Transcript Drug resistance highly complex

Predictive Biomarkers and Drug Resistance
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Acquisition of tumour multidrug resistance inevitable in most advanced solid tumours
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Drug resistance highly complex:
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Failing to cure the majority of advanced solid tumours
Declining therapeutic benefits at higher drug cost
Approx 10% of kinases alter resistance to one or more drugs (Swanton et al 2007 Cancer Cell ; Swanton et al 2007 Cell Cycle)
Failure of Biomarker Validation
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150,000 biomarkers only 100 for clinical use
Intratumour Heterogeneity
• Evidence of intratumour heterogeneity
• Possible Implications for biomarker studies
• Practical approaches to address heterogeneity
Breast Cancer Intra-tumour Heterogeneity
Sector Ploidy Profiling and DNA Copy Number Analysis
• Multiple intermixed cell subpopulations within one tumour
differ by large genomic events/focal amplifications/ deletions
Navin N, et al. Genome Res 2010
Navin N, et al Nature 2011
Geyer and Reis-Filho J Path 2010
Shah and Aparicio Nature 2012
Does a Single Tumour Biopsy:
 Represent the tumour somatic/transcriptomic landscape ?
 Provide robust biomarkers of outcome ?
 Demonstrate that all mutations are ubiquitously present in every region of a tumour
 Predicted by a linear/clonal sweep model of tumour evolution
 Provide reliable data following Deep Sequencing Analysis to stratify patients for trials ?
Primary Mets
Ubiquitous
Shared
Primary
Shared
Mets
Private
65% mutations are heterogeneous and not present in every biopsy
Re-construct Phylogenetic Evolution of Tumour
Evidence for Convergent Evolution
SETD2 Loss of Function: H3K36 tri-methylation
Normal
3 distinct SETD2 mutations associated with loss of function: Mutational capacity?
Evidence intratumour heterogeneity may impact upon
drug response?
 6 weeks of Everolimus therapy
 Assess status of mTOR pathway across different regions of the tumour
 Evidence of Differential Pathway Activity post-Everolimus exposure?
mTOR active in all primary regions except R4 and metastases
Heterogeneous Kinase Domain mTOR mutation L2431P
mTOR mutation L2431P
Kinase Domain mTOR mutation L2431P Associated with
Constitutive Activation of the mTOR Kinase
Kinase Domain mTOR mutation L2431P Lies in A Repressor
Domain Close to Activation Loop of Kinase
Tracking Tumour Growth
R9
Normal
Chest Wall Metastasis
M2a,b
Seeding of metastatic sites can be tracked to one tumour region
Perinephric Metastasis
M1
Primary
TumourRegions
Regions
Primary Tumour
Metastatic
Sites
Metastatic Sites
Allelic Imbalance: ITH within Chest wall metastasis
R9
Chest Wall Metastasis
M2a,b
Perinephric Metastasis
M1
Onlysomatic
somatic mutations
with
>20x>20x
coverage
Only
mutations
with
coverage
wereincluded
included
were
Primary
TumourRegions
Regions
Primary Tumour
Metastatic
Sites
Metastatic Sites
Genes upregulated in ccA
Genes in ccB
Heterogeneity of RCC Prognostic Signature Expression
Median
ccA 103 months
ccB 24 months
Onlysomatic
somatic mutations
with
>20x>20x
coverage
Only
mutations
with
coverage
wereincluded
included
were
Darwin and cancer branched evolution
Relevance of ITH and Cancer Branched Evolution
Tumour Diversity Supports Evolutionary Fitness
(Maley et al 2006)
Tumour Adaptation and Selection for
• Drug resistance (Su et al 2012; Lee et al 2011)
• Metastatic growth (Yachida and Campbell 2010, Shah 2009)
Tumour Sampling Bias
• Different tumour biopsies different results
• Sites of disease evolve independently
Clonal Dominance and Actionable Mutations?
• Mutations present at one site but not another
Patient 1