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Regular Article

CLINICAL TRIALS AND OBSERVATIONS

Impact of BCR-ABL transcript type on outcome in patients with

chronic-phase CML treated with tyrosine kinase inhibitors
Preetesh Jain,1,2 Hagop Kantarjian,1 Keyur P. Patel,3 Graciela Nogueras Gonzalez,4 Rajyalakshmi Luthra,3
Rashmi Kanagal Shamanna,3 Koji Sasaki,1 Elias Jabbour,1 Carlos Guillermo Romo,1 Tapan M. Kadia,1 Naveen Pemmaraju,1
Naval Daver,1 Gautam Borthakur,1 Zeev Estrov,1 Farhad Ravandi,1 Susan O’Brien,1,5 and Jorge Cortes1
1
Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX; 2Department of Internal Medicine, University of Texas
Medical School at Houston, Houston, TX; 3Department of Hematopathology and 4Department of Biostatistics, The University of Texas MD Anderson Cancer
Center, Houston, TX; and 5Chao Family Comprehensive Cancer Center, University of California Irvine Medical Center, Orange, CA

The most common breakpoint cluster region gene-Abelson murine leukemia viral
Key Points
oncogene homolog 1 (BCR-ABL) transcripts in chronic myeloid leukemia (CML) are
• Patients with e13a2 e13a2 (b2a2) and e14a2 (b3a2). The impact of the type of transcript on response and
transcripts have inferior survival after initial treatment with different tyrosine kinase inhibitors is unknown. This
outcomes with imatinib 400; study involved 481 patients with chronic phase CML expressing various BCR-ABL
e14a2 has favorable transcripts. Two hundred patients expressed e13a2 (42%), 196 (41%) expressed e14a2,
and 85 (18%) expressed both transcripts. The proportion of patients with e13a2, e14a2,
outcomes regardless of
and both achieving complete cytogenetic response at 3 and 6 months was 59%, 67%, and
treatment modality.
63% and 73%, 81%, and 82%, respectively, whereas major molecular response rates were
• Multivariate analysis showed 27%, 49%, and 50% at 3 months, 42%, 67%, and 70% at 6 months, and 55%, 83%, and 76% at
that the expression of e14a2 or 12 months, respectively. Median (international scale) levels of transcripts e13a2, e14a2,
both e14a2 and e13a2 predicts and both at 3 months were 0.2004, 0.056, and 0.0612 and at 6 months were 0.091, 0.0109,
optimal ELN responses and and 0.0130, respectively. In multivariate analysis, e14a2 and both predicted for optimal
longer EFS and TFS. responses at 3, 6, and 12 months. The type of transcript also predicted for improved
probability of event-free (P 5 .043; e14a2) and transformation-free survival (P 5 .04 for
both). Compared to e13a2 transcripts, patients with e14a2 (alone or with coexpressed e13a2) achieved earlier and deeper responses,
predicted for optimal European Leukemia Net (ELN) responses (at 3, 6, and 12 months) and predicted for longer event-free
and transformation-free survival. (Blood. 2016;127(10):1269-1275)

Introduction
The Philadelphia (Ph) chromosome resulting from the balanced recip-
rocal translocation between chromosomes 9 and 22 t(9;22)(q34;q11.2)
is the cytogenetic hallmark of chronic myeloid leukemia (CML).1-3
This balanced reciprocal translocation results in the formation of
the BCR-ABL1 oncogene, which is translated into a protein with
constitutive tyrosine kinase activity, possibly the most effectively
therapeutically targeted oncoprotein.4,5 The breakpoints in the BCR
gene on chromosome 22 most commonly occur between exons
e12 (b2) and e13 (b3) or between e13 (b3) and e14 (b4), in the major
breakpoint cluster region (M-BCR), generating 2 slightly different
chimeric transcripts.6-8 The breakpoint in the ABL1 gene is usually
located between exons a1 and a2. These breakpoints result in various
BCR-ABL rearrangements, most commonly the e13a2 (b2a2) and
e14a2 (b3a2), which code for a 210-kDa protein: p210. In some
patients, both transcripts can be coexpressed: e13a2 (b2a2) with
e14a2 (b3a2). Less frequently, the break in BCR occurs between
exons 1 and 2, generating the e1a2 transcript, which codes for a
190-kDa protein, or between exons 19 and 20, generating the e19a2
transcript that codes for a 230-kDa protein.6,9-13 More rarely, other
variants such as e14a3 (b3a3)14 and e8a2 transcripts15 are described.
The prognostic significance of the BCR-ABL1 transcripts16,17 has
been reported from patients treated with interferon alone18 or imatinib
400 mg.19 Improved response has been reported in patients carrying the
e14a2 (b3a2) transcript compared with those with the e13a2 (b2a2)
transcripts after treatment with standard-dose imatinib.14,19-24 This
observation correlates with higher activity of phospho CrKL (CT10
regulator of kinase-like) a surrogate marker of BCR-ABL1 tyrosine
kinase activity in patients with e13a2 transcripts.25 Secondary structure
elements are different in e14a2 due to the presence of extra 25 amino
acids not seen in e13a2 transcripts, possibly indicating that e14a2
and e13a2 transcripts may have different roles in mediating signal
transduction pathways in CML.26
Our group has previously reported higher rates of molecular
response and a better trend for transformation-free survival (TFS) for
patients treated with imatinib who presented with e14a2 transcripts.24
The second-generation tyrosine kinase inhibitors (2GTKIs) dasatinib

