REVIEWs

Chronic lymphocytic leukaemia:

from genetics to treatment
Francesc Bosch   1,2,3* and Riccardo Dalla-​Favera3
Abstract | Chronic lymphocytic leukaemia (CLL), the most frequent type of leukaemia in adults,
is a lymphoproliferative disorder that is characterized by the expansion of monoclonal, mature
CD5+CD23+ B cells in the peripheral blood, secondary lymphoid tissues and bone marrow. CLL is
an incurable disease with a heterogeneous clinical course, for which the treatment decision still
relies on conventional parameters (such as clinical stage and lymphocyte doubling time).
During the past 5 years, relevant advances have been made in understanding CLL biology.
Indeed, substantial progress has been made in the identification of the putative cell of origin of
CLL , and comprehensive studies have dissected the genomic, epigenomic and transcriptomic
landscape of CLL. Advances in clinical management include improvements in our understanding
of the prognostic value of different genetic lesions, particularly those associated with
chemoresistance and progression to highly aggressive forms of CLL , and the advent of new
therapies targeting crucial biological pathways. In this Review , we discuss new insights into the
genetic lesions involved in the pathogenesis of CLL and how these genetic insights influence
clinical management and the development of new therapeutic strategies for this disease.

1
Department of Haematology,
University Hospital Vall
d’Hebron, Autonomous
University, Barcelona, Spain.
2
Laboratory of Experimental
Haematology, Vall d’Hebron
Institute of Oncology (VHIO),
Barcelona, Spain.
3
Institute for Cancer Genetics,
Columbia University,
New York, NY, USA.
*e-​mail: fbosch@vhio.net
https://doi.org/10.1038/
s41571-019-0239-8
With an estimated incidence of 4.7 new cases per 100,000
individuals, chronic lymphocytic leukaemia (CLL) is the
most common form of chronic leukaemia in the USA and
in Europe1. In 2017, the estimated number of newly diag-
nosed cases was 20,110, representing ~1.2% of all cancers
in the USA2. By contrast, the incidence of CLL among
individuals from African, Caribbean and Asian countries
is ~1.4 new cases per 100,000 individuals, suggesting
that genetic factors have a role in this racial disparity3,4.
Accordingly, relatives of patients with CLL have a higher
risk of developing CLL and other lymphoproliferative dis-
orders than the general population, although the basis for
this genetic susceptibility remains elusive5–7. The median
age at diagnosis is 70 years, with a male predominance
(1.3:1) in all ethnic subgroups2,8. As life expectancy and
the use of blood testing increase, the prevalence of CLL
and the proportion of asymptomatic patients diagnosed
with early stage disease will continue to increase, whereas
the median age at diagnosis will decrease2,8.
CLL is a chronic lymphoproliferative disorder9,10
diagnosed by the presence of ≥5,000 clonal CD5+CD23+
B lymphocytes per microlitre of peripheral blood for more
than 3 months, or by the presence of its non-​leukaemic
variant, small lymphocytic lymphoma (SLL)9,10. CLL
remains an incurable disease with a heterogeneous clin-
ical course, for which prognostication is based on sim-
ple and highly reproducible clinical parameters that
were used to develop two clinical staging systems11,12.
The  modified Rai classification, which was derived
from the original Rai staging system with five risk sub-
groups (stages 0–IV)13, defines patients with low-​risk CLL
who solely display lymphocytosis, intermediate-​risk dis-
ease with palpable lymph nodes or hepatosplenomegaly,
and high-​risk disease with anaemia (haemoglobin <110 g/l)
or thrombocytopenia (platelet count <100 × 109/l)13. The
Binet classification (Binet A–C) relies on similar physical
examination and laboratory findings12. On the basis of the
enormous advances in the biology and treatment of CLL,
these historical staging systems have been complemented
by a plethora of new prognostic and predictive parame-
ters based on CLL genetics and bio­logy for the purpose of
predicting patient outcomes and response to treatment14–17.
In this Review, we focus on insights into the genetic
lesions involved in the pathogenesis of CLL gained over the
past 7 years, referring readers to other reviews on the role
of the tumour microenvironment18. We discuss the
genetic lesions in CLL and their value as both prognostic
indicators of clinical course and as predictive biomarkers
of response to chemotherapy and targeted therapies.
Genetics and pathogenesis of CLL
Emerging knowledge of CLL genetics and biology indi-
cates that CLL is not a homogeneous disease, informing
the current understanding of the distinct cell types from
which this malignancy can originate and the complex set of
genetic lesions that are associated with its pathogenesis.

Nature Reviews | Clinical Oncology

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Key points
• Next-​generation sequencing of the coding genome has identified the most common
somatic genetic alterations associated with the pathogenesis of chronic lymphocytic
leukaemia (CLL).
• Specific genetic alterations provide biomarkers for prognostication of the clinical
course and prediction of response to chemotherapy and targeted therapy.
• Recurrent genetic alterations identify cellular pathways that present potential
therapeutic targets.
• This new knowledge is informing novel treatment algorithms for the clinical
management of patients with CLL.
Cell of origin
The identification of the cell of origin of any given
malignancy (that is, the non-​maligant cell from which
the malignant transformation originated) can be useful
as a reference to identify the alterations in the cell that
caused its malignant transformation. Over the years,
several cell types have been proposed as putative cells of
origin (also sometimes referred to as the ‘normal counter­
part’) of CLL on the basis of progressive increases in the
understanding of B cell biology and differentiation.
The observed presence of clonal rearrangements
of immunoglobulin (IG) genes along with expression of
specific cell surface markers has established that CLL
is derived from a mature B cell that is characterized
by weak expression of B cell markers (surface mem-
brane immunoglobulins (Ig), CD19 and CD20) and is
positive for expression of CD23 (also known as FcεRII;
a B cell and dendritic cell marker) and of the CD200
and CD5 antigens10. The expression of CD5 led to the
hypothesis that CLL is derived from IgM-​s ecreting
B1 lineage of B cells that are contributors to innate
immunity19,20, as opposed to the B2 lineage, which is
involved in adaptive immunity. Subsequently, the dis-
covery that two subgroups of patients with CLL can be
distinguished on the basis of the presence or absence
of mutations in the immunoglobulin heavy chain var-
iable region (IGHV) genes, which encode part of the
B cell receptor (BCR), unequivocally indicated that
the IGHV-​mutated (IGHV-M) CLLs are derived from
antigen-​experienced B cells that have transited through
the germinal centre (GC) of secondary lymphoid
organs, the site of immunoglobulin somatic hyper­
mutation21. Conversely, whether the IGHV-​unmutated
(IGHV-​UM) CLLs are derived from pre-​GC (naive)
B cells or GC-​independent antigen-experienced B cells
remains unclear21.
Comparative gene expression profiling of CLL speci­
mens and subsets of non-​transformed human B cell has
shown that both IGHV-​M and IGHV-​UM subtypes are
similar to CD27+ memory B cells21, suggesting that both
CLL subtypes originate from antigen-​experienced CD27+
B cells, with IGHV-​M and IGHV-​UM subtypes having
been derived from post-​GC or GC-​independent cells,
respectively21,22. In 2012, transcriptome analyses of sub-
sets of non-​transformed B cells suggested that IGHV-M
CLLs are derived from a previously unrecognized
CD27+CD5+ post-​GC subset, whereas IGVH-​UM CLLs
resemble CD5+CD27− IGHV-​UM-naive B cells23 (Fig. 1).
A 2012 study comparing the epigenetic profiles of
patients with CLL showed that the degree of genome
methylation in CLL cells is generally similar to that in
memory B cells, although CLL-​associated differences
might reflect the existence of a currently unknown
non-malignant B cell subpopulation24. Overall, the dis-
tinction between IGHV-​M CLL putatively derived from
GC-​experienced B cells and IGHV-​UM CLL arising
from pre-​GC-naive B cells or GC-​independent mem-
ory B cells still remains a valid, although not universally
accepted, model.
Patients with IGHV-​M CLL and those with IGHV-​
UM CLL have a highly restricted repertoire of IG genes,
suggesting a role for antigen selection in the patho-
genesis of the disease25,26. Approximately one-​third of
patients with CLL, particularly those with IGHV-​UM
CLL, exhibit stereotypic BCRs, which are based on
their complementary-​determining regions26,27. To date,
>200 different CLL stereotype subsets have been iden-
tified25, which can be further subdivided into several
subsets with distinct biological and clinical features28:
IGHV-​UM CLLs tend to express low-​affinity, poly-​
reactive and self-​reactive BCRs, whereas IGHV-​M
CLLs usually express oligo-​reactive and mono-​reactive
BCRs25. Notably, both IGHV-​M and IGHV-​UM sub-
types might also rely on antigen-​independent, cell-​
autonomous BCR signalling, providing a potential
rationale for the therapeutic targeting of the BCR
signalling pathway29.
Finally, the very early genetic and epigenetic events
that eventually lead to CLL have been suggested to
occur in haematopoietic stem cells (HSCs)30. Consistent
with this notion, in some patients with allogeneic HSC
transplantation (HSCT), pre-​malignant lymphoid cells
were transmitted from the donor to the recipient and
eventually led to CLL development30. In addition, HSCs
from patients with CLL, but not those from healthy
donors, have been shown to engraft in immunodeficient
mice and induce B cell lymphoproliferations in vivo31.
Finally, specific lesions in genes implicated in lymphoid
tumours (for example, NOTCH1, SF3B1 and EGR) have
been found in purified HSCs from some patients with
CLL32. Overall, the conclusion that the initial genetic
lesions favouring CLL development might occur in
HSCs remains controversial, particularly considering
the difficulties in purifying CLL-​free HSC populations
from bone marrow32,33, and the emerging evidence that
healthy elderly individuals have clonal haematopoiesis,
which can increase the risk of haematological malignan-
cies, including CLL34,35, and is associated with subsets of
genetic lesions also detected in CLL.
Overall, the cell of origin of CLL is a subject of con-
tinued debate, with regard to both the cell type in which
the first genetic lesion occurs (HSCs versus mature
B cells) and to the mature B cell type (pre-​GC, post-​GC
or GC-​independent) from which the clonal expansion
of overt CLL can originate.
Recurrent genetic lesions
The development of genome-​wide sequencing and
copy-​number analysis has enabled the thorough charac­
terization of the genomic landscape of CLL (Fig.  2).
Whole-​e xome sequencing (WES) of >1,000 CLL
specimens and whole-​genome sequencing (WGS) of
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Early/immature Mature
• Lymphoid-lineage priming • Clonal selection • Clonal selection
• Expansion • Expansion • Transformation

