TP53 Mutations with Low Variant Allele Frequency Predict Short Survival in Chronic Lymphocytic Leukemia

Abstract

Purpose: In chronic lymphocytic leukemia (CLL), TP53 mutations are associated with reduced survival and resistance to standard chemoimmunotherapy (CIT). Nevertheless, the clinical impact of subclonal TP53 mutations below 10% to 15% variant allele frequency (VAF) remains unclear. Experimental Design: Using a training/validation approach, we retrospectively analyzed the clinical and biological features of TP53 mutations above (high-VAF) or below (low-VAF) the previously reported 10.0% VAF threshold, as determined by deep next-generation sequencing. Clinical impact of low-VAF TP53 mutations was also confirmed in a cohort (n = 251) of CLL treated with fludarabine-cyclophosphamide-rituximab (FCR) or FCR-like regimens from two UK trials. Results: In the training cohort, 97 of 684 patients bore 152 TP53 mutations, while in the validation cohort, 71 of 536 patients had 109 TP53 mutations. In both cohorts, patients with the TP53 mutation experienced significantly shorter overall survival (OS) than TP53 wild-type patients, regardless of the TP53 mutation VAF. By combining TP53 mutation and 17p13.1 deletion (del17p) data in the total cohort (n = 1,220), 113 cases were TP53 mutated only (73/113 with low-VAF mutations), 55 del17p/TP53 mutated (3/55 with low-VAF mutations), 20 del17p only, and 1,032 (84.6%) TP53 wild-type. A model including low-VAF cases outperformed the canonical model, which considered only high-VAF cases (c-indices 0.643 vs. 0.603, P < 0.0001), and improved the prognostic risk stratification of CLL International Prognostic Index. Clinical results were confirmed in CIT-treated cases (n = 552) from the retrospective cohort, and the UK trials cohort. Conclusions: TP53 mutations affected OS regardless of VAF. This finding can be used to update the definition of TP53 mutated CLL for clinical purposes.

Impact of Low-Burden TP53 Mutations in the Management of CLL

“…The clinical consequence of TP53 mutations was similar when patients with low VAF were stratified into subclasses <1%, between 1% and 5% or 5% and 10%. Shorter OS was also confirmed when separately considering patients with single or multiple mutations classified as high VAF or low VAF ( 15 , 20 ).…”

“…Focusing on studies designed to assess overall survival (OS) between cases harboring the wild-type TP53 gene versus cases with low-burden TP53 variant (15,18,20,35), the frequencies of TP53 mutation ranged from 10.6 to 27.5%, of which 26.8 to 45.2% cases exclusively harbored low-burden TP53 mutations depending on the threshold used to discriminate between lowand high-VAF TP53 mutations. Blakemore et al failed to demonstrate a clinical impact of low-burden TP53 mutations but identified an intermediate-risk group.…”

“…While TP53 abnormalities account for approximately 10% of naïve-treatment patients, these abnormalities are found in greater than 40% of patients with fludarabine-refractory CLL, which highlights the phenomenon of clonal evolution of TP53 mutation induced by chemotherapy (13). Despite the current recommendations that consider <10% of minor clones to be of uncertain significance, accumulating evidence based on longitudinal studies argues for the clinical relevance to report TP53 minor clones (15,18,20,(23)(24)(25). NGS sequencing of serial samples before and after treatment has allowed characterization of the dynamics of the minor clones under treatment and demonstrated their biological and clinical relevance.…”

“…First, CLL lymphocyte population purity greater than 80% reduces the possibility of dilution in nontumoral DNA that could underestimate a very low-burden mutation. Second, sufficient DNA corresponding to >6,000 diploid genomes and a third high target read depth is required to detect a very low-burden mutation with VAF<1% ( 20 ). Finally, robust bioinformatic workflows were developed to call true variants distinguished from background error noise.…”

“…In most studies focusing on the clinical impact of TP53 minor clones, an arbitrary threshold of 10–12% VAF was chosen to define patients with low- or high-burden TP53 -mutated clones. Most studies conducted in untreated patients ( 15 , 18 , 20 ) showed that low-burden TP53 mutations significantly reduced the OS compared to cases with unmutated TP53 genes. Moreover, the impact on OS was the same for patients harboring minor clones or high-burden TP53 mutations ( Table 1 ).…”