Submitted October 7, 2015; accepted December 18, 2015. Prepublished The publication costs of this article were defrayed in part by page charge
online as Blood First Edition paper, January 4, 2016; DOI 10.1182/blood-2015- payment. Therefore, and solely to indicate this fact, this article is hereby
10-674242. marked “advertisement” in accordance with 18 USC section 1734.

The online version of this article contains a data supplement. © 2016 by The American Society of Hematology

BLOOD, 10 MARCH 2016 x VOLUME 127, NUMBER 10 1269

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1270 JAIN et al BLOOD, 10 MARCH 2016 x VOLUME 127, NUMBER 10

and nilotinib have improved the responses in patients when used Table 1. Patient characteristics according to the type of BCR-ABL
either as front-line therapy or as second-line treatment after imatinib transcript
failure.27-29 To our knowledge, none of the previously published No. (%),or median [interquartile range]
studies have systematically analyzed the responses and survival e13a2 and
outcomes in patients treated with imatinib 400, imatinib 800, and Characteristic e13a2 e14a2 e14a2 P

2GTKI as initial therapy for CML according to the type of BCR-ABL1 N 200 (42) 196 (41) 85 (18)
transcripts. Age, years [range] 47 [37-57] 49 [39-58] 52 [41-61] .11
In this analysis, we evaluated the prognostic relevance of commonly Hemoglobin (g/dL) 12 (11-13) 12 (11-13) 13 (12-14) .32
WBC (K/mL) 31 (12-71) 28 (17-63) 30 (13-70) .94
expressed BCR-ABL1 transcripts in patients with chronic phase
Platelet (K/mL) 288 (200-418) 405 (276-592) 358 (268-493) .001
CML treated with 4 different front-line TKI modalities. The objective
Sokal score
of this analysis was to determine the prognostic significance of High 11 (5) 11 (6) 9 (11) .53
transcript types across patients with CML–chronic phase treated Intermediate 47 (23) 48 (24) 21 (25)
with different TKI modalities. Low 142 (71) 137 (70) 55 (65)
Treatment type
Imatinib 400 mg 31 (15) 28 (14) 10 (12) .32
Imatinib 800 mg 82 (41) 89 (45) 28 (33)
Dasatinib 41 (20) 38 (19) 26 (31)
Patients and methods Nilotinib 46 (23) 41 (21) 21 (25)
Median follow-up 88 [43-122] 98 [49-127] 84 [46-115] .18
Patients (months)

