Genetic Biomarkers

In addition to these extra clinical and laboratory parameters, an increasing number of biomarkers are being recognised as having prognostic significance in chronic lymphocytic leukaemia (CLL). Together these factors allow for the classification of patients as having low, intermediate or high risk of disease progression (Oscier et al., 2012).

Chromosomal deletions del 11q, del 17p and TP53 gene mutations are associated with poorer outcomes in terms of treatment-free and overall survival compared to patients with a normal karyotype, del 13q or trisomy 12 (Efremov & Laurenti, 2014; Stilgenbauer et al., 2014).

More recent next generation sequencing has enabled the identification of a number of further genetic mutations in CLL, including notably NOTCH1, MYD88, ATM, SF3B1, and BIRC3, some of which encode proteins that are involved in DNA damage signalling and repair. Many, but not necessarily all, acquired genetic abnormalities may have an important role in CLL pathogenesis and may confer different levels of prognosis. A four-category model has been proposed (Table 7) and these genetic risk factors are discussed below, although the impact of some of these genetic lesions (e.g. BIRC3) have not yet been confirmed in clinical trials (Hallek, 2015; Puiggros et al., 2014; Rossi et al., 2013; Landau et al., 2015).

Although UK guidelines recommend screening for TP53 abnormality prior to initial and subsequent treatment, the presence of high-risk markers is not currently used as an indication for initiating treatment (Oscier et al., 2012). However, the presence of specific markers may aid treatment decision making patient counselling follow-up planning (Stilgenbauer et al., 2015).

Table 7. Prognostic subgroups and associated risk genetic factors in CLL at diagnosis (adapted from Rossi et al., 2013 and Puiggros et al., 2014)
Category Associated genetic factors Therapeutic strategies 10-year survival

Very high risk

del 17p/TP53 mutation
 

p53-independent drugs such
as BCR signalling or BCL2 inhibitors

Allogeneic stem cell transplantation

29%

High risk

del 11q/ATM mutation
and/or
NOTCH1 mutation and /or
SF3B1 mutation

FCR

37%

Intermediate risk

Trisomy 12
Normal karyotype and FISH

Not recommended

57%

Low risk

Isolated del 13q

Not recommended

69%

FCR: fludarabine, cyclophosphamide, and rituximab; FISH, fluorescent in situ hybridisation.

TP53 Aberrations

Loss of the tumour suppressor gene TP53 confers very poor prognosis (i.e. ultra/very high risk CLL). (Landau et al., 2015; Puente et al., 2015). It is seen in up to 10% of patients at diagnosis (including 3-5% with early-stage CLL) and in 30% of patients with fludarabine-refractory disease (Hallek, 2017; Oscier et al., 2012; Rossi et al., 2009; Stilgenbauer et al., 2015).

In addition, ca. 5% of patients at diagnosis and 12% with refractory disease have a TP53 mutation without loss of the other allele which would not be detected by fluorescence in situ hybridisation (FISH) (Oscier et al., 2012). Most TP53 aberrations (>80%) will include the deletion 17p. Mutations in TP53 without del 17p are less common but also confer short survival and chemorefractoriness (Efremov & Laurenti, 2014; Hallek, 2015; Landau et al., 2015; Puente et al., 2015; Rossi et al., 2009; Stilgenbauer et al., 2014).

Studies have shown that patients with TP53 loss and/or mutation have a significantly lower response rates, and shorter PFS and OS, when treated with an alkylating agent, purine analogue, bendamustine, chlorambucil, mitoxantrone and rituximab, alone or in combination (Oscier et al., 2012; Sun & Weistner 2015). In the Phase III studies CLL8 (FC vs. FCR) and CLL4 (fludarabine, chlorambucil or FC), TP53 mutations and del 17p were shown to significantly affect OS and PFS (Oscier et al., 2012; Stilgenbauer et al., 2014). Other studies also support these findings (Stilgenbauer et al., 2015). However, TP53 (or del 17p) status has much less effect on the response of patients treated with drugs which kill CLL cells through a TP53-independent mechanism such as alemtuzumab, ibrutinib, idelalisib or venetoclax (Oscier et al., 2012; Sun & Weistner 2015, Roberts et al., NEJM 2016).

Del 17p

Approximately 5-8% of patients with chemotherapy-naïve CLL and up to 30% chemorefractory patients are found to have deletions in the short arm of chromosome 17 (del 17p) (Hallek, 2017; Puiggros et al., 2014). These deletions usually include the region 17p13 where the tumour suppressor gene TP53 is. Patients with del 17p have increased resistance to chemotherapy, which cannot be overcome by addition of anti-CD20 antibody therapy and therefore del 17p confers poor prognosis/high risk CLL (Hallek, 2017). However, as seen with TP53 aberrations, small molecule B cell receptor (BCR) signalling inhibitors idelalisib and ibrutinib and venetoclax, and the monoclonal antibody alemtuzumab, which operate in a TP53-independent manner, are effective treatment options in high risk patients irrespective of del 17p status (Sun & Weistner 2015).

Del 11q and ATM Mutations

Approximately 25% of patients with chemotherapy-naïve advanced stage CLL and 10% of patients with early stage disease have a deletion in the long arm of chromosome 11 (del 11q). Deletions in 11q vary greatly in size and often overlap with the region containing the ATM gene which encodes the DNA damage response kinase ATM, as well as other genes including BIRC3 (Hallek 2017; Puiggros et al., 2014). Del 11q confers poor prognosis; patients typically have bulky lymphadenopathy, rapid progression and reduced OS (Hallek 2017; Puiggros et al., 2014).