MBL IGHV-M CLL

TD

GC Post-GC
B cell CD5+CD27+ • BCR signalling
B cell • T cells
• Microenvironmental factors
‘CLL HSC’ Naive
HSC B cell B cell
(?) TD
progenitor

Pre-GC
TI CD5+CD27–
B cell

MBL IGHV-UM CLL

Clonal/polyclonal Oligoclonal Monoclonal

Fig. 1 | The cellular origin of chronic lymphocytic leukaemia. The genetic and epigenetic events leading to chronic
lymphocytic leukaemia (CLL) have been suggested to occur in haematopoietic stem cells (HSCs)31, although this
hypothesis remains controversial32,33. After HSCs acquire genetic and epigenetic lesions (indicated by lightning symbols),
the nature of which are still unknown, the cellular output of these lesions could be a polyclonal expansion of B cell
progenitors. Subsequent antigenic stimulation might lead to oligoclonal selection and expansion of mature B cells.
CLL cells with mutations in the immunoglobulin heavy chain variable region genes (IGHV-​M) seem to originate from
post-germinal centre (GC) CD5+CD27+ B cells, which are most likely derived from CD5+CD27+ B cells that have undergone
the GC reaction23. Conversely , IGHV-​unmutated (IGHV-​UM) CLL seems to be derived from pre-​GC CD5+CD27− B cells,
which might arise from naive B cells or from a separate lineage of precursor B cells, probably in a T cell-​independent
process23. The evolution from these progenitors to monoclonal B lymphocytosis (MBL) and, ultimately , to overt CLL is
dictated by additional genetic and epigenetic abnormalities (indicated by lightning symbols), B cell receptor (BCR)
stimulation, microenvironmental factors and T cells. The dashed arrows indicate a hypothetical mechanism. TD,
T cell-dependent antigen; TI, T cell-​independent antigen. Figure adapted from ref.48, Springer Nature Limited.

~200 patients with CLL have revealed the presence of
~0.9 mutations per megabase (including point muta-
tions, copy number alterations and exceedingly rare
chromosomal translocations) and a load of ~10–30
non-​silent events per patient, with a higher number of
somatic substitutions in IGHV-​M CLL (~2,800) than in
IGHV-​UM CLL (~2,000)36–45. Overall, the mutational
load in CLL is lower than in other lymphoid neoplasms
and epithelial tumours, and is similar to that in acute
leukaemias46,47. In this section, we summarize the major
pathways that are recurrently altered in a sizeable pro-
portion of patients with CLL, and discuss their prog-
nostic value as individual biomarkers (Table 1). We refer
to other reviews that provide detailed reports of the full
spectrum of genetic alterations in CLL48,49.
Regulation of the cell cycle and apoptosis. The most
frequent genetic lesions in CLL (~50–60% of patients)50
are deletions of 13q14 (del13q14) (Fig.  2; Table  1) ,
which are generally monoallelic (~80% of del13q14
events) and more prevalent in IGHV-​M CLL than in
IGHV-​UM CLL41,50–52. These lesions are often found
to be the unique cytogenetic abnormality detectable
in some CLLs, suggesting their role in the early stages
of CLL development41,50,51. Despite the fact that the size of
13q14 deletion is variable across patients, the minimal
deleted region contains two long non-​coding RNA
genes (DLEU2 and DLEU1) and the microRNA gene
cluster MIR15A–MIR16-1 (refs53–57). The pathogenetic
role of these deletions has been confirmed in mice with
conditional deletions of the murine locus equivalent
to that of the minimal deleted region in patients with
CLL, which developed clonal lymphoproliferations,
recapitulating the different steps of CLL initiation and
progression, including monoclonal B lymphocytosis
(MBL), CLL, and progression to diffuse large B cell
lymphoma (DLBCL)51,53. In vitro studies have indicated
that the main mechanisms by which MIR15A–MIR16-1
exert their pathogenetic roles in B cells is through
regu­lation of the cell cycle and apoptosis, specifically
by modulating the expression of genes involved in the
G0/G1–S transition (for example, inducing activation of
G1–S-​specific cyclin D2 (CCND2) and CCND351) and
the anti-​apoptotic gene BCL2 (ref.58).
Since the seminal study by Döhner and colleagues50,
the detection of del13q14 has been associated with the
best prognosis among the different copy number
abnormalities (del17p, del11q and trisomy 12) (Table 1).
Patients with CLL and del13q14 tend to have a prolonged
time to first treatment (TTFT), mutations in the IGHV
genes and prolonged overall survival (OS) compared
with patients with other genetic abnormalities15,50.

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NOTCH1 BCR signalling Inflammatory Not recurrently mutated

signalling pathway
<5%
Brontictuzumab Fostamatinib BCR TLR 5–10%
Entospletinib IL-1R
RO4949097 10–20%
LY3039478 TAK659
>20%
Cerdulatinib
PF03084014
NOTCH1

γ-secretase Ibrutinib SNS-062 LYN

Acalabrutinib M7583 MYD88 IMO-8400
PLCγ2
SYK NFKBIE BIRC3 CA-4948
FBXW7 BGB-3111 DTRMWXHS
CT-1530 CC-292 BLNK TRAF2/
BTK Venetoclax
Tirabrutinib TRAF3 BA
Navitoclax X
Idelalisib PI3K NF-κB MIK665 BAK
Duvelisib KRAS (anti-MCL1)
Umbralisib NRAS AMG176
AKT (anti-MCL1) PUMA BIM
YY-20394
BRAF
RNA processing
BCL2
RPS15 mTOR MAPKs
Chromatin
modification APR-246
NXF1 Cell cycle COTI-2
XPO1 and apoptosis DNA damage response
ICN1

CDH2 CB-103 MED12

ATM p53
H2B H2A SF3B1 • Cyclin D2
• Cyclin D3 NF-κB
H4 H3 POT1

SETD2 Target
genes AZD6738
ASXL1 Selinexor BAY1895344
SL-801 del13q14 del11q del17p
Trisomy 12 (MIR15A–MIR16-1, (ATM) (TP53)
DLEU1 and DLEU2)

Fig. 2 | Cll genetic landscape and currently tested targeted drugs. The schematic depicts the complexity of the
chronic lymphocytic leukaemia (CLL) genetic landscape revealed by fluorescence in situ hybridization (FISH) and next-​
generation sequencing (NGS). The most frequent chromosomal abnormalities detected by FISH include deletions of
chromosome 13q14 (del13q14; which contains MIR15A–MIR16-1, DLEU1 and DLEU2), trisomy 12, del11q (which contains
ATM) and del17p (which contains TP53)50. Del13q14 has been implicated in the regulation of the cell cycle and apoptosis,
whereas del11q (ATM) and del17p (TP53) affect the response to DNA damage. Recurrent genetic alterations identified by
NGS include mutations in genes involved in chromatin modification (such as CHD2), nuclear factor-​κB (NF-​κB) signalling
(BIRC3 and MYD88), the NOTCH1 pathway (NOTCH1 and FBXW7), RNA processing (SF3B1 and XPO1) or the DNA damage
response (for example, ATM, TP53 and POT1)38–40. The frequencies of the genetic lesions and/or the encoded proteins are
indicated by their colour (see the key). Proteins that are not recurrently mutated in CLL are shown in blue. Targeted
therapies that are currently being tested in clinical trials involving patients with CLL are indicated as light-​grey boxes;
approved agents are in bold text. BCR , B cell receptor.

NOTCH1 signalling. The most commonly mutated gene
detected at diagnosis in patients with CLL is NOTCH1,
a well-​characterized oncogene in T cell acute lympho­
blastic leukaemia (T-​A LL) 59, with a prevalence of
~4–20%36,38–41 (Fig. 2; Table 1). NOTCH1 encodes a trans-
membrane receptor that, upon binding to its ligand, is
proteolytically processed to generate the transcriptionally
active nuclear intracellular domain of NOTCH1 (ICN1),
which transactivates genes involved in proliferation,
metabolism and survival, including the activation of the
MYC proto-​oncogene60. In contrast to the mutations in
T-​ALL, NOTCH1 mutations in CLL remove the PEST
domain of the NOTCH1 protein, preventing proteasomal
degradation of ICN1 by the ubiquitin ligase F-box/WD
repeat-​containing protein 7 (FBXW7)36,37,39,40,42. Of note,
3% of CLLs that are devoid of NOTCH1 lesions har-
bour FBXW7-inactivating mutations41, suggesting an
analogous functional outcome via abnormally stabilized
NOTCH1 signalling. The pathogenetic role of NOTCH1
in CLL might not be limited to patients harbouring gene
mutations, given that CLL cells in the lymph nodes display
frequent NOTCH1 activation independent of mutation61
and that ICN1 and a NOTCH1 gene expression signature
are detectable in ~50% of peripheral blood CLL cells lack-
ing NOTCH1 mutations62. These findings highlight the
need to revisit the role of NOTCH1 in CLL pathogenesis
and its prognostic and therapeutic implications.
The frequency of NOTCH1 mutations in patients
with CLL varies according to the clinical stage in which
it is analysed. Indeed, NOTCH1 lesions are very rare
(<5%) in patients with ultra-​stable CLL, but are present
at diagnosis in ~12% of unselected patients with CLL63.
The frequency of NOTCH1 mutation is increased in
patients with advanced-​stage CLL and in those with CLL

