modified from Dr. Richard Schilsky
Five Types of Biomarker Studies
• Prospective biomarker/drug
co-development studies
• Prospective biomarker development
studies
• Prospective biomarker validation
studies
Modified from Dr. Richard Schilsky
Current studies and trials
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Prognostic and predictive markers
Assays for markers and targets
Subpopulation, niche, enrichment trials
Rare tumors
Discovery, test, validation studies
Both level of evidence (Level I from
prospective marker-directed trials)
and weight of evidence
Integral vs. Integrated
Biomarker Studies
• Integral studies: Tests must be
performed in order for the trial to
proceed, i.e. tests are essential
to the trial (includes markerdirected trials with CLIA
compliance).
Modified from Dr. Richard Schilsky
Integral marker trials
• Diverse solid-tumor types
• Logistics for tumor tissue and
control specimens
• Biomarker assay resources
• Regulatory compliance with Clinical
Laboratory Improvement
Amendments of 1988 (CLIA-88)
• Turnaround time for risk assessment
and therapy assignment
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Integral vs. Integrated
Biomarker Studies
• Integrated studies: Studies that are
intended to identify and validate
assays or marker tests that might
be used in future trials, but the
assay results are not used to make
decisions in the current trial.
Modified from Dr. Richard Schilsky
Correlative
Biomarker Studies
• Correlative studies: Studies to
develop biomarkers/assays or
imaging tests that are performed
retrospectively, are exploratory in
nature, and do not meet the criteria
of being an integral or integrated
study
Modified from Dr. Richard Schilsky
Key Issues in Clinical
Biomarker Development
• Define intended clinical use
• Prospectively study the population
and specimens for the intended use
• Use an analytically validated
biomarker test
• Hypothesis and sample size must be
adequate to demonstrate improved
clinical outcomes when the
biomarker test is applied.
From Dr. Richard Schilsky
Clinical Trial Study Designs
• If we are confident that the therapy will not
work in marker-negative patients
AND
• We have a validated assay that can reliably
assess the status of the marker
THEN
• We might design and conduct clinical trials
only in marker-positive patients
Modified from Dr. Richard Schilsky
Prospective Marker
Validation Studies
The most informative design
Marker+
Marker−
Randomization
Randomization
Targeted
Therapy
Standard
Therapy
Targeted
Therapy
Standard
Therapy
E5202 trial schema
High-Risk Patients
18q LOH
are
Stratify:
RANDOMIZED
Disease stage
IIA or IIB
Microsatellite instability
(stable/low vs high)
18q LOH
Low-Risk Patients
MSS/MSI-L with
retention of 18q alleles
or MSI-H are OBSERVED
MSI-L = low-level microsatellite instability
MSI-H = high-level microsatellite instability
*Bevacizumab continued for an additional 6 months
Arm A:
mFOLFOX6
q2w × 12
Arm B:
mFOLFOX6 +
bevacizumab*
q2w × 12
Arm C:
Observation only
TAILORx
NODE NEGATIVE BREAST CANCER STUDY
ER/PR + tumors
ONCOTYPE DX ASSAY
Score < 11
29% of pts
Score 11-25
44% of pts
Score >25
27% of pts
R
Endocrine
Therapy
Endocrine
+
Chemotherapy
Chemotherapy +
Endocrine Therapy
Accrual goal= 4800 randomized patients, 11000 screened
Non inferiority = decrease in 5 year DFS from 90 to 87% or less
(Slide courtesy of Dr. Richard Schilsky)
Obstacles to
Biomarker Research
• Adequacy of biospecimen
acquisition, processing and storage
• Access to CLIA-certified labs
• Funding for biomarker studies
• Regulatory requirements
• Contractual agreements with
commercial partners
Modified from Dr. Richard Schilsky
Advantages of Centralized Core Labs
• Standardization for trials
– Sample collection, processing, and
assays
• Expertise of trained personnel
• Availability of state-of-the-art
technologies
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Advantages of Centralized Core Labs
• Assay development, validation,
consultation, and interpretation
• Quality and reliability
• Cost-effectiveness
• Uniform access to non-renewable
specimens for investigators
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Integral Biomarker Specimen Flow – E5202
Fax results – avg 4 working days
5 working days
Surgery
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m
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Site registers
patient, ships
2 blocks
(1 tumor,
1 normal)
PCO-RL*
Laboratory
QC and
Processing
ECOG
Rando
MDACC* tests
for 18qLOH,
MSI
Fax results – avg 4 working days
Site registers
patient to
Treatment
*CAP-certified lab for CLIA-88 compliance
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Advantages of Decentralized Labs
• “Real-world”
• Access
• Convenience
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Biomarkers in CRC:
Recent Advances
• Complexity of microRNA alterations
in the adenoma-adenocarcinoma
sequence
• Gene expression profiling for
prognosis in Stage II colon cancer
• Markers for EGFR antibody therapy
• Heterogeneity
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• miRNA
– Cell differentiation
– Cell cycle
progression
– Apoptosis
– Regulation of
gene expression
• Over 100 miRNAs
implicated in
colorectal cancer
He L. et al. (2004) Nat Rev Genet: 522–531
Mucosa-Adenoma-Adenocarcinoma Sequence
NNM
ALG
AHG
CA
p < 0.001
Red: p< 0.01
Grey: p< 0.05
Black: p> 0.05
Significant Pairwise Comparisons for 230 miRS
hsa-miR-224
hsa-miR-877*
hsa-miR-1
hsa-miR-632
hsa-miR-130a
NM: Non-neoplastic mucosa
ALG: Adenoma with lowgrade dysplasia
AHG: Adenoma with highgrade dysplasia
CA: Adenocarcinoma
Example of Group 1A:
Early Persistent
Example of Group 2B:
Late
Conclusions
• Large number of miRNAs deregulated in
progression from non-neoplastic mucosa
to adenoma to adenocarcinoma
• Complex patterns of dysregulation
dependent on the phase in progression
• Dysregulation often an early event
• Use of miRNAs as biomarkers or as
therapeutic targets or agents dependent
upon the timing of altered expression.
