1. Samuel Aparicio, B.M., B.Ch., Ph.D., and Carlos Caldas, M.D.
The Implications of Clonal Genome Evolution for Cancer Medicine N ENGL J MED 2013;368: (Feb 28, 2013)
Samuel Aparicio, B.M., B.Ch., Ph.D., and Carlos Caldas, M.D.
R3 변자민

2. INDEX Darwinian Evolution & Cancer
The Decipherment of Clonal Evolution
Implications for Clinical Oncology
Genomic stratification
Tumor monitoring
The emergence of treatment resistance
Mutational and clonal assessment in practice
Implications for Drug Development and Clinical Testing of New agents
It has long been hypothesized that screening for colorectal cancer can affect mortality from the disease in two ways:
By detecting cancers at an early and curable stage
By detecting and removing adenomas

3. DARWINIAN EVOLUTION & CANCER
Darwin’s theory of evolution: “speciation”
fundamental property of cancer
“Tumor evolution”
now a hot issue with the advent of comprehensive cancer genome sequencing technology
It has long been hypothesized that screening for colorectal cancer can affect mortality from the disease in two ways:
By detecting cancers at an early and curable stage
By detecting and removing adenomas

4. ‘Clonal structure and evolution in cancers’ by Peter Nowell in 1976
Clone: a group of cells related to each other by descent from a unitary origin
Clonal relationship among cells arise with ‘selection’ operating on phenotypes
Stable phenotype
Consequence of fixed mutation (e.g. oncogenic mutations, drug-sensitivity mutations)
Consequence of genetic drift (mutation over time) without selection
Transient or unstable phenotype
Not evident as lineage relationship in the genome

5. Figure 1. Clonal Evolution and Clonal Relationships

6. Human tumors are composed of evolving clones
Hallmarks of Cancer
Existence of clonal genotypes (i.e., not all mutations occur in the same cells)
Expansion and decline of clonal population over time
Existence of internal spatial variation in tumor composition
Partial tumor responses to therapy and the emergence of drug-resistant malignant cells
Seeding of metastatic cells from subclones
Absence of an observable clonal structure based on genome aberrations in some cancers
Existence of neutral clonal relationship without discernible phenotypic consequences

7. DECIPHERMENT of CLONAL EVOLUTION
The next-generation sequencing device now provides a measure of allele prevalence for almost any aberration found in a genome !
It has long been hypothesized that screening for colorectal cancer can affect mortality from the disease in two ways:
By detecting cancers at an early and curable stage
By detecting and removing adenomas

8. Figure 2. Next-Generation Sequencing Measurements of Allele Prevalence and Clonal Analysis

9. 3 key concepts
Clonal-mutation prevalence is a compound measure of the population abundance of the mutation in question
A clonal genotype refers to the set of common fixed mutations that define a clone
Clonal lineage defines the relationship between clones as they evolve over time

10. → Another important implication:
Figure 3. Changes in Clonal Composition over Time, Estimated on the Basis of Changes in Clonal-Mutation Prevalence
Determination of clones with genotypes that confer risk of progression or drug resistance
→ Another important implication:
spatial and temporal variation in the composition of primary cancer (e.g. breast cancers, renal cancers)
→ important consequence:

11. IMPLICATIONS for CLINICAL ONCOLOGY
I. Genomic Stratification
Genomically distinct clones → variable tx responses
Distinguish clinically relevant minor subclones
Multiple sampling of primary tumors with or without assistance from functional imaging
Stratification of targeted tx in metastatic disease
Discordance of mutations between primary and corresponding metastatic disease
Characterizing and measuring clonal heterogeneity is the key: important to rebiopsy tumors in metastatic disease
II. Tumor Monitoring
III. Emergence of Treatment Resistance
IV. Mutational & Clonal Assessment in
Practice

12. IMPLICATIONS for CLINICAL ONCOLOGY
I. Genomic Stratification
II. Tumor Monitoring
III. Emergence of Treatment Resistance
IV. Mutational & Clonal Assessment in
Practice

13. Blood sample as liquid biopsy
Bloodstream
dissemination
Blood sample as liquid biopsy
Circulating tumor DNA sequencing: assess tumor dynamics (recurrence and tumor burden monitoring)
Direct sequencing of plasma DNA: identify new mutations in circulating tumor (ctDNA) → early identification of resistance to targeted therapies
death in situ
Tumor DNA

14. post curative lobectomy
Primary tumor c chromosomal rearrangement (e.g. ROS1 translocation)
Post-mastectomy chemoTx
Figure 4-1. Concept of Plasma DNA for Monitoring Circulating Tumor DNA and Clonal Evolution

15. KRAS wild type metastaic colorectal cancer
Cetuximab treatment
3 months
BRCA1 germline mutation ovarian cancer
TP53 mutation in ctDNA
Figure 4-2. Concept of Plasma DNA for Monitoring Circulating Tumor DNA and Clonal Evolution

16. IMPLICATIONS for CLINICAL ONCOLOGY
I. Genomic Stratification
Systemic genomic sampling of tumors
a) before treatment, b) at the completion of treatment, and
c) at the time of relapse
Determining the mechanism of drug resistance
Finding combinations of drugs to suppress clonal evolution
II. Tumor Monitoring
III. Emergence of Treatment Resistance
IV. Mutational & Clonal Assessment in
Practice
Treatment of recurrent disease

17. IMPLICATIONS for CLINICAL ONCOLOGY
I. Genomic Stratification
II. Tumor Monitoring
How might clonal analysis be used in practice in the near term?
III. Emergence of Treatment Resistance
IV. Mutational & Clonal Assessment in
Practice
Provision of targeted deep-sequence coverage for analysis of clonal-mutation prevalence by clinical genomics laboratories
Example: KRAS mutations to stratify patients with colon cancer for EGFR mutations to predict benefits from erlotinib or gefitinib

18. IMPLICATIONS for DRUG DEVELOPMENT & CLINICAL TESTING of NEW AGENTS
The genetic variability of cancer and its capacity to evolve mean that most single-target approaches are not sufficient
The ability to follow which clonal genotypes are sensitive and which are resistant could be valuable in both the and late stages of drug development
The mutational landscape of cancers suggests a vast array of possible potentially targetable pathways
by prospectively developing sequenced polyclonal xenografted human tumors
by mapping clonal genotypes of therapeutic resistance and sensitivity in patients

19. Mutation sequencing is gradually becoming adopted
CONCLUSIONS
Mutation sequencing is gradually becoming adopted
→The clinical-trials community will need to retool to incorporate tissue biopsies and ongoing studies of tumor evolution as part of the correlative science of clinical trials