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Table 1 | Prognostic influence of Cll genetic lesions at diagnosis

genetic lesion Study number of patients Frequency TTFT 5-year additional features
(%) (months) OS (%)
Isolated del13q14 Döhner et al.50 325; 52% with early stage CLL 55a ~90b >90b • Enriched in early stages
• Enriched in IGHV-​M
NOTCH1 Rossi et al.63 637; 75% with early stage CLL 11 NA 50b • Enriched in advanced stages
mutation • Associated with trisomy 12
Weissmann et al.116 643; 0% with early stage CLL 12 42b 55b • Enriched in IGHV-​UM
Baliakas et al.64 2697; 78% with early stage CLL 7 40b NA
Nadeu et al.82 396; 84% with early stage CLL 22 <12b ~70b,c
Jeromin et al. 125
908; 0% with early stage CLL 12.3 40 b
80b
Mansouri et al.185 359; 77% with early stage CLL 5 5b ~50b
FBXW7 mutation Jeromin et al. 125
908; 0% with early stage CLL 2.5 NA NA NA
del17p or TP53 Döhner et al.50 325; 52% with early stage CLL 7a <12b 40b • Enriched in advanced stages
disruption • Enriched in IGHV-​UM
Zenz et al.71 125; 65% with early stage CLL 10d NA 40
Puente et al.40 452; 68% with early stage CLL 5 <12b NA
Rossi et al.15 637; 75% with early stage CLL 8.5 27b 50b
Baliakas et al.64 1691; 78% with early stage CLL 9 36 35b
del11q or ATM Döhner et al. 50
325; 52% with early stage CLL 18 a
13 b
68b • Enriched in advanced stages
disruption • Associated with bulky disease
Nadeu et al.82 398; 84% with early stage CLL 11 <12b NS • Associated with young age
Wierda et al.186 930; 87% with early stage CLL 9a <24b NA • Enriched in IGHV-​UM
POT1 mutation Ramsay et al.83 127; 82% with early stage CLL 3 NA NA Enriched in IGHV-​UM
SF3B1 disruption Wang et al. 37
91 ; 79% with early stage CLL
e
15 <12 b
NA • High male:female ratio
• Associated with high white
Rossi et al.63 637; 75% with early stage CLL 6.8 <12b 2.5 yearsb,f blood cell count
Baliakas et al.64 1715; 78% with early stage CLL 8 36b NA • Enriched in advanced stages
• Associated with del11q
Jeromin et al.125 1160; 0% with early stage CLL 9 40b 64b • Enriched in IGHV-​UM
Mansouri et al. 185
360; 77% with early stage CLL 3.6 3b
~55b
BIRC3 disruption Rossi et al.187 637; 75% with early stage CLL 6.2 NA 3.1 yearsb,f • Enriched in advanced stages
• Associated with del11q
Baliakas et al. 64
919; 78% with early stage CLL 2.5 32 b
NA • Enriched in IGHV-​UM
Nadeu et al.82 399; 84% with early stage CLL 4 NS NA
MYD88 mutation Martínez-​Trillos et al. 87,88
587; 81% with early stage CLL 4 NS 100b • Increased prevalence in males
• Associated with young ageg
Baliakas et al.188 1080; 78% with early stage CLL 2.2 ~79b NA • Enriched in advanced stages
Rossi et al.63 637; 75% with early stage CLL 4.1 NA 96b • Enriched in IGHV-​M
CLL , chronic lymphocytic leukaemia; NA , not available; NS, not significant; OS, overall survival; TTFT, time to first treatment. aFluorescence in situ hybridization;
b
Statistical prognostic significance of the lesion; cNot statistically significant at the subclonal level; dSanger sequencing; eTwo-​thirds untreated; fMedian survival;
g
Controversial data.

harbouring trisomy 12, and ~80% of patients harbouring
NOTCH1 mutations have IGHV-​UM CLL63,64 (Table 1).
Moreover, their presence has been associated with
unfavourable OS (5-year OS 50–70%), even in patients
with IGHV-​M CLL, and with an increased risk of Richter
syndrome36,65,66. Of note, patients with genetic lesions
of the 3′ untranslated region of NOTCH1 tend to have
a poor prognosis similar to that of patients with other
NOTCH1 mutations40. Finally, NOTCH1-mutated CLLs
have decreased surface expression of CD20, which might
partially explain why such patients derive limited benefit
from anti-​CD20-based therapies36,63,67–70.
DNA damage response. Deletions of the 17p13 chromo-
somal region (del17p) are found at different frequencies
in CLL depending on the clinical stage of the disease,
ranging from 1% in MBL to 20% in chemorefractory
disease70–72 (Fig. 2; Table 1). Typically, 17p losses involve
the entire short arm of chromosome 17 and invariably
encompass the locus of the tumour suppressor gene
TP53 (ref.73). Missense mutations in the second TP53
allele, usually located in the DNA-​binding domain,
are found in ~80% of CLLs with del17p, with an addi-
tional 9% of mutations discovered using ultra-​deep
next-​generation sequencing (ultra-​deep NGS)71,74–76.
Consistent with the increased genomic instability
caused by the inactivation of TP53, CLLs with del17p
have a higher degree of genomic complexity than
TP53-wild-type CLLs77.
The prognostic implication of TP53 dysregulation
is linked to its association with resistance to DNA-​
damaging agents (chemotherapy or radiotherapy), and
the presence of this genetic lesion at diagnosis is associ-
ated with a decreased TTFT and unfavourable OS15,40,50,71
(Table 1) . Accordingly, TP53 inactivation is a major
determinant of therapeutic decisions.

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ATM, an upstream regulator of the TP53 gene located
in the 11q22-23 region, is involved in deletions (del11q)
in ~10% of patients with CLL, with an increased fre-
quency in those with IGHV-​UM CLL with nodal
disease37,50,78 (Fig. 2; Table 1). In general, del11q is mon-
oallelic, large in size (>20 Mb) and is associated with
mutations in the remaining ATM allele in more than
one-​third of patients with del11q CLL, suggesting that
the ATM gene is the major target of these deletions78.
In some patients, deletions of 11q do not involve ATM,
but affect the BIRC3 gene, a negative regulator of the
non-​canonical nuclear factor-​κB (NF-​κB) pathway79.
Both del11q and ATM genetic lesions are found in up to
20% of patients at diagnosis39,48,50,78, and these patients
tend to be younger, have enlarged lymph nodes at diag-
nosis and have a shorter TTFT and OS than patients
with del13q, trisomy 12 or those without chromosomal
abnormalities, particularly when ATM genetic lesions
are biallelic78,80–82.
POT1 is involved in telomere protection and is
mutated in 3–7% of patients with CLL83. POT1 mutations
alter the telomeric DNA binding domain, resulting in
increased structural aberrations and chromosomal breaks
that favour tumour progression83. These lesions have
been reported to be strongly associated with IGHV-UM
CLL, SF3B1 mutations and advanced clinical stage83.
RNA processing. Recurrent mutations in different genes
encoding spliceosome machinery have been identified
in patients with CLL, with the gene encoding the splicing
factor 3B subunit 1 (SF3B1) reported as the most fre-
quently mutated gene37,42,84, with a mutational frequency
of ~10%37,40,41 (Fig. 2; Table 1). Although the role of SF3B1
lesions is not yet fully understood, they might lead to
splicing changes affecting the structure and coding
potential of gene transcripts across multiple pathways,
including the DNA damage response and NOTCH1
signalling85. Along with SF3B1, genetic lesions in other
genes involved in RNA processing (for example, NFX1,
XPO1 and MED12) have also been reported, albeit at
lower frequencies48,85 (Fig. 2). In addition to the genetic
lesions affecting the spliceosome, mutations in RPS15,
a gene encoding a component of the 40S ribosomal
subunit, have been associated with aggressive CLL and
TP53 abnormalities1. Assuming that all of these lesions
in genes encoding spliceosome components function
via the same mechanism, dysregulation of RNA pro-
cessing would be observed in ~30% of patients, suggest-
ing a common pathogenetic pathway in CLL41,42,85. The
frequency of genetic abnormalities in the SF3B1 gene
tend to increase from ~10% in newly diagnosed patients
to a higher frequency of ~17% in patients refractory to
fludarabine treatment64,84, and are more frequent in
patients with del11q, del13q14 or trisomy 12 (refs64,84).
These lesions are also more frequent in males than
females, and their presence correlates with a decreased
TTFT and unfavourable OS (Table 1).
Inflammatory pathway and constitutive NF-​κB acti-
vation. Several lesions found in large-​scale genome
sequencing projects in patients with CLL seem to con-
verge on the activation of the NF-​κB transcriptional
complex36–41,86. Monoallelic BIRC3-truncating muta-
tions are found at diagnosis in 2.2–4.3% of patients with
CLL and cause the removal of the C-​terminal RING fin-
ger domain of the BIRC3 protein, leading to constitutive
NF-​κB activation79,84 (Fig. 2; Table 1). In addition, the
MYD88 gene is mutated in ~3% of patients with CLL,
exclusively those with IGHV-M ​ CLL40,41 (Fig. 2; Table 1).
MYD88, a cytosolic protein adaptor involved in the
Toll-​like receptor (TLR) pathway, has pleiotropic func-
tions in B cells, including NF-​κB activation. The most
common recurrent MYD88 mutation (MYD88L265P) in
CLL, which is also found in Waldenström macroglob-
ulinaemia and activated B cell (ABC)-type DLBCL,
leads to increased binding of MYD88 to interleukin-1
receptor-​associated kinase 1 (IRAK1) and subsequent
downstream activation of NF-​κ B 39. Finally, other
lesions in genes involved in the inflammatory pathway
(TRAF2, TRAF3 and NFKBIE) are observed at frequen-
cies <2% and are all hypothesized to lead to NF-​κB acti-
vation86 (Fig. 2). However, a definitive assessment of the
frequency of NF-​κB activation and the role of NF-​κB
complexes in CLL pathogenesis is still lacking.
Among the different genetic lesions that could acti-
vate the NF-​κB signalling pathway, BIRC3 lesions have
been positively associated with chemorefractory dis-
ease, advanced clinical stages, IGHV-​UM disease and
an increased prevalence of del11q79. However, although
the presence of BIRC3 aberrations seems to be associ-
ated with shorter OS, their influence on TTFT has not
been proved82. The prognostic implications of MYD88
lesions remain controversial because of conflicting
data, presumably owing to their low frequency. One
study, mainly involving patients with early stage CLL
and a low median age, revealed that MYD88 lesions
were positively associated with IGHV-​M status (90%),
Binet A stage, and young age and had a small influence
on TTFT and, surprisingly, OS87,88. Conversely, analy­
sis of larger cohorts of patients with advanced-​stage
CLL showed that MYD88 mutations are not preferen-
tially associated with age or prognosis64,84 and are not
associated with an adverse outcome in patients with
IGHV-​M CLL89.
Trisomy 12. Trisomy of chromosome 12 is a relevant
and recurrent cytogenetic abnormality found in ~15% of
patients with CLL at diagnosis50, for which no functional
explanation has been found to date (Fig. 2). Trisomy 12
has been associated with an atypical morphology of the
lymphocytes, and its prevalence is markedly high in SLL,
the tumoural counterpart of CLL, in which it is found
in ~30% of patients90. Although trisomy 12 has classi-
cally been considered as an intermediate-​risk genetic
lesion, the co-​occurrence of NOTCH1 mutations has
been associated with poor outcomes67,91. This finding is
in line with the observation of an increased frequency of
trisomy 12 in patients with Richter syndrome92.
Epigenetic changes in CLL
Epigenetic studies, defined by the analysis of DNA-​
modifying marks in the genome of tumour cells, can
provide biologically and clinically important informa-
tion in two different areas. By comparing tumour and
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 Reviews

