Detailed analysis of therapy-driven clonal evolution of TP53 mutations in chronic lymphocytic leukemia

Abstract

In chronic lymphocytic leukemia (CLL), the worst prognosis is associated with TP53 defects with the affected patients being potentially directed to alternative treatment. Therapy administration was shown to drive the selection of new TP53 mutations in CLL. Using ultra-deep next-generation sequencing (NGS), we performed a detailed analysis of TP53 mutations' clonal evolution. We retrospectively analyzed samples that were assessed as TP53-wild-type (wt) by FASAY from 20 patients with a new TP53 mutation detected in relapse and 40 patients remaining TP53-wt in relapse. Minor TP53-mutated subclones were disclosed in 18/20 patients experiencing later mutation selection, while only one minor-clone mutation was observed in those patients remaining TP53-wt (n=40). We documented that (i) minor TP53 mutations may be present before therapy and may occur in any relapse; (ii) the majority of TP53-mutated minor clones expand to dominant clone under the selective pressure of chemotherapy, while persistence of minor-clone mutations is rare; (iii) multiple minor-clone TP53 mutations are common and may simultaneously expand. In conclusion, patients with minor-clone TP53 mutations carry a high risk of mutation selection by therapy. Deep sequencing can shift TP53 mutation identification to a period before therapy administration, which might be of particular importance for clinical trials.

Evaluation of 230 patients with relapsed/refractory deletion 17p chronic lymphocytic leukaemia treated with ibrutinib from 3 clinical trials

“…CpG mitogen‐stimulated methods increase the sensitivity to detect karyotype abnormalities in CLL (Thompson et al , 2015), and our data provide a strong rationale for considering more routine application of this method, particularly among patients with del(17p). The extent of prior exposure to cytotoxic chemotherapy is associated with clonal evolution to genetically high‐risk disease, including del(17p) and cytogenetic complexity (Brejcha et al , 2014; Malcikova et al , 2015), further suggesting that precision therapeutics should be used earlier in the course of disease. Likewise, the likelihood that patients in this high‐risk group with R/R disease may develop resistance to a single‐agent targeted therapy provides a compelling rationale for combination treatment approaches (Woyach et al , 2014).…”

An ultra-deep sequencing strategy to detect sub-clonal TP53 mutations in presentation chronic lymphocytic leukaemia cases using multiple polymerases

“…Chronic lymphocytic leukemia (CLL) is a heterogeneous disorder, characterised by clonally expanded CD5 positive B-cells carrying a range of genetic abnormalities some of which segregate with disease severity 3,7,8 . As with many other forms of cancer, an important abnormality associated with poor overall outcome and refractoriness to DNA damaging therapy, is dysfunctional p53 [9][10][11][12][13][14][15][16] .…”

“…The reported frequency of TP53 mutations in CLL ranges from approximately 10% without treatment, rising to 50% in relapsed disease, refractory to DNA damaging therapy 12,15,16 . As recent next-generation sequencing studies suggest, the rise in frequency of clonal TP53 mutated populations following DNA damaging therapy most likely reflects an expansion of low abundance, TP53 mutated sub-clones often undetectable at presentation by conventional sequencing 2, 4, 16,20 .…”

“…As recent next-generation sequencing studies suggest, the rise in frequency of clonal TP53 mutated populations following DNA damaging therapy most likely reflects an expansion of low abundance, TP53 mutated sub-clones often undetectable at presentation by conventional sequencing 2, 4, 16,20 . The majority of TP53 mutations reported in CLL lie within the p53 DNA binding domain (exons 4 -10) 21,22 , which can alter its capacity to bind to target DNA sequences and induce transcription; such abnormalities would offer a distinct survival advantage when a cell is exposed to agents that irreversibly damage DNA 8, 15,16,23,24 .…”

“…Deep sequencing platforms have the potential to solve the issue of sensitivity, and have identified sub-clones with a mutation frequency as low as 0.3% in CLL 2-4, 15,16 .…”