Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia

Abstract

Key Points• Small TP53 mutated subclones have the same unfavorable prognostic impact as clonal TP53 defects in chronic lymphocytic leukemia.TP53 mutations are strong predictors of poor survival and refractoriness in chronic lymphocytic leukemia (CLL) and have direct implications for disease management. Clinical information on TP53 mutations is limited to lesions represented in >20% leukemic cells. Here, we tested the clinical impact and prediction of chemorefractoriness of very small TP53 mutated subclones. The TP53 gene underwent ultra-deep-next generation sequencing (NGS) in 309 newly diagnosed CLL. A robust bioinformatic algorithm was established for the highly sensitive detection of few TP53 mutated cells (down to 3 out of ∼1000 wild-type cells). Minor subclones were validated by independent approaches. Ultra-deep-NGS identified small TP53 mutated subclones in 28/309 (9%) untreated CLL that, due to their very low abundance (median allele frequency: 2.1%), were missed by Sanger sequencing. Patients harboring small TP53 mutated subclones showed the same clinical phenotype and poor survival (hazard ratio 5 2.01; P 5 .0250) as those of patients carrying clonal TP53 lesions. By longitudinal analysis, small TP53 mutated subclones identified before treatment became the predominant population at the time of CLL relapse and anticipated the development of chemorefractoriness. This study provides a proof-of-principle that very minor leukemia subclones detected at diagnosis are an important driver of the subsequent disease

The long‐term outcome of patients in the LRF CLL4 trial: the effect of salvage treatment and biological markers in those surviving 10 years

“…TP53 ‐mutated sub‐clones not detected initially by conventional methods) can become predominant after relapse (Rossi et al , 2014; Sutton & Rosenquist, 2015). Further longitudinal genomic studies are required to determine whether therapies such as FC, which induce a powerful DNA damage response, select for small drug resistant clones that impair response to subsequent chemo or chemo‐immunotherapy (Rosenwald et al , 2004; Landau et al , 2013; Rossi 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 .…”