Risk factors
• TP53 aberrations
• NOTCH1 mutations
• IGHV4-39
del13q14 >50%
NOTCH1 ~40%
CDKN2A/B ~30% RS (5–10%)
del9p21 ~30%
MYC ~30%
• BCR signalling Risk factors
• Microenvironment • TP53 aberrations
• Advanced-stage • Bone marrow
CLL CLL disease RS under
involvement
Early stage Advanced stage ibrutinib (5%)
MBL • Clonally related
MYC gains
Ibrutinib
(<2 years)

TP53 >40%
del13q14 60% del13q14 60% BIRC3 ~24% CLL resistant
TP53 2% TP53 5% SF3B1 ~17% to CIT
SF3B1 4% SF3B1 8% del13q14 50% ATM ~20%
TP53 7% CIT
NOTCH1 6% NOTCH1 12%
ATM 5% ATM 10% SF3B1 21%
BIRC3 4% BIRC3 8% NOTCH1 10% BTK mutations
ATM 15% PLCG2 mutations CLL resistant
BIRC3 6% del8p to ibrutinib
ITPKB mutations (15%)
Ibrutinib MYC gains
(>2 years)

Fig. 3 | genetics of chronic lymphocytic leukaemia progression. The overall genomic mutation load seems to be
similar in monoclonal B lymphocytosis (MBL) and early stage chronic lymphocytic leukaemia (CLL), as determined in
both whole-exome sequencing and whole-​genome sequencing studies38–41. When CLL evolves from early stages to
overt disease, discrete acquisition of genetic lesions occurs, suggesting that B cell receptor (BCR) signalling and/or
the microenvironment contribute to disease progression41. After the constraints exerted by treatment with
chemoimmunotherapy (CIT) or the BCR signalling inhibitor ibrutinib, CLL cells with genetic lesions conferring drug
resistance become clonally selected (orange cells)15,41,45. Finally , CLL can transform from advanced-​stage disease to
an aggressive lymphoma termed Richter syndrome (RS), although the concurrent diagnosis of CLL and RS is rare
(reviewed in113). In most cases, the RS cells (red cells) derive from the original CLL clone (blue cells) by developing
additional genetic lesions65,66,92. NOTCH1 mutations, MYC activation and TP53, CDKN2A and CDKN2B disruptions are
characteristic genetic lesions of RS65. Patients with CLL receiving ibrutinib can progress in two different ways. First, in
approximately 5% of patients, the disease can evolve in <2 years on treatment to a RS that is clonally related to the
underlying CLL119,120. The time and clinical presentation suggest that ibrutinib selects for a pre-​existing RS clone.
Second, 15% of patients, who typically show progression after >2 years of treatment, can develop mutations associated
with resistance to ibrutinib (that is, BTKC481S, PLCG2 or ITPKB mutations)45,119,147. These mutations can be detected using
highly sensitive techniques even before the start of ibrutinib treatment (orange cells) and up to 15 months preceding
clinical progression, which is characterized by an increase in the size of the lymph nodes and a rise in lymphocyte count
and serum lactate dehydrogenase (LDH) levels119,120,147.

non-​transformed cells, epigenetic studies provide rele- Genetics of tumour progression

vant information on the putative cell of origin. In fact,
the comparative analysis of DNA methylation profiles
of IGHV-​UM and IGHV-​M cells has suggested a rela-
tionship with naive and memory B cells, respectively24.
Furthermore, high levels of intra-​sample methylation
heterogeneity correlate with high-​risk genetic lesions,
clonal evolution and an adverse prognosis93. Finally,
comprehensive analyses are unveiling relationships
between some epigenetic profiles and specific genetic
lesions (for example, MYD88 mutations or trisomy 12)94.
These observations suggest that CLL-​associated epi­
genetic changes can complement the analysis of genetic
alterations in the characterization of disease subgroups,
intraclonal heterogeneity and response to therapy, and
that they are also of direct therapeutic interest since
these epigenetic changes can be efficiently modulated
by specific drugs94–96.
Clinical and biological evidence indicates that CLL is
preceded by a pre-​malignant stage of MBL, and can
evolve in later, more aggressive stages, including trans­
formation into an aggressive lymphoma (Richter
transformation) (Fig. 3).
MBL and the clonal evolution of CLL. In 2008, the WHO
recognized MBL as a diagnosis based on the presence of
monoclonal B cell populations in the peripheral blood
at concentrations of up to 5,000 cells per microlitre (with
the phenotype of CLL, atypical CLL or non-​CLL (CD52+)
B cells) in the absence of other clinical features, such as
disease-​related symptoms, cytopenia or lymphadeno­
pathies97. MBL is detectable in up to 12% of healthy adults
when analysed using a high-​sensitivity eight-​colour flow
cytometry approach to screen >5 × 106 total peripheral
blood B lymphocytes98, and in up to 25% of individuals

Nature Reviews | Clinical Oncology

Reviews
older than 70 years99. The updated WHO classification
distinguishes ‘high-​count’ MBL from ‘low-​count’ MBL,
the latter being defined by a peripheral blood CLL count
of <500 cells per microlitre (refs10,100). High-​count MBL
has been recognized as a pre-​malignant state because it
precedes CLL in virtually all patients101,102. In addition,
high-​count MBL carries mutated IGHV genes and a BCR
repertoire and stereotype that resemble those of CLL103.
Conversely, low-​count MBL has an immunoglobulin G
(IgG) genetic repertoire that is usually found in elderly
individuals and that differs from those observed in
patients with IGHV-​M or IGHV-​UM CLL, suggesting
that low-​count MBL is not a pre-​malignant state, but
rather a consequence of age-​related immune senes-
cence104. In addition, the distinction between high-count
and low-​count MBL is based on data from a small cohort
(n = 31) and reflects a continuum of lymphocyte counts
that is associated with the risk of developing overt CLL52.
Thus, the updated International Workshop on Chronic
Lymphocytic Leukemia (iwCLL) guidelines do not
re­cognize low-​count MBL as a pathological entity and
do not recommend that affected patients are clinically
followed105. Finally, further genomic and epidemiologi-
cal analysis of MBL is necessary to conclusively validate
these notions106,107.
The overall genomic mutational load seems sim-
ilar in CLL and MBL, as evidenced by both WES and
WGS studies39. However, the load of putative driver
genetic lesions is significantly lower in MBL than in CLL
(1.2 versus 1.7 mutations per megabase for IGHV-M
CLL; P = 0.0008)40,108, except when MBL is compared
with ultra-​stable CLL107. This notion was also verified in
a study specifically evaluating the prevalence of lesions
in genes such as NOTCH1, SF3B1 and TP53 in MBL,
which showed that the presence of these lesions is of prog-
nostic significance109. Intriguingly, progression from MBL
to overt CLL does not seem to be accompanied by acqui-
sition of novel genetic lesions, but rather by an expansion
of the clones that already harbour driver mutations109.
Overall, the precise genetic boundaries between MBL and
CLL remain difficult to identify, but a consensus exists in
defining del13q14, trisomy 12 and MYD88 mutations as
early initiating lesions commonly present in CLL38,41,109,
whereas TP53, ATM and SF3B1 mutations seem to be
genetic events that occur during tumour progression41.
Similar to other neoplasias, CLL is genetically hetero­
geneous and contains multiple clonal and subclonal
populations38,110,111. The interplay among these sub-
clones along with their response to internal or external
constraints, such as the selection induced by drug treat-
ment, will determine the abundance and identity of the
selected subclones and their evolution38,41,70,75,79,112 (Fig. 3).
Richter syndrome. Analogous to other low-​grade lympho­
proliferations, CLL can transform into Richter syndrome,
a lymphoma with an aggressive phenotype that has an
annual incidence of 0.5% among all patients with CLL
(reviewed in113). The WHO classification recognizes
two distinct pathological variants of Richter syndrome,
namely the DLBCL variant and the Hodgkin lym-
phoma variant10. Richter syndrome-​associated DLBCL
is commonly clonally related to the founder CLL clone
(in >85% of patients with Richter syndrome), but has a
poorer outcome than de novo DLBCL and is character-
ized by chemoresistance and unfavourable OS66,92. Risk
factors for the development of Richter syndrome include
the presence of TP53 disruptions, NOTCH1 mutations
and IGHV4-39 usage (reviewed in114). In patients receiv-
ing BCR signalling inhibitors, the presence of tetraploid
karyotypes and TP53 aberrations have been associated
with an increased risk of Richter syndrome115. Activation
of the NOTCH1 pathway is the most characteristic
genetic feature of clonally related Richter syndrome, con-
sistent with the observations that NOTCH1 mutations in
CLL at diagnosis are associated with an increased likeli-
hood of developing Richter syndrome and can be found
at subclonal levels by ultra-​deep NGS in the original CLL
founder clones36,63,65,116,117. Since NOTCH1 mutations are
rarely acquired during CLL progression, patients with
this genetic lesion should be closely monitored as they
are at risk of developing Richter syndrome and could be
candidates for NOTCH1-targeted therapy118. In contrast
to clonally related Richter syndrome, the less common
clonally unrelated Richter syndromes (<15% of patients
with Richter syndrome) have a similar survival outcome
to that of de novo DLBCL and, therefore, should be con-
sidered either as independent second malignancies or as
divergent pathogenetic variants derived from a common
precursor cell66,113.
Genomic analysis has revealed that, in most patients,
Richter syndrome is derived from the original predom-
inant CLL clone via a linear pathway of genetic evolu-
tion involving the development of additional genetic
lesions65,66,92. The final genetic landscape of Richter syn-
drome displays similarities to as well as marked differ-
ences from de novo DLBCL. In particular, mutations that
are commonly found in Richter syndrome and are also
found in de novo DLBCL include MYC-​activating events
and disruption of TP53, CDKN2A and CDKN2B, which
are found collectively in ~90% of patients with Richter
syndrome65 (Fig. 3). Conversely, some lesions common
in all DLBCL subgroups are rare in Richter syndrome,
including biallelic inactivation of the TNFAIP3 (also
known as A20) and PRDM1 (also known as BLIMP1)
tumour suppressor genes, and BCL6 translocations. One
of the most distinguishing features of Richter syndrome
DLBCL is a high frequency of trisomy 12, which is rare
in de novo DLBCL65,66,92.
Approximately 5–10% of patients with CLL receiv-
ing ibrutinib develop Richter syndrome, usually within
2 years on treatment, suggesting that this drug selects for
a pre-​existing transformed clone. Pathological data on
Richter syndrome associated with ibrutinib treatment are
limited, and this transformation has been associated with
advanced-​stage disease with TP53 dysfunctions and is
usually clonally related to the underlying CLL and asso-
ciated with MYC copy number gains119,120. Finally, Richter
syndrome has been described in some patients receiving
the BCL2 inhibitor venetoclax121,122, although the exact
prevalence and characteristics of this transformation
remain to be determined. Some of these patients had
previously characterized TP53 mutations in the CLL, and
this transformation was associated with the acquisition of
mutations in the CDKN2A, CDKN2B or SF3B1 (ref.122).
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 Reviews