It is not clear, but the addition of immunotherapy such as anti-CD20 antibody to chemotherapy may overcome the adverse prognostic significance for patients with del 11q, as seen with data from the CLL8 trial comparing FC to FCR (Efremov & Laurenti, 2014; Oscier et al., 2012; Puiggros et al., 2014). In this trial, chemoimmunotherapy with FCR improved outcomes including ORR, CR, PFS and OS in patients with del 11q compared to FC (Hallek et al., 2010, Stilgenbauer et al., 2014).

BIRC3 Mutations

In a study of the prevalence of BIRC3 mutations at different clinical stages of CLL, BIRC3 genetic mutations were rarely seen at diagnosis (in 4% of patients) but were more prevalent in fludarabine-refractory CLL without TP53 abnormalities (in 24%). Results from this study suggest that BIRC3 mutations are associated with chemorefractory CLL and poorer outcomes similar to those seen in patients with TP53 abnormalities, although this has not currently been confirmed in clinical trials. However, from analyses of the Phase III CLL4 and CLL8 trials, the prognostic impact of BIRC3 mutations was unclear and less pronounced than for TP53 mutations/del 17p (Oscier et al., 2012, Landau et al., 2015; Stilgenbauer et al., 2015).

Del 13q

Over 50% of CLL patients have the deletion 13q14 (del 13q14) which, when occurring a sole abnormality, is associated with low risk CLL. However, there is large heterogeneity in the prognosis of patients with del 13q and large deletions in this region lead to shorter time to first treatment (TTFT) and OS than smaller deletions in 13q. It is hypothesised that a number of genes in this region may be involved in tumour suppressor activity (Puiggros et al., 2014).

Trisomy 12

An extra copy of chromosome 12 (trisomy 12) is found in up to 20% of CLL patients at diagnosis and is the third most common genetic aberration in CLL. Trisomy 12 is associated with intermediate risk prognosis (Efremov & Laurenti, 2014). However, little is known about the genes that are involved in CLL pathogenesis for patients with trisomy 12 (Hallek 2017). It is hypothesised that direct gene-dosage up regulation as a result of trisomy 12 may lead to an increase in proliferative activity of CLL cells (Puiggros et al., 2014).

NOTCH1 Mutations

The NOTCH1 gene is strongly associated with trisomy 12. High NOTCH1 mutation rates are seen in trisomy 12 CLL patients and especially in those having a poor outcome (patients with unmutated IGHV status and ZAP-70+) (Rossi et al., 2013). NOTCH1 mutations occur in approximately 10% of de novo CLL and 15-20% of relapsed, refractory or progressive CLL, and are associated with high-risk CLL with shorter survival and increased risk of transformation (Sun & Weistner 2015; Zhang & Kipps 1981). Patients with NOTCH1 mutations treated with fludarabine-based regimens or chlorambucil have more rapid disease progression and decreased OS compared to patients with wild-type phenotype. Furthermore, rituximab added to FC does not offer any benefit over FC alone and indeed showed reduced benefit by the addition of rituximab to FC in patients with NOTCH1 mutations in the CLL8 trial (Stilgenbauer et al., Blood 2014). In the Phase III UK Leukaemia Research Fund (LRF) CLL4 trial, comparing chlorambucil, fludarabine or fludarabine and cyclophosphamide (FC) in treatment naïve patients, the impact of NOTCH1 and SF3B1 genetic mutations on outcomes was determined. 10% of patients had NOTCH1 mutations which correlated with unmutated IGHV status, trisomy 12, high expression of CD38/ZAP70 and conferred significantly poorer prognosis in terms of overall- (median 54.8 vs. 74.6 months) and progression-free survival (median 22.0 vs. 26.4 months) (Oscier et al., 2013).

SF3B1 Mutations

SF3B1 encodes a splicing factor sub-unit (SF3B1), which is involved in pre-mRNA processing for genes controlling cell cycle progression and apoptosis. Around 10% of newly diagnosed CLL and 17% of progressive late-stage CLL have mutations in SF3B1 which may promote cell proliferation and/or survival and is associated with a more rapid disease progression (Sun & Weistner 2015; Zhang & Kipps 1981). In the Phase III UK Leukaemia Research Fund CLL4 trial, 17% of treatment-naïve patients had SF3B1 mutations which were significantly associated with high expression of CD38 and reduced overall survival (median 54.3 vs. 79.0 months) (Oscier et al., 2013). However, the prognostic role of SF3B1 mutations is not clear and the effect of such mutations was less pronounced than for TP53 mutations/del 17p in the Phase III CLL4 and CLL8 trials (Stilgenbauer et al., 2014).

MYD88 Mutation

MYD88 encodes an adaptor protein involved in interleukin-1/toll-like receptor signalling and tends to be associated with mutated IGHV CLL and more favourable outcomes (Sun & Weistner 2015).

IGHV Mutational Status

Patients with CLL can be divided into two groups based on the mutational status of the CLL B-cell immunoglobulin heavy chain variable region (IGHV) genes, namely unmutated or mutated. Approximately 50% of CLL patients will have unmutated IGHV status (U-CLL), which confers worse prognosis than for patients with mutated IGHV status (M-CLL) (OS 9 years vs. 24 years, respectively). Furthermore, patients with U-CLL are more likely to have advanced stage disease at diagnosis, progress more rapidly, require earlier and more frequent treatment, are more likely to have disease transformation and are more likely to have infections/infection-related mortality.

Unfavourable genetic aberrations such as del 17p and del 11q occur more frequently in U-CLL whereas del 13q (associated with low-risk prognosis) occurs more often in M-CLL (Stilgenbauer et al., 2014; Sun & Weistner 2015).