Clonal Evolution, Genomic Drivers, and Effects of Therapy in Chronic Lymphocytic Leukemia

Abstract

Purpose The identification of gene mutations and structural genomic aberrations that are critically involved in CLL pathogenesis is still evolving. One may postulate that genomic driver lesions with effects on CLL cell proliferation, apoptosis thresholds or chemotherapy resistance should increase in frequency over time when measured sequentially in a large CLL cohort. Experimental Design We sequentially sampled a large well-characterized CLL cohort at a mean of 4 years between samplings and measured acquired copy number aberrations (aCNA) and LOH using SNP 6.0 array profiling and the mutational state of TP53, NOTCH1 and SF3B1 using Sanger sequencing. The paired analysis included 156 patients, of whom 114 remained untreated and 42 received intercurrent therapies, predominantly potent chemo-immunotherapy, during the sampling interval. Results We identify a strong effect of intercurrent therapies on the frequency of acquisition of aCNAs in CLL. Importantly, the spectrum of acquired genomic changes was largely similar in patients that did or did not receive intercurrent therapies; therefore, various genomic changes that become part of the dominant clones are often already present in CLL cell populations prior to therapy. Further, we provide evidence that therapy of CLL with pre-existing TP53 mutations results in outgrowth of genomically very complex clones which dominate at relapse. Conclusions Using complementary technologies directed at the detection of genomic events that are present in substantial proportions of the clinically relevant CLL disease bulk, we capture aspects of genomic evolution in CLL over time, including increases in the frequency of genomic complexity, specific recurrent aCNAs and TP53 mutations.

Clinical impact of clonal and subclonal TP53, SF3B1, BIRC3, NOTCH1, and ATM mutations in chronic lymphocytic leukemia

“…We confirmed the expansion of most TP53-mutated clones after therapy observed also in other studies. 12,20,24 However, TP53, SF3B1, and NOTCH1 mutations appeared de novo or expanded before any therapy in some patients, indicating that progressive dynamics of these clones are not only dependent on therapy selection. On the contrary, small ATM-mutated clones seem to be more stable, although the time between samples in our study was relatively short.…”

“…6, [12][13][14] Combined copy number analysis 13,[15][16][17][18][19][20] and NGS 11,12,21 have shown that CLL cases may be composed of heterogeneous tumor cell populations with subclonal mutations that may evolve over the course of the disease and influence its biological behavior. The acquisition and selection of genomic aberrations over the disease course may be critical to understanding the progression and resistance to treatment.…”

Clinical impact of small subclones harboring NOTCH1 , SF3B1 or BIRC3 mutations in chronic lymphocytic leukemia

“…[1][2][3][4] The application of ultra-deep-next generation sequencing (NGS) to track TP53 mutated subclones in CLL has provided a proof-of-concept that small tumor cell populations of very low clonal abundance can drive the overall disease course, and may represent informative and highly sensitive biomarkers of chemorefractoriness. 5 In addition to TP53, other cancer genes known to be recurrently mutated in CLL and significantly associated with poor survival include NOTCH1, SF3B1, and BIRC3.…”

Targeting the Ataxia Telangiectasia Mutated-null phenotype in chronic lymphocytic leukemia with pro-oxidants

“…Indeed, in CLL, oxidative stress is present early in the genesis of disease and is detectable at the stage of premalignant monoclonal B-lymphocytosis. 46 Thus to avoid the selection of adverse subclones with ATM-deficiency that occurs with conventional genotoxic agents, 7,8 it is preferable to target stress phenotypes common to all tumor cells and, as in this case, potential mechanisms of diversification. 47 Furthermore, elevated oxidative stress may provide a selective advantage for ATM-null CLL cells regarding their interactions with immune cells within lymphoid tissues.…”

“…6 More recent reports of the dynamic nature of clonal progression has led to the understanding that the selective pressure imparted by DNA damaging agents favors the expansion of pre-existing subclones with defective DDR and consequently successive rounds of treatment with these agents are less effective. 7,8 There is, therefore, a need for therapeutic strategies that act independently of the DDR pathway that can target ATM-null CLL cells.…”