Routine sequencing in CLL has prognostic implications and provides new insight into pathogenesis and targeted treatments

Abstract

Summary Chronic lymphocytic leukaemia (CLL) is a genetically heterogeneous disease characterised by genomic alterations and gene mutations that may portend worse survival or resistance to treatments. A total of 680 blood or bone marrow samples underwent targeted sequencing of 29 genes previously identified as being mutated in CLL, which were correlated to known prognostic clinical characteristics. Overall, 400 (59%) patients were treatment‐naïve (TN) and 280 (41%) were relapsed/refractory (R/R). Most patients (70%) had ≥1 mutation, with TP53 (22%), SF3B1 (18%), NOTCH1 (13%) and ATM (13%) being the most commonly mutated genes. A higher proportion of R/R patients had mutations in SF3B1 (P = 0·01) and TP53 (P < 0·001). Patients with mutated IGHV CLL more often had mutations in KLHL6 (P = 0·001) and MYD88 (P < 0·001). Pairwise associations showed mutational co‐occurrences in the TN group including SF3B1/ATM [false discovery rate (FDR) < 0·05] and NOTCH1/POT1 (FDR < 0·01). Recurrent mutations resulting in premature truncation prior to the ubiquitination domains of NOTCH1 in its PEST domain and BIRC3 in its RING domain can produce proteins that constitutively activate CLL. Frequent missense mutations, such as K700E in SF3B1 and E571K in XPO1, have unknown function but are most likely to be activating mutations. Future directions include using these mutations to identify pathways for therapeutic targeting and rational drug design.

Altered Nuclear Export Signal Recognition as a Driver of Oncogenesis

“…Prior work suggests that XPO1 muta tions in CLL are clonal at diagnosis and likely to be present at relapse as well, suggesting an early founder mutation (23). Consistent with this notion, XPO1 E571 mutations have been tracked in plasma cellfree DNA in patients with Hodgkin lymphoma (24), where their presence correlates with tumor regression or progression, and the frequency of XPO1 muta tions in CLL does not appear to be significantly different between the treatmentnaïve or relapsed/refractory state (42).…”

Association of gene mutations with time‐to‐first treatment in 384 treatment‐naive chronic lymphocytic leukaemia patients

“…Very little is understood regarding mutations within KLHL6 in CLL with a previously reported frequency of 1·8% (Puente et al , ) and a frequency of 4·2% in our TN cohort. We and others have associated mutated KLHL6 with mutated IGHV (Puente et al , ; Hu et al , ) with a postulated mechanism through the non‐canonical activation of the nuclear factor‐κB pathway (Bertocci et al , ). In this study, mutated KLHL6 was associated with a 66·3‐month increase in mTTFT as compared to KLHL6 wildtype patients.…”

“…Furthermore, mutations in ATM, BIRC3, SF3B1 and NOTCH1 were also associated with shorter TTFT, consistent with previous reports (Table ) (Wang et al , ; Cortese et al , ; Jeromin et al , ; Nadeu et al , ). Because these mutations do not truly exist in isolation and have been shown to co‐occur with other mutations and prognostic clinical factors (Wang et al , ; Jeromin et al , ; Landau et al , ; Takahashi et al , ; Hu et al , ), the lack of significance of SPEN and CXCR4 in the univariable analysis (Table S2) is not surprising and suggests that their role in leukaemogenesis and disease progression is eclipsed by other intrinsic disease factors.…”

“…ATM protein is one of the initial identifiers of double-stranded DNA breakage and through downstream activation of TP53 and BRCA1, aids in cell cycle arrest and recruitment of other DNA damage repair proteins and apoptosis of the cell (Stankovic & Skowronska, 2014). Within CLL, mutated ATM was previously shown to correlate with decreased responses to therapy, shorter TTFT and OS independent of the initial clonality of the mutation (Landau et al, 2015;Hu et al, 2019). Similar to other DNA destabilizing mutations, such as XPO1 and POT1, the role of ATM mutations in leukaemogenesis may be attributable to inducing genomic instability, thereby allowing CLL cells to acquire "second hits" of other mutations (Poncet et al, 2008;Turner et al, 2012;Ramsay et al, 2013).…”

Prevalence, distribution and predictive value of XPO1 mutation in a real‐life chronic lymphocytic leukaemia cohort

“…Given the suggested role of XPO1 in the nuclear export of p53, we particularly focused on TP53 and XPO1 mutation co‐occurrence. By re‐analysing the data from three large CLL cohorts, we observed that concurrent TP53 and XPO1 mutations were mostly rare (4 of 1697 patients harboured XPO1 and TP53 mutations) 1,2,12 . In our cohort, the co‐occurrence of XPO1 and TP53 mutations was found in three patients (Fig 1; Figure S3).…”