• Acquisition of tumour multidrug resistance inevitable in most advanced solid tumours– Failing to cure the majority of advanced solid tumours– Declining therapeutic benefits at higher drug cost
• Drug resistance highly complex: – 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– 150,000 biomarkers only 100 for clinical use
Predictive Biomarkers and Drug Resistance
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 2010Navin N, et al Nature 2011
Geyer and Reis-Filho J Path 2010Shah 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 ?
Ubiquitous
SharedPrimary
SharedMets
Private
65% mutations are heterogeneous and not present in every biopsy
Primary Mets
Re-construct Phylogenetic Evolution of Tumour
Normal
Evidence for Convergent EvolutionSETD2 Loss of Function: H3K36 tri-methylation
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
Seeding of metastatic sites can be tracked to one tumour region
M2a,b M1
Chest Wall Metastasis Perinephric Metastasis
NormalR9
Primary Tumour Regions Metastatic SitesPrimary Tumour Regions Metastatic Sites
Allelic Imbalance: ITH within Chest wall metastasis
Only somatic mutations with >20x coverage were included
Only somatic mutations with >20x coverage were included
M2a,b M1
Chest Wall Metastasis Perinephric Metastasis
R9
Primary Tumour Regions Metastatic Sites
Only somatic mutations with >20x coverage were included
Only somatic mutations with >20x coverage were included
Primary Tumour Regions Metastatic Sites
Heterogeneity of RCC Prognostic Signature Expression
MedianccA 103 monthsccB 24 months
Gen
es u
preg
ulat
ed in
ccA
Gen
es in
ccB
Darwin and cancer branched evolution
Relevance of ITH and Cancer Branched Evolution
Patient 1
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