Clinical implications using variables with independent prognostic value and

The extensive knowledge derived from the genomic
analysis of CLL reveals marked heterogeneity in this
malignancy. Emerging evidence indicates that this hetero­
geneity can inform prognostication and predict resistance
to both chemotherapy and targeted therapy.
Genetic lesions as prognostic markers
The mutational status of the IGHV genes remains sta-
ble throughout the course of the disease and is one of
the most important prognostic biomarkers in CLL. In
comparison with patients with IGHV-​M CLL (~60% at
diagnosis), those with IGHV-​UM CLL are characterized
by the presence of high-​risk genetic lesions, an increased
propensity to undergo clonal evolution and an associa-
tion with a shorter TTFT and unfavourable OS38,40,123,124.
In addition, ~30% of patients carrying stereotyped BCRs
have distinct clinical outcomes, particularly in specific
subsets (reviewed in ref.28), but further investigation of
the prognostic value of BCR stereotype is warranted.
Finally, surrogates of the mutational status of IGHV
genes, such as tyrosine protein kinase ZAP-70, CD38 or
CD49d expression, have been found to be of prognostic
importance for TTFT and OS14.
The complexity and individually variable prognostic
value of the aforementioned genetic lesions have stimu­
lated the development of integrated prognostic scores
combining multiple genetic lesions alone or in combi-
nation with established clinical variables (Table 2). The
main clinical value of these scores is the simplification
of the prognostic assessment of patients with CLL by
the identification of subgroups of patients who are likely
to progress and, therefore, might need early treatment.
The identification of such patients is now of parti­cular
importance because the overwhelming majority of
new patients with CLL are diagnosed at early stages8.
Unfortunately, most prognostic markers have been
identified in patients with CLL treated with chemo­
immunotherapy, thus some variables (for example,
IGHV mutational status) might have minor prognos-
tic value in patients treated with newer targeted treat-
ments. Thus, different prognostic indexes are needed for
patients receiving these new therapies.
One integrated score enabled the identification of
four novel prognostic subgroups by combining fluo-
rescence in situ hybridization (FISH)-based analysis
of chromosomal aberrations with molecular data from
1,274 patients at diagnosis15 (Table 2). Importantly, this
approach identified subgroups with a poor prognosis
within previously established groups with a good prog-
nosis. Thus, ~20% of the lower-​risk patients accord-
ing to the FISH cytogenetic model were stratified
into higher-risk groups by integrating the mutational
information.
A second score, the CLL International Prognostic
Index (CLL-​IPI), was established in a large cohort
of patients who were included in eight clinical trials
evaluating chemotherapy or chemoimmunotherapy
combinations (chlorambucil, chlorambucil plus ritux-
imab, fludarabine, fludarabine plus cyclophosphamide
and fludarabine plus cyclophosphamide plus rituximab),

Table 2 | Prognostic scores combining clinical and molecular variables in Cll

Study number of independent variables predicting independent variables
patients TTFT predicting OS
Rossi et al.15 1274 – • High-​risk: TP53 and/or BIRC3
mutation
• Intermediate-​risk: NOTCH1
mutation, SF3B1 mutation or
del11q
• Low-​risk: trisomy 12 or normal
cytogenetics
• Very low-​risk: del13q14
Jeromin et al.125 1160 • SF3B1 mutation • SF3B1 mutation
• IGHV-​UM • IGHV-​UM
• del11q • TP53 disruption
• Male sex
• Age
CLL-​IPI17 3472 • TP53 disruption (mutation or • TP53 disruption (mutation or
deletion) deletion)
• IGHV-​UM • IGHV-​UM
• Serum β2-microglobulin level • Serum β2-microglobulin level
>3.5 mg/l >3.5 mg/l
• Binet B or C (Rai I–IV) stage • Binet B or C (Rai I–IV) stage
• Age >65 years • Age >65 years
Nadeu et al.126 406 • IGHV-​UM • Age >65 years
• Binet B–C • del17p
• SF3B1 mutation • IGHV-​UM
• BRAF mutation • FBXW7 mutation
• ATM mutation • NOTCH1 mutation
• NOTCH1 mutation • SF3B1 mutation
• MGA mutation • TP53 mutation
CLL , chronic lymphocytic leukaemia; CLL-​IPI, Chronic Lymphocytic Leukemia International Prognostic Index; OS, overall survival;
TTFT, time to first treatment.

Nature Reviews | Clinical Oncology

Reviews
and validated in two independent datasets17 (Table 2).
Five parameters were predictive of OS and TTFT, namely
TP53 status (considering either del17p or TP53 lesions),
IGHV mutational status (mutated versus unmutated),
serum β2-microglobulin levels (cut-​off >3.5 mg/l),
clinical stage (Binet A versus B or C) and age (cut-​off
age >65 years). The value of this score is its ability to
predict OS, both for treatment decisions and at diag­
nosis. Jeromin et al.125 analysed the prognostic influence
of a group of genes (NOTCH1, FBXW7, MYD88, XPO1
and TP53) and their prognostic value along with age and
sex in 1,160 untreated patients with CLL (Table 2). They
found that SF3B1 mutations, IGHV-​UM and del11q
are predictive of a short TTFT, whereas SF3B1 muta-
tion, IGHV-​UM, TP53 disruption, male sex and age are
correlated positively with a short OS duration.
Finally, the prognostic model developed by Nadeu
et al.126 was obtained in a cohort of patients with mostly
early stage disease. Despite its complexity, this model has
important features, including the observation that the
accumulation of driver alterations in addition to clonal
architecture are of prognostic significance126. Of note,
SF3B1, but not TP53, disruptions had an independent
prognostic influence on the TTFT, but both were key
factors in predicting OS in the aforementioned models
by Nadeu et al.126 and Jeromin et al.125 (Table 2).
Given the low frequency of genetic lesions at diag­
nosis, larger studies are warranted to reveal the real
influence of these genetic lesions in early stage disease.
More importantly, until comprehensive genomic ana­
lysis is widely incorporated into clinical practice, prog-
nostic scores should be kept as simple as possible and
easy to apply.
Genetic lesions as predictive markers
For almost 40 years, chlorambucil was the mainstay in
the treatment of CLL, but had little influence on the sur-
vival outcomes of patients16. During the past 15 years,
several new treatment regimens — particularly chemo-
immunotherapy combinations — have been shown to
be active in CLL, achieving deep responses and prolong-
ing survival of patients127–132. Over the past 5 years, an
impressive number of targeted therapies have emerged
that are changing most of the therapeutic paradigms in
CLL133–138. Some parameters (such as IGHV mutational
status) that are useful predictive markers, defined as clin-
ical or molecular features that provide information on
the probability that a patient will derive benefit from a
specific treatment, for chemoimmunotherapy regimens
no longer remain valid when applied to targeted ther-
apies. Hence, identification of the underlying mecha­
nisms of therapeutic response and resistance in CLL
is of the utmost relevance. Thus, analysis of the afore-
mentioned main genetic lesions should be included in
prospective clinical trials to enable selection of patients
who will derive the most benefit from a given treatment.
Response to chemoimmunotherapy. Recent genomic
studies have unveiled the phenomenon of intratumoural
heterogeneity, characterized by the presence of partially
genetically diverse clones and subclones that interact
and compete110. As chemoimmunotherapy regimens
comprise drugs that induce DNA damage, clones and
subclones carrying genetic lesions that hamper DNA
repair, particularly TP53 gene disruptions, are resist-
ant to, and are therefore selected by, chemoimmuno­
therapy 38,75,82 (Fig.  3; Table  3) . Accordingly, several
studies have shown that clonal evolution occurs more
frequently in tumours receiving chemoimmunotherapy
treatments, whereas an equilibrium exists in the clonal
architecture in untreated tumours41. This notion has
important therapeutic implications, although the pos-
sibility that the detection of aggressive clonal evolution
might in fact lead to early treatment cannot be excluded.
Nonetheless, sequential analysis of patients in relapse
after chemoimmunotherapy has shown that subclonal
evolution can follow three general patterns41,139. First,
CLL subtypes with del13q, trisomy 12 or del11q tend to
remain clonally stable. Second, the frequency of TP53
gene disruptions increases upon relapse and are associ-
ated with inferior response rates as well as unfavourable
progression-​free survival (PFS) and OS after treatment.
Thus, all patients with CLL who are eligible for therapy
should be tested for the existence of TP53 disruptions
before the initiation of chemoimmunotherapy. Third,
CLL subtypes with SF3B1 and ATM lesions have a vari-
able evolution (increases or decreases in the abundance
of the subclones), although genetic lesions in SF3B1
are associated with shorter PFS durations with minor
influences on response rates and OS.
Notably, NOTCH1 abnormalities do not correlate
with response or OS after chemoimmunotherapy41,70,72,
except in one study70, in which the presence of NOTCH1
lesions was correlated with a lack of PFS benefit from
the addition of rituximab to fludarabine plus cyclophos-
phamide (thus forming the FCR regimen). This find-
ing might be related to the observation that CLL cells
with mutated NOTCH1 exhibit decreased expression of
CD20 (ref.140) (Table 3). However, the prognostic influ-
ence of the detection of the intracellular (ICN1) portion
of NOTCH1, an indicator of its constitutive activity, has
not yet been assessed62.
Finally, analysis of predictive markers of a poor
response to fludarabine in patients with refractory CLL
has unveiled the involvement of most of the genetic
alterations associated with clinical progression in CLL,
including TP53 (27.5%), NOTCH1 (24.1%), SF3B1
(18.9%) and BIRC3 (15.5%)141. Remarkably, alloge-
neic HSCT is able to overcome the adverse predic-
tive influence of these genetic lesions in patients with
fludarabine-​refractory CLL142, demonstrating that thera-
pies for which the mechanism of action does not directly
induce DNA damage should be preferred treatments for
patients with TP53 lesions (Table 3).
Response to targeted therapies. The BCR signalling
pathway has been targeted using several small-​molecule
inhibitors, with ibrutinib and idelalisib currently
approved for the treatment of CLL. Ibrutinib is an irre-
versible inhibitor of BTK that strongly inhibits BCR sig-
nalling, leading to decreases in proliferation, adhesion
and homing of CLL lymphocytes as well as to abroga-
tion of the tumour-​protective effects from the micro­
environment (reviewed in143). Owing to its mechanism
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 Reviews