Biomarkers in CRC:
Recent Advances
• Complexity of microRNA alterations
in the adenoma-adenocarcinoma
sequence
• Gene expression profiling for
prognosis in Stage II colon cancer
• Markers for EGFR antibody therapy
• Heterogeneity
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The 12-Gene Oncotype DX® Colon Cancer Recurrence
Score®
7 CANCER RELATED GENES
Cell Cycle
Stromal
Ki-67
C-MYC
MYBL2
FAP
BGN
INHBA
GADD45B
5 REFERENCE GENES
ATP5E
PGK1
GPX1
UBB
VDAC2
QUASAR Results: Colon Cancer Recurrence
Score® Predicts Recurrence Following Surgery
Prospectively-Defined Primary Analysis in Stage II Colon Cancer (n=711)
Risk of Recurrence at 3 years
35%
30%
25%
20%
15%
10%
p=0.004
5%
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0%
0
10
20
30
40
50
60
70
Recurrence Score
Kerr et al., ASCO 2009, #4000
QUASAR Results: Recurrence Risk in
Pre-specified Recurrence Risk Groups
1.0
Low
Intermediate
High
Range
of RS
Proportion of
patients
<30
43.7%
30-40
30.7%
≥41
25.6%
Comparison of High vs. Low
Recurrence Risk Groups using Cox
Model: HR = 1.47 (p=0.046)
0.8
Proportion Event Free
Recurrence
Risk Group
0.6
0.4
Recurrence Risk Group
0.2
Low
12%
( 9% -16%)
Intermediate
18%
22%
(13%-24%)
High
0.0
0
n=711
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Kaplan-Meier Estimates (95% CI)
of Recurrence Risk at 3 years
2
(16%-29%)
3
4
5
Years
Kerr et al., ASCO 2009, #4000
Biomarkers in CRC:
Recent Advances
• Complexity of microRNA alterations
in the adenoma-adenocarcinoma
sequence
• Gene expression profiling for
prognosis in Stage II colon cancer
• Markers for EGFR antibody therapy
• Heterogeneity
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JNCI 101:1310, 2009
PLoS One 4: e7287, 2009
PLoS ONE 4: e7287, 2009
Biomarkers in CRC:
Recent Advances
• Complexity of microRNA alterations
in the adenoma-adenocarcinoma
sequence
• Gene expression profiling for
prognosis in Stage II colon cancer
• Markers for EGFR antibody therapy
• Heterogeneity
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PROJECT T9
Delivering on the promise of
personalized molecular medicine
PROJECT T9 Two-stage analysis
Sequenom screen
Dynamic
Orthologous confirmation
Sanger Sequencing
Any activating mutations in >5% in any major tumor lineage
PI3K/AKT
MEK
Pathway
Pathway
Receptors
Downstream
Effectors
EGFR
CDK4
AKT1, 2, 3
BRAF
FGFR1,2,3
CTNNB1
PIK3CA
HRAS
KIT
FBXW7
PHLPP2
KRAS
VEGF
JAK2
FRAP (mTOR)
MEK1,2
PDGFRA
RET
RICTOR
NRAS
GNAQ
FLT3
PDPK1
RAF1
ERa
IDH1,2
PIK3R1
PRKAG1/2
MET
Dear1
MC1R
ALK
TNK2(ACK1)
ABCB1
Heterogeneity of Biomarkers
• Intra-tumoral
• Primary cf. synchronous metastasis
• Multiple metastases
• Primary cf. metachronous recurrence
• Recurrence cf. recurrence after
chemotherapy
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Heterogeneity of Biomarkers
• Co-mutation heterogeneity:
The rule, not the exception
• Discordance varies with genes
• Primary cf. synchronous liver
metastasis
– KRAS: 30%, most acquired
– NRAS: 100%, 75% acquired and
25% lost
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Opportunities for future progress
• Ability to complete the various types of
biomarker studies including validation
trials to contribute to personalized
cancer care
• Large numbers of patients required
Opportunities for future progress
• Funding
- Patient accrual (cf. industry trials)
- Effort of faculty for salary support
- Marker studies
Sources
Phasing with protocol development
Opportunities for future progress
• Complexity and duration of protocol
review process
• Regulatory issues
• Informatics
• Markers to be valued and addressed like
drugs
• “A bad marker is as harmful as a bad
drug.”