Download Deep sequencing identifies genetic heterogeneity and recurrent

Ojha J, Ayres J, Secreto C, Tschumper R, Rabe K, Van Dyke D, Slager S, Shanafelt T, Fonseca
R, Kay NE, Braggio E. Deep sequencing identifies genetic heterogeneity and recurrent
convergent evolution in chronic lymphocytic leukemia. Blood. 2015 Jan 15;125(3):492-8.
In the paper entitled ‘Deep Sequencing Identifies Genetic Heterogeneity and Recurrent Convergent
Evolution in Chronic Lymphocytic Leukemia’, the group from the Mayo Clinic in Rochester takes
advantage of next generation sequencing to detect multiple subclones and clonal evolution in
sequential samples from patients with chronic lymphocytic leukemia.
The authors have focused on patients treated with the PCR regimen that involves treatment with
Pentostatin, Cyclophosphamide and Rituximab. They identified 12 patients for whom blood samples
were available for at least two time points 6 months apart. For all of the selected patients, the
purity of malignant cells indentified by four-colour immunophenotypic analysis ranged from 66-99%.
Following whole exome sequencing, deep targeted sequencing of 24 genes relevant to CLL and
comparative genome hybridisation the authors come to some very interesting conclusions.
First, based on the identified mutations the authors discovered two patterns of clonal architecture
through the disease course. In 33% of patients they observed linear evolution characterized by the
existence of a unique clone that acquired mutations over time, while in 67% of patients they
detected multi-branching evolution with the frequency of 2 or more subclones fluctuating over time.
Interestingly, whereas stable clonal composition was confirmed in 4 of the 5 untreated patients, for
the majority of those who were treated and experienced disease progression (4 of 7) the subclonal
dominance changed after therapy.
The most intriguing result of the study is the identification of convergent evolution that involved
genomic alterations that are putatively implicated in CLL, such as del (11q23) and mutations in
NOTCH1, SF3B1, or DDX3X. This means that that multiple subclones with similar genetic alterations
can compete over time during disease progression under the treatment and that irrespective of
which subclone(s) becomes dominant, the final outcome will be alteration of the same pathway(s).
This is documented most clearly in the case of CLL33 where both competing subclones carry
different mutations in the DDX3X and SF3B1 genes and different breakpoints in chromosome 11.
Additionally, del 17p, a TP53 mutation and a NOTCH mutation were identified in the final dominnat
subclone B.
The authors conclude that, in Darwinian terms, their findings suggest that different subclones
respond to the same enviromental pressures and therefore evolve with a similar phenotype.
Consequently, it appears that in the future, the task will be to identify the selective growth
advantages under different therapies. This will certanly aid our understanding of drug resistance
mechanisms and thus ability to design novel therapeutic combinations.