All patients with chronic phase CML enrolled in consecutive or parallel clinical
trials at The MD Anderson Cancer Center using TKI as front-line therapy from
July 31, 2000 to September 10, 2013 were included in this analysis. Patients were
treated on protocols approved by the institutional review board, and informed
consent was obtained in accordance with the Declaration of Helsinki. Eligibility
criteria, follow-up, and response assessment were similar for all trials:
cytogenetic analysis every 3 months for the first year, then every 6 months
for the next 2 to 3 years, and then every 1 to 2 years. Real-time polymerase
chain reaction was generally assessed every 3 months for the first year and
then every 6 months. Response criteria were as previously described.30
Only patients with BCR-ABL transcripts e13a2 (previously b2a2), e14a2
(previously b3a2), and coexpressed e13a2 (b2a2) with e14a2 (b3a2) were
included in the analyses. Demographic and baseline disease characteristics
were collected at baseline. The differences between variables were analyzed
by the x2 test and the Kruskal-Wallis test for categorical and continuous
variables. Of note, all patients treated with imatinib 400 initiated therapy
between May 2001 and June 2001 when molecular analysis was not routinely
done before achievement of complete cytogenetic response (CCyR); therefore,
molecular response at 3 months is not available for the imatinib 400 cohort.
Statistical analysis
Event-free survival (EFS) was measured from the start of treatment to the
date of any of the following events (as defined in the International
Randomized Study of Interferon and STI571)31 while on therapy: loss of
complete hematologic remission, loss of major cytogenetic response
(MCyR), progression to accelerated (defined as blasts $15%, blasts 1
promyelocytes $30%, basophils $20%, platelets ,100 3 109/L, unrelated
to therapy, or cytogenetic clonal evolution) or blast phase (defined as
blasts $30%, or extramedullary disease), or death from any cause at any
time while on study. Overall survival (OS) was measured from the time
treatment was started to the date of death from any cause at any time or date
of last follow-up. TFS was measured from the start of therapy to the date of
transformation to accelerated or blast phase while on therapy or deaths on
study (ie, deaths on initial TKI).
Survival probabilities were estimated by the Kaplan-Meier method
and compared by the log-rank test. Univariate and multivariate analyses
were performed to identify whether the type of transcript can predict
for cytogenetic and molecular responses at different time points and/or
survival outcomes. Variables with P # .10 in the univariate analysis were
entered into a multivariate model and analyzed using the Cox proportional
hazard regression. P , .05 was considered significant. Survival end points
were analyzed using the Kaplan-Meier method, and differences were
calculated by the log-rank test. Statistical analyses were carried out using
STATA/SE version 13.1 statistical software (Stata Corp. LP, College
Station, TX).
Results
Patients
Overall, 487 patients with previously untreated chronic phase CML
were treated with different TKI modalities, of which 481 patients
expressing e13a2, e14a2, or coexpression of e13a2 with e14a2 tran-
scripts (both) were included in this analysis. Six patients with variant
transcripts (e1a2, n 5 4; b3a3, n 5 2) were excluded from this analysis.
Patients were treated with 4 different frontline TKI modalities: imatinib
400 mg daily (n 5 69), imatinib 800 mg daily (n 5 199), dasatinib
50 mg twice daily or 100 mg daily (n 5 105), or nilotinib 400 mg twice
daily (n 5 108). The baseline characteristics of the patients are
summarized in Table 1. Two hundred patients (42%) expressed e13a2,
196 (41%) expressed e14a2, and 85 (18%) expressed both transcripts.
Patients with e13a2 had significantly lower platelets (median, 288 K/mL;
range, 15-1906 K/mL) compared with e14a2 or both (median,
405 K/mL; range 77-1476 K/mL; and 358 K/mL; range, 100-2928 K/mL,
respectively; P , .001). Patient characteristics were also comparable for
patients treated with the different TKI modalities. Median follow-up
was longer for patients treated with imatinib than with 2GTKI. Disease
transformation occurred in 21 patients (4%) (blast phase, n 5 7;
accelerated phase, n 5 14), and 14 (3%) patients died on study. Of
the 21 patients with transformation to accelerated or blast phase, 15
expressed e13a2 (representing 8% of all patients with e13a2), 6 patients
expressed e14a2 (3% of all e14a2 patients), and none coexpressed both
transcripts (P 5 .04). The distribution of patients who transformed to
accelerated or blast phase (n 5 21) by Sokal risk categories were as
follows: low risk, 13 (62%); intermediate, 6 (28%); high risk, 2 (9%). A
total of 52 (11%) patients died (n 5 26 for e13a2, n 5 20 for e14a2, and
n 5 6 for both), including the 14 who died while on study. Events
occurred in 77 (16%) patients.
Cytogenetic and molecular responses according to
transcript type
Only patients with values available at the time of assessment were
included in this analysis. Absolute numbers of evaluable patients
according to type of transcript are shown in Figure 1. Cumulative
response rates according to the transcript type were as follows: CCyR,
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BLOOD, 10 MARCH 2016 x VOLUME 127, NUMBER 10 BCR-ABL TRANSCRIPTS AND TKI IN CML 1271