Table 3 | Predictive value of genetic lesions according to type of treatment

genetic Treatment Study treatments (setting) number of ORR (%) mPFS (months) mOS (months)
lesion type patients
(% mutated)
TP53 CIT Alemtuzumab versus 297 (7.5) • Mutant: 64 versus 20a • Mutant: 10 versus 2a NR
chlorambucil (frontline)189 • WT: 83 versus 55a • WT: 15 versus 12a
Fludarabine versus fludarabine 378 (8.5) Mutant 67 versus WT Mutant 23 versus WT Mutant 30 versus WT
plus cyclophosphamide 91 (both arms) 62 (both arms)a NR (both arms)a
(frontline)72
Chlorambucil versus fludarabine 466 (7.6) Mutant 27 versus WT Mutant 5% versus WT Mutant 20% versus WT
versus fludarabine plus 83 (all arms)a 27% (all arms)a,b 59% (all arms)a,b
cyclophosphamide (frontline)74
Chlorambucil versus 161 (9.9) Odds ratio for WT HR for WT versus HR for WT versus
chlorambucil plus rituximab versus mutant: 8.6 mutant: 1.8 (all arms) mutant: 3.8 (all arms)a
versus chlorambucil plus (all arms)a
obinutuzumab (frontline)190
Fludarabine plus 628 (11.5) • Mutant 52 versus WT • Mutant 12 versus WT • Mutant 30 versus WT
cyclophosphamide versus 92 (fludarabine plus 36 (fludarabine plus 90 (fludarabine plus
FCR (frontline)70 cyclophosphamide cyclophosphamide cyclophosphamide
arm)a arm)a arm)a
• Mutant 75 versus WT • Mutant 15 versus WT • Mutant 42 versus WT
98 (FCR arm)a 59 (FCR arm)a NR (FCR arm)a
Allo-​HSCT R/R142 72 (30) – HR for mutant versus HR for mutant versus
WT: 0.66 WT: 1.03
Targeted Ibrutinib (R/R)191 144 (100) Mutant 83 Mutant 63%c Mutant 75%c
Ibrutinib versus ofatumumab 154 (51) Mutant 91 versus WT Mutant 66% versus WT Mutant 86 versus WT
(R/R)145 (ibrutinib 92 (ibrutinib arm) 81% (ibrutinib arm)d 81 (ibrutinib arm)d
arm)
Idelalisib–rituximab versus 110 (46) – Mutant ~75% versus –
rituximab (R/R)135 WT 74% (idelalisib–
rituximab arm)e
Idelalisib–rituximab (frontline)154 64 (14) Mutant 100 versus Mutant 100% versus Mutant 100% versus
WT 96 WT 90%c WT 90%c
Venetoclax (R/R)138 107 (72) 79 (all patients) ~70% (all patients)e ~85% (all patients)e
ATM CIT Chlorambucil versus 161 (12.4) Odds ratio for WT HR for WT versus HR for WT versus
and/or chlorambucil plus versus mutant: 1.3 mutant: 1.5 (all arms) mutant: 0.8 (all arms)
del11q rituximab versus (all arms)
chlorambucil plus
obinutuzumab (frontline)190
Targeted Ibrutinib versus ofatumumab 154 (19) Mutant 93 versus Mutant 78% versus WT –
(R/R)145 WT 91 (ibrutinib arm) 73% (ibrutinib arm)d
Idelalisib–rituximab 160 (21) Mutant 85 versus – –
(frontline, R/R)192 WT 76
SF3B1 CIT Chlorambucil versus 437 (17) – Mutant 29 versus WT Mutant 54 versus
fludarabine versus fludarabine 39 (all arms)a WT 79 (all arms)a
plus cyclophosphamide
(frontline)193
Chlorambucil versus 161 (15.5) NS NS NS
chlorambucil plus
rituximab versus
chlorambucil plus
obinutuzumab (frontline)190
Fludarabine plus 628 (18) • Mutant 89 versus WT • Mutant 29 versus WT • Mutant 76
cyclophosphamide versus 88 (fludarabine plus 34 (fludarabine plus versus WT 86
FCR (frontline)70 cyclophosphamide cyclophosphamide (fludarabine plus
arm) arm)a cyclophosphamide
• Mutant 96 versus WT • Mutant 43 versus WT arm)
96 (FCR arm) 59 (FCR arm)a • Mutant NR versus
WT NR (FCR arm)
Allo-​HSCT Allo-​HSCT (R/R)142 72 (26) – HR for mutant versus HR for mutant versus
WT: 0.63 WT: 0.79
Targeted Ibrutinib versus ofatumumab 154 (31) Mutant 96 versus WT Mutant 65% versus –
(R/R)145 95 (ibrutinib arm) WT 79% (ibrutinib
arm)d

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Table 3 (cont.) | Predictive value of genetic lesions according to treatment type.

genetic Treatment Study treatments (setting) number of ORR (%) mPFS (months) mOS (months)
lesion type patients
(% mutated)
NOTCH1 CIT Chlorambucil versus fludarabine 466 (10) – Mutant 22 versus WT Mutant 55 versus WT
versus fludarabine plus 27 (all arms)a 75 (all arms)a
cyclophosphamide (frontline)193
Chlorambucil versus 161 (20) NS NS NS
chlorambucil plus rituximab
versus chlorambucil plus
obinutuzumab (frontline)190
Fludarabine plus 628 (10) • Mutant 87 versus WT • Mutant 33 versus WT • Mutant 86 versus WT
cyclophosphamide versus 88 (fludarabine plus 34 (fludarabine plus 84 (fludarabine plus
FCR (frontline)70 cyclophosphamide cyclophosphamide cyclophosphamide
arm) arm) arm)
• Mutant 90 versus WT • Mutant 34 versus WT • Mutant 79 versus WT
96 (FCR arm) 57 (FCR arm)a NR (FCR arm)
Allo-​HSCT Allo-​HSCT (R/R)142 72 (14) – HR for mutant versus HR for mutant versus
WT: 0.69 WT: 0.68
Targeted Ibrutinib versus ofatumumab 154 (28) Mutant 93 versus WT Mutant 72% versus WT –
(R/R)145 91 (ibrutinib arm) 74% (ibrutinib arm)d
POT1 CIT Chlorambucil versus 161 (8.7) NS NS HR for WT versus
chlorambucil plus rituximab mutant: 2.9 (CIT arms)a
versus chlorambucil plus
obinutuzumab190 (frontline)
BIRC3 Targeted Ibrutinib versus ofatumumab 154 (14) Mutant 95 versus WT Mutant 81% versus WT –
(R/R)145 95 (ibrutinib arm) 72% (ibrutinib arm)d
Allo-​HSCT, allogeneic haematopoietic stem cell transplantation; CIT, chemoimmunotherapy ; FCR , fludarabine plus cyclophosphamide plus rituximab; HR , hazard
ratio; mOS, median overall survival; mPFS, median progression-​free survival; NR , not reached; NS: not significant; ORR , overall response rate; R/R , relapsed and/or
refractory ; WT, wild-​type. aStatistically significant; bAt 60 months; cAt 24 months; dAt 18 months; eAt 12 months.

