Predictive Biomarkers and Drug Resistance

• 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