Figure 1. Analysis of major cytogenetic and molec-

ular responses (£10% or £1%) for BCR-ABL at 3 and
6 months according to the type of BCR-ABL transcript
(e13a2, e14a2, or both). (A) Achievement of MCyR
(#35% Ph-positive metaphases). (B) Achievement of
molecular response (#1% and #10% BCR-ABL-IS) at
3 and 6 months. Percentages are shown at the top, and
the absolute numbers of evaluable patients are shown
at the bottom of each graph. (C) Pattern of changes in
median BCR-ABL transcript levels (IS) over time (3, 6,
12, 18, 24, 36, and 60 months) according to the type of
BCR-ABL transcript (log scale). IS, international scale.

e13a2 (89%), e14a2 (94%), and both (94%), P 5 not significant;
MMR, e13a2 (79%), e14a2 (91%), and both (95%), P 5 .0001; and
MR4.5, e13a2 (57%), e14a2 (79%), and both (80%), P 5 .00001
(supplemental Figure 1A, available on the Blood Web site). We then
assessed the response rates by TKI modality for each transcript cohort
(supplemental Figure 1B-D). For CCyR, patients with e13a2 who
received imatinib 400 had an inferior response rate (77%) compared
with other TKI modalities (90-95%); this trend was not observed in
patients with e14a2 or both transcripts where CCyR rate with imatinib
400 (93%) was similar to other treatment modalities (93-96%). Sim-
ilarly, for MMR and MR4.5, patients with e13a2 treated with imatinib
400 had a trend for an inferior response rate compared with those treated
with other TKI modalities. Of note, MMR and MR4.5 rates were
generally similar in all TKI modalities for patients with e14a2
transcripts except for patients treated with nilotinib, who showed a
somewhat inferior rate of MR4.5 in both the e13a2 and e14a2 cohorts
compared with patients treated with imatinib 800 or dasatinib (sup-
plemental Figure 1D).
We then analyzed response rates at different time points. For e13a2,
e14a2, and coexpression cohorts, the proportion of patients achieving
CCyR at 3 months was 59%, 67%, and 63%, respectively, and 73%,
81%, and 82% at 6 months, respectively (supplemental Figure 2A).
Corresponding rates of MCyR were 83%, 94%, and 88% at 3 months
and 87%, 93%, and 93% at 6 months, respectively (Figure 1A). The
trend for lower rates of CCyR and MCyR for the e13a2 transcript cohort
compared with the e14a2 cohort persisted even at 60 months.
Rates of MMR for the e13a2, e14a2, and coexpression cohorts were
27%, 49%, and 50% at 3 months, 42%, 67%, and 70% at 6 months,
and 55%, 83%, and 76% at 12 months (equivalent to optimal European
Leukemia Net [ELN] response32), respectively (supplemental Figure 2B).
Similarly, rates of MR4.5 were lower for the e13a2 cohort over time
compared with the e14a2 and coexpression cohorts (supplemental
Figure 2C). Patients with e13a2 transcripts achieved lower rates of
MMR or MR4.5 at all time points compared with those with e14a2.
Patterns of decline in different transcripts after treatment
We then analyzed the changes in transcript levels (in international scale)
over time. The median transcripts levels (e13a2, e14a2, and both) at
3 months were 0.2004, 0.056, and 0.0612 and at 6 months were 0.091,
0.0109, and 0.0130, respectively. Patients with e13a2 transcripts
demonstrated a slower rate of decline over time after start of treatment
compared with the e14a2 and coexpression cohorts (Figure 1C). When
analyzing the decline in transcript levels according to TKI used,
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1272 JAIN et al BLOOD, 10 MARCH 2016 x VOLUME 127, NUMBER 10

consider this end point depends on the achievement of sustained

MR4.5, defined as MR4.5 that has been observed consecutively
for $2 years with assessments at least every 6 months. We thus
analyzed the cumulative incidence of achievement of sustained
MR4.5 by transcript type. Patients with e14a2 and coexpressed
transcripts demonstrated a significantly higher incidence of sustained
MR4.5 compared with those with e13a2 (8-year probability, 43% vs
24%; P 5 .0021; supplemental Figure 4).
The times to achieve CCyR, MMR, and MR4.5 are shown in
supplemental Figure 5A. The median time to CCyR was similar
(3 months each) for the 3 transcript cohorts. However, time to MMR
and MR4.5 was longer in patients with e13a2 transcripts compared
with those with e14a2 and coexpressed transcripts (6, 3.5, and
3.5 months for MMR and 20, 10, and 11 months for MR4.5, respec-
tively). When analyzing the time to CCyR, MMR, and MR4.5 ac-
cording to the TKI modality used (supplemental Figure 5B-D), patients
treated with imatinib 400 had the longest time to response, irrespective
of type of transcripts, with patients with e13a2 generally having longer
times to MMR and MR4.5 across all treatment types.