of action, ibrutinib is active against CLL subtypes with
genetic lesions traditionally associated with resistance
to chemoimmunotherapy, namely TP53 or SF3B1
lesions144 (Table 3). Post-​hoc analyses performed in the
RESONATE trial, in which ibrutinib was compared with
ofatumumab in patients with relapsed and/or refractory
(R/R) CLL, showed that the overall response rate (ORR),
PFS and OS in the ibrutinib arm were not influenced
by the presence of genetic lesions in ATM, NOTCH1,
SF3B1 or BIRC3, although longer follow-​up is needed
to conclusively validate these findings145. Conversely, the
presence of genetic lesions in TP53 is correlated with
inferior ORR and PFS in patients with R/R CLL treated
with ibrutinib, suggesting that, despite their superior
activity over chemoimmunotherapy in CLLs with TP53
lesions, current targeted therapies are not the final
curative solution for CLL146.
Sequential analysis of clonal dynamics in patients
with CLL treated with ibrutinib did not reveal the
expansion of clones displaying common genetic driv-
ers, for example SF3B1 or TP53 mutations45,147, which
is in contrast to the observation in patients treated with
chemoimmunotherapy41. Conversely, genetic analysis of
patients with CLL with disease progression during ibru-
tinib treatment enabled the identification of potential
mechanisms of resistance (Fig. 3). Ibrutinib binds cova-
lently to the sulfhydryl group of C481 in the active site of
BTK, resulting in the irreversible inhibition of its kinase
activity. More than 80% of patients with acquired resist-
ance to ibrutinib harbour recurrent mutations involving
the ibrutinib binding site of BTK (BTKC481S) or the BCR
signalling gene PLCG2 (PLCG2R665W, PLCG2L845F and
PLCG2S707Y)147–149. BTKC481S mutations prevent the cova-
lent binding of ibrutinib to the BTK active site, resulting
in a loss of inhibition of BTK enzymatic activity148,150.
In addition, PLCG2 mutations are potentially gain-​of-
function lesions that promote BCR-​mediated signal-
ling independent of BTK inhibition148. Notably, the use
of highly sensitive technologies (for example, droplet
microfluid technologies) has enabled the detection of
these mutations before the start of ibrutinib treatment147,
reinforcing the concept that external selection pressure
exerted by targeted therapies contributes to the selection
of rare subclones that are already present before ther-
apy. Indeed, BTK and PLCG2 gene mutations have been
described in ibrutinib-​treated patients with CLL up to
15 months preceding the clinical relapse149,151, and they seem
to occur with greater frequency in elderly patients with a
complex karyotype or TP53 disruptions149. Accordingly,
serial exome and transcriptome sequencing of patients
with CLL treated with ibrutinib revealed the presence of
baseline mutations in pivotal downstream regulators
of BTK (for example, ITPKB and CDIPT) in one-​third of
patients, which were associated with unfavourable PFS45.
In addition, mutations in ITPKB45, which have previ-
ously been described in lymphomas, and expansion
of clones with deletions of 8p (del8p), which induces
haploinsufficiency of the TRAIL receptor (TRAIL-​R), are
genetic abnormalities that arise in patients who develop
resistance to ibrutinib45,147. Nevertheless, additional
experimental data, including analyses in animal models,
are needed to determine the exact role of these mutations
in the emergence of resistance to ibrutinib. A small frac-
tion of patients (~5%) receiving ibrutinib can develop a

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 Reviews

Active CLL the definition of a complex karyotype, the best method

to assess it, and its predictive influence with respect to
the targeted therapies remains to be established.
The BCR pathway has also been targeted by down-
TP53 wild type del17p and/or
TP53 mutation stream inhibition of PI3K. Idelalisib, a selective small-​
molecule inhibitor of PI3K catalytic subunit δ isoform
(PI3Kδ; also known as p110 δ isoform), which is speci­
IGHV-M, del13q IGHV-UM fically expressed in the haematopoietic compartment,
or trisomy 12 or del11q
has shown activity alone and in combination with rituxi­
mab in several B cell lymphoproliferative disorders135,154.
Although idelalisib is active in CLLs harbouring TP53
Fit Unfit Ibrutinib • Ibrutinib
• Ibrutinib • Ibrutinib • Venetoclax (if disruptions, data on the activity of this drug in the pres-
• FCR (BR >65 years) • Chlorambucil not candidate ence of other genetic lesions in CLL are limited (Table 3).
and CD20 mAb for ibrutinib) Along the same lines, little is known about the potential
molecular mechanisms of resistance to idelalisib.
In CLL, the BCL2 protein family members that regu-
R/R disease late the apoptotic process are skewed towards preventing
apoptosis for reasons that are not fully elucidated58,155,156.
Accordingly, blocking BCL2 protein function using the
BCL2 homology region 3 (BH3) mimetic venetoclax
R/R to CIT Intolerant of R/R to ibrutinib
ibrutinib leads to apoptosis in CLL cells and excellent oncologi­cal
control of the disease137. Venetoclax is highly active in
• Venetoclax patients with CLL with del17p and/or TP53 gene dys-
• Idelalisib + rituximab
• Clinical trial
regulation, which is consistent with its p53-independent
mechanism of action137,138. However, complex karyo­
types, but not TP53 disruption, predict progression
• Ibrutinib • Venetoclax + rituximab Cell therapy in patients treated with venetoclax121. A comparative
• Venetoclax + rituximab • Idelalisib + rituximab • Allo-HSCT
• Idelalisib + rituximab • CAR T cells genomic analysis of eight patients with CLL that was
resistant to or had progressed after venetoclax treatment,
Fig. 4 | Therapeutic algorithm for patients with Cll. Patients with chronic lymphocytic half of whom had a Richter syndrome transformation,
leukaemia (CLL) should be treated when they fulfil the International Workshop on Chronic showed acquisition of lesions in SF3B1 (subclonal), loss
Lymphocytic Leukemia (iwCLL) criteria8 for active disease. CLLs with TP53 disruptions of CDKN2A and/or CDKN2B, mutations in BRAF and
should be treated with ibrutinib or venetoclax (in patients who are not candidates for amplifications of CD274 (which encodes programmed
ibrutinib)158. In fit patients with low-​risk (that is, IGHV-​M status, del13q4 or trisomy 12) TP53 cell death 1 ligand 1 (PD-​L1))122. Functional studies in
wild-​type CLL , chemoimmunotherapy (CIT) combinations lead to similar outcomes to the same small panel of patients revealed that BRAF
ibrutinib, whereas the preferred treatment in unfit patients with low-​risk CLL is ibrutinib mutations, but not CDKN2A and/or CDKN2B deletions,
over combinations of chlorambucil and obinutuzumab or other anti-​CD20 antibodies
were associated with venetoclax resistance. Importantly,
(rituximab or ofatumumab)158,161. A general consensus exists on the use of front-​line ibrutinib
in patients with high-​risk CLL , even those without TP53 abnormalities. In patients with at the end of 2018, a study revealed that some patients
relapsed/refractory (R/R) disease after CIT, the most recommended options are ibrutinib or who are resistant to venetoclax acquire the hetero­
venetoclax plus rituximab, whereas idelalisib plus rituximab can be considered as the third zygous BCL2G101V mutation, which reduces sensitivity to
option133,135,145,158,167,184. Patients with R/R disease who are intolerant of ibrutinib can be venetoclax in vitro. The clinical influence of this muta-
salvaged with venetoclax plus rituximab or idelalisib plus rituximab. Finally , patients tion, usually detected at a low variant allele fraction,
progressing after ibrutinib can be treated with venetoclax plus rituximab or idelalisib plus requires confirmation157.
rituximab, or included in clinical trials, and subsequently considered for a cell therapy
depending on the characteristics of the patient and donor. Allo-​HSCT, allogeneic Influence on treatment strategies
haematopoietic stem cell transplantation; BR , bendamustine plus rituximab; During the past 5 years, the dissection of the genetic
CAR , chimeric antigen receptor ; FCR , fludarabine plus cyclophosphamide plus rituximab;
lesions underpinning CLL, along with the advent
mAb, monoclonal antibody.
of novel drugs, has shifted the treatment strategy in
patients with CLL from universal chemoimmunotherapy
Richter syndrome that is clonally related to the under- to a more individualized approach. At diagnosis, assess-
lying CLL, usually during the first 2 years of treatment ment of IGHV mutational status, molecular cytogenetics
and sometimes with bone marrow involvement120 (Fig. 3). (using FISH) and mutational analysis of the TP53 gene
These transformations typically exhibit MYC gains and are currently recommended in the iwCLL guidelines to
lack the common BTK and PLCG2 mutations. ascertain the prognostic risk in a given patient105. In a
The presence of complex karyotypes has been asso- patient requiring treatment, these molecular tests are
ciated with inferior responses to both chemoimmuno­ mandatory because they help in identifying the best
therapy and ibrutinib 149, suggesting that genomic therapeutic strategy (Fig. 4). In patients included in clini­
instability has an unfavourable effect on response to cal trials, the additional analysis of biomarkers directly
treatment. Data from 2018 suggest that the adverse influ- informing the response to targeted therapy is advisable.
ence of complex karyotypes in half the patients treated Finally, complex karyotype analysis, although poten-
with ibrutinib is independent of the presence of TP53 tially useful in predicting response, is still considered
genetic abnormalities152,153. Nonetheless, a consensus on investigational.

Nature Reviews | Clinical Oncology

Reviews
First-​line treatment algorithm
A general consensus exists that treatment-​naive patients
requiring therapy should be tested for the presence of
del17p and TP53 disruptions (Fig. 4). If these lesions
are present, even at the subclonal level75, these patients
should not be treated with genotoxic drugs (alkylating
agents, anthracyclines or purine analogues), given that
genetic lesions hampering DNA repair predict a poor
response38,75,82. Indeed, the median PFS of patients with
CLL harbouring TP53 lesions treated using FCR or
other chemoimmunotherapy combinations is less than
18 months71. Thus, these patients are candidates for ther-
apies with mechanisms of action not requiring the pres-
ence of an intact and functional DNA repair machinery.
Ibrutinib is the most recommended upfront treatment in
patients with TP53 mutations158, leading to an estimated
median PFS of more than 30 months152. In patients who
are not eligible to receive ibrutinib (for example, owing
to specific comorbidities, drug interactions or patient
choice), venetoclax is an excellent alternative138.
In patients without TP53 disruptions, assessment of
the IGHV mutational status and physical fitness are key
to individualized treatment. Long-​term follow-up data
from patients with CLL treated with FCR, the mainstay
of chemoimmunotherapy in CLL, show that approxi-
mately half of the patients with IGHV-​M CLL have a
durable response of more than 10 years128,130. Thus, FCR
or bendamustine plus rituximab (BR) have been the pre-
ferred chemoimmunotherapy regimens for fit patients
with IGHV-​M disease, whereas less intense combina-
tions of chlorambucil with a CD20 monoclonal antibody
(such as obinutuzumab, ofatumumab or rituximab) can
be recommended for those patients who will probably
not tolerate FCR or BR128–130,159. However, data published
in 2018 and 2019 from three indepen­dent randomized
clinical trials showed that, in low-​risk patients with
CLL, ibrutinib with or without monoclonal anti-​CD20
antibodies leads to PFS outcomes similar to those of
chemoimmunotherapy160–162Although additional follow-​
up monitoring is still required, these data indicate that
ibrutinib should be placed at the same level as chemo­
immunotherapy in the therapeutic algorithm. Notably, in
the clinically unfit patients with TP53 wild-​type disease,
ibrutinib is usually the preferred option owing to both
its high activity leading to an estimated PFS of 75% at
4 years, and its good safety profile145,158,163. By contrast,
patients with IGHV-​UM CLL have a PFS of 33% at
5 years when treated with chemoimmuno­therapy130. For
this high-​risk population, a growing consensus exists on
the use of ibrutinib in the front-​line setting, regardless of
age and comorbidities (reviewed in164). This consensus
is based on the observation that IGHV mutational status
does not influence PFS in patients treated with ibruti-
nib146, which was confirmed in 2019 by the results of the
aforementioned clinical trials160–162.
An important aspect of BTK inhibitor therapy is that
it should be administered continuously because minimal
residual disease (MRD)-negative responses cannot be
achieved with these agents145. This characteristic trans-
lates into several issues relating to long-​term toxicities,
compliance, drug interactions and cost. Thus, the use
of ibrutinib before chemoimmunotherapy in patients
with low-​risk CLL will still be a subject of debate until
mature results from ongoing randomized clinical trials
comparing both treatments provide conclusive data on
this issue.
Treatment of relapsed/refractory CLL
Salvage chemoimmunotherapy in patients with R/R CLL
who have previously been treated with chemotherapy
leads to short-​lasting responses, with a median PFS of
less than 2 years165,166. This suboptimal response is mainly
due to the acquisition of resistant clones selected by pre-
vious therapies (Fig. 3) and to difficulties in completing
the planned treatment owing to their excessive toxicity.
In the setting of R/R CLL after chemoimmunotherapy,
a clear indication exists for the use of targeted therapies
(Fig. 4). The median PFS in heavily pretreated patients
receiving salvage therapy with ibrutinib is 51 months146.
The combination of venetoclax plus rituximab was
approved in 2018 by the FDA for this indication, and
is an interesting early option for the treatment of R/R
CLL167. Approximately 15% of patients in the frontline
and the R/R settings develop resistance to ibrutinib
(parti­cularly those with TP53 disruptions), which is
probably attributable to the aforementioned molecular
mechanisms of resistance to ibrutinib. Around 65% of
these patients respond to venetoclax168, but they should
be further considered for allogeneic HSCT, chimeric
antigen receptor (CAR) T cell therapy or participation
in clinical trials, given that the median time to progres-
sion of patients failing to ibrutinib and treated with
venetoclax is ~25 months.
Several additional BTK inhibitors are currently
being tested, alone and in combination, in the front-
line and the R/R settings (Fig. 2). Acalabrutinib (ACP-
196), which was approved for treatment of mantle cell
lymphoma in 2018, seems to have a better toxicity pro-
file than ibrutinib owing to its greater specificity and,
therefore, fewer off-​target effects. Despite the fact that
acalabrutinib results in an ORR of 95% in patients with
R/R disease169, whether this agent is more active than
ibrutinib requires a longer follow-​up and the results
of a phase III study comparing acalabrutinib versus
ibrutinib (NCT02477696). Vecabrutinib (SNS-062) is
another BCR inhibitor that seems to be active in vitro
in CLL cells with the common BTKC481S resistance muta-
tion170 and in a preliminary study using a CLL adop-
tive transfer model171. Whether or not this will translate
into adequate clinical activity is currently being eval-
uated in a clinical trial (NCT03037645)172. Other BTK
inhibitors (BGB-3111 (NCT03336333), CT-1530
(NCT02981745), tirabrutinib (NCT03740529), M7583
(NCT02825836), DTRMWXHS (NCT02891590) and
CC-292 (NCT01744626)) and SYK inhibitors (entos-
pletinib (NCT02983617), TAK-659 (NCT02954406)
and cerdulatinib (NCT01994382)) are currently under
investigation in R/R CLL (Fig. 2).
Idelalisib, an inhibitor of PI3Kδ, has also been
approved in combination with rituximab for the
treatment of CLL135. Unfortunately, PI3Kδ inhibition
has been associated with a particular toxicity profile
characterized by autoimmune complications and an
increased risk of opportunistic infections, particularly
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 Reviews

in treatment-​naive patients (diarrhoea 42%, pneumo-
nitis 20% and hepatotoxicity 16%)173. Thus, the use of
idelalisib is usually restricted to patients with R/R dis-
ease after treatment with ibrutinib or venetoclax. In addi-
tion, duvelisib was approved at the end of 2018 for the
treatment of R/R CLL based on a randomized clinical
trial (NTC02004522) comparison of this agent against
ofatumumab174. Other PI3K inhibitors, some of which
have toxicity profiles distinct from that of idelalisib,
are currently under investigation in clinical trials in
patients with CLL and other lymphoproliferative dis­
orders in the R/R setting (umbralisib (NCT02268851)
and YY-20394 (NCT03757000)). Finally, other com-
pounds targeting specific pathways, including NOTCH1
signalling (CB-103 (NCT03422679), brontictuzumab
(NCT01703572), RO4929097 (NCT01158274),
LY3039478 (NCT01695005) and Pf-03084014
(NCT00878189)), inhibition of nuclear export of proteins
(selinexor (NCT02303392), RNA processing (SL-801
(NCT02667873)), inflammatory pathways (IMO-8400
(NCT02363439) and CA-4948 (NCT03328078)), MCL-1
inhibitors (MIK665 (NCT02992483) and AMG176
(NCT03797261)) and the DNA damage response
pathway (AZD6738 (NCT01955668), BAY1895344
(NCT03188965), APR-246 (NCT00900614) and COTI-2
(NCT02433626)) are currently under investigation in
early phase clinical trials (Fig. 2).
No standard treatment strategy exists for patients
with Richter syndrome. Most of these patients have
TP53 disruptions, which preclude the response to the
rituximab–cyclophosphamide, doxorubicin, vincristine
and prednisone (R-​CHOP)-like chemotherapy regimens
that are usually used in patients with high-​grade lym-
phoma (reviewed in114). Of note, interesting data have
been obtained with the combination of ibrutinib or other
BCR inhibitors and immune-​checkpoint inhibitors175,176.
Of patients with Richter transformation who were pre-
viously refractory to chemoimmunotherapy, 65% had
a response to treatment with ibrutinib plus nivolumab.
Unfortunately, responses to chemotherapy or immune-​
checkpoint inhibitors are generally less than 12 months.
Thus, patients with Richter transformation usually
undergo consolidation cell therapy with allogeneic
HSCT or CAR T cell therapy177,178.
Novel targeted therapies have been combined with
the aim of achieving synergistic activities that could
translate into deeper responses and shorter treatment
schedules than those associated with continuous admin-
istration of ibrutinib (reviewed in179). Preliminary results
with the combinations of ibrutinib and venetoclax,
venetoclax and obinutuzumab or the triplet bendamus-
tine, obinutuzumab and venetoclax showed ORRs of
>90%, including a substantial number of patients with
undetectable MRD responses, with a low toxicity pro-
file in patients with R/R CLL180–183. Nonetheless, iden-
tification of the long-​term activity or toxicity as well as
the best way to combine or sequence these treatments
await the results of the numerous ongoing clinical trials
(NCT02756897, NCT03128879 and NCT02950051).
Conclusions
During the past 5 years, great progress has been made
in the clinical application of new genomic methods for
dissecting the genetic aetiology of CLL as well as in the
identification of patterns of clonal evolution, clinical
progression and therapeutic resistance. Accordingly,
new prognostic and predictive biomarkers and novel
targeted therapies have been developed, which are
being translated into improved risk stratification tools,
prolonged PFS and, ultimately, extended OS in patients
with CLL. However, this progress has opened the door
to new challenges in several major areas. Clear evi-
dence is emerging that most genetic events leading to
tumour progression or drug resistance are present in
very early pretreatment stages of the disease, and that
their stochastic accumulation is positively correlated
with the number of tumour cells and their divisions.
Thus, future studies should explore earlier therapeutic
interventions at diagnosis or even during clinical remis-
sions in patients with high-​risk disease, when the hetero­
geneity and abundance of different subclones are still
generally low. Furthermore, the responses to targeted
therapies, for instance to ibrutinib and venetoclax, are
very encouraging, yet the determinants of response or
non-​response are only partially understood. Thus, the
coupling of each clinical trial with extensive, prospective
searches for biomarkers of response is needed. Finally,
the enormous and growing costs of the new drugs pose
formidable socioeconomic challenges that go far beyond
any strictly biomedical considerations.
Published online xx xx xxxx

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Acknowledgements
The work of the authors is supported by grants to F.B. from
the Ministry of Economy and Competitiveness, Instituto de
Salud Carlos III (17/00943) and to R.D.-F. from the US
Department of Health & Human Services, NIH, National
Cancer Institute (NCI) (1R35CA210105).
Author contributions
The authors contributed equally to all aspects of the article.
Competing interests
The authors declare no competing interests.
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Reviewer information
Nature Reviews Clinical Oncology thanks S. Stilgenbauer,
J. Burger and M. Hallek, for their contribution to the peer
review of this work.
Related links
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