Survival outcomes according to the type of transcript

There were more events, transformations, and deaths among patients

with e13a2, resulting in a general trend for inferior survival outcomes
in such patients (Figure 2A-C). The 5-year probabilities for EFS
for patients expressing e13a2, e14a2, and both transcripts were 79%,
89%, and 87%, respectively (P 5 .09). The corresponding figures for
TFS were 91%, 97%, and 99% (P 5 .01), respectively. Five-year
probabilities of survival were 88%, 95%, and 98% (P 5 .34) for each
cohort, respectively. Because achievement of MCyR at 3 months or
BCR-ABL #10% is an important hallmark for response to treatment,
we compared survival outcomes in different transcripts based on the
achievement of optimal ELN response at 3 months.32 Only TFS was
significantly longer in patients who expressed e14a2 and/or both
transcripts and achieved optimal response at 3 months (P 5 .03;
supplemental Figure 6). Other survival outcomes, EFS and OS,
were not significantly different in the 3 types of transcripts when
categorized by 3- and 6-month optimal ELN response (Table 2).
Furthermore, survival outcomes based on ELN responses categories

Table 2. Summary of time to event outcomes of patients expressing

different BCR-ABL transcripts (e13a2, e14a2, and coexpressed
e13a2 and e14a2) according to optimal ELN responses achieved at
the 3- and 6-month landmark: EFS, TFS, and OS
% 5-year outcome EFS/TFS/OS
e13a2 e14a2 Both

Cytogenetic response*
3 months MCyR 83/90/90 90/94/95 91/99/97
No MCyR 54/78/85 61/90/91 61/100/100†
Figure 2. Survival outcomes according to the type of BCR-ABL transcript 6 months CCyR 88/91/93 94/96/97 94/100/99
(e13a2, e14a2, or both). (A) EFS; median survival not reached in all for all No CCyR 50/77/80 65/84/93 63/100/100†
transcripts (P 5 .091). (B) TFS; median survival not reached for all transcripts Molecular response‡
(P 5 .01). (C) OS; median survival not reached in any group (P 5 .346).
3 months #10% 82/89/91 90/95/96 87/99/97
.10%§ 2/2/100 2/2/2 2/2/2
6 months ,1% 89/92/94 94/96/97 94/100/98
generally the decline was slowest with imatinib 400 compared with $1% 55/71/79 43/91/89 30/100/100
imatinib 800 and dasatinib. Patients who received imatinib 400 or *Optimal ELN response by cytogenetic response: major cytogenetic response at
800 mg or dasatinib demonstrated similar pattern of decline in all types 3 months or complete cytogenetic response at 6 months.
of transcripts, with the slowest decline seen among the e13a2 cohort. †n 5 11 for coexpressed transcripts with no MCyR at 3 months and n 5 14 with
no MCyR at 6 months.
This difference was less noticeable among those treated with nilotinib
‡Optimal ELN response by molecular response: BCR-ABL1 #10% at 3 months
(supplemental Figure 3A-D). Treatment discontinuation is an important or ,1% at 6 months.
treatment goal for patients receiving TKI therapy, and the possibility to §Less than 5 patients in this group.
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BLOOD, 10 MARCH 2016 x VOLUME 127, NUMBER 10 BCR-ABL TRANSCRIPTS AND TKI IN CML 1273

Table 3. Factors predictive of EFS including the type of BCR-ABL significant for predicting OS (HR 5 0.45, 95% CI 5 0.18-1.11;
transcripts P 5 .08).
N Events Log-rank HR 95% CI HR P value We also assessed whether the type of transcript can predict for
Univariate* optimal ELN response at different time points (at 3, 6, and 12
TKI type months).32 The expression of e14a2 transcripts predicted for improved
Imatinib 400† 69 21 0.013 probability of MCyR at 3 months (supplemental Table 3). Expression
Imatinib 800 199 38 0.58 (0.34-0.99) .045 of e14a2 or coexpressed transcripts predicted for MMR at 6 and 12
Dasatinib 104 7 0.28 (0.12-0.67) .004
months (optimal ELN response; supplemental Table 4). Similarly,
Nilotinib 108 11 0.45 (0.22-0.95) .035
expression of e14a2 transcripts predicted for 6-month CCyR (P 5 .04;
Transcript type
e13a2‡ 199 40 0.091
supplemental Table 5). In addition, the type of transcript (e14a2 and
e14a2 196 24 0.57 (0.35-0.95) .032
both) predicted for MMR at 12 months (Table 4), OR for e14a2 was
Both 85 13 0.74 (0.40-1.39) .355 5.85, 95% CI (3.01-11.37; P , .001) and for both transcripts OR was
Splenomegaly ($10 cm) 3.18, 95% CI (1.50-6.74; P 5 .003).
No 453 68 0.012
Yes 27 9 2.38 (1.19-4.77) .014
Multivariate
TKI type
Imatinib 400† 69 21 Discussion
Imatinib 800 199 38 0.55 (0.32-0.94) .030
Dasatinib 104 7 0.28 (0.12-0.67) .004 In this study, we analyzed the influence of the transcript type on
Nilotinib 108 11 0.44 (0.21-0.92) .029 molecular and cytogenetic responses achieved in response to
Transcript type different TKI regimens in newly diagnosed chronic phase CML
e13a2‡ 199 40 patients and also compared different transcripts with respect to
e14a2 196 24 0.59 (0.36-0.98) .043 survival outcomes. Patients who expressed e14a2 (and to some
Both 85 13 0.80 (0.43-1.50) .489 extent those with coexpression of e14a2 and e13a2) achieved
Splenomegaly ($10 cm)
earlier and deeper cytogenetic and molecular responses compared
No 453 68
with those with only e13a2 transcripts and maintained these
Yes 27 9 2.18 (1.07-4.44) .031
responses longer. In multivariate analysis, the expression of e14a2 or
*White blood cell count, age, Sokal score, hemoglobin, platelet count, peripheral
blood blasts, and serum lactate dehydrogenase are not significant (P 5 not significant;
Table 4. Factors predictive for MMR at 12 months (optimal
data not shown).
response) including the type of BCR-ABL fusion transcript
†Imatinib 400 is the reference for comparison with the other 3 TKI modalities.
‡e13a2 is the reference for comparison with e14a2 and both (coexpressed No MMR, MMR,
transcripts). N (%) N (%) OR 95% CI OR P

Univariate*
TKI type
were not significantly different in various transcript types, Imatinib 400† 20 (23) 24 (8)
irrespective of the TKI modality used (supplemental Table 1). This Imatinib 800 33 (38) 140 (45) 3.54 (1.75-7.15) ,.001
could be due to lower number of patients in each transcript type Dasatinib 22 (25) 72 (23) 2.73 (1.27-5.84) .010
when analyzed according to the TKI modality and type of ELN Nilotinib 11 (13) 77 (25) 5.83 (2.45-13.88) ,.001
Transcript type
response. In general, survival outcomes were inferior in patients with
e13a2‡ 60 (70) 101 (32)
e13a2 transcripts in response to different TKI modalities.
e14a2 15 (17) 151 (48) 5.98 (3.22-11.11) ,.001
Both 11 (13) 61 (19) 3.29 (1.61-6.75) .001
Type of BCR-ABL transcript predict for survival and response: Splenomegaly ($10 cm)
multivariate analysis No 76 (88) 300 (96)
Yes 10 (12) 13 (4) 0.33 (0.14-0.78) .012
We then conducted univariate and multivariate analyses to determine Platelets (.300 K/mL)
whether effect of transcript on outcome is independent of other No 46 (53) 123 (39)
variables. Table 3 shows the results of these analyses for EFS. Yes 40 (46) 190 (61) 1.78 (1.10-2.87) .019
Covariates with P , .10 were included in the final multivariate model Multivariate§
TKI type
for EFS. Compared with e13a2, e14a2 (but not coexpressed e13a2
Imatinib 400† 20 (23) 24 (8)
and e14a2 transcripts) significantly predicted for longer EFS (e14a2
Imatinib 800 33 (38) 140 (45) 4.83 (2.20-10.62) ,.001
hazard ratio [HR] 5 0.59, 95% confidence interval [CI] 5 0.36-0.98 Dasatinib 22 (25) 72 (23) 3.39 (1.45-7.89) .005
[P 5 .04], coexpressed transcripts HR 5 0.80, 95% CI 5 0.43-1.50 Nilotinib 11 (13) 77 (25) 8.24 (3.16-21.43) ,.001
[P 5 .48]). Treatment with imatinib 800, dasatinib, and nilotinib also Transcript type
predicted for longer EFS (P 5 .03, .004, and .02, respectively) and e13a2‡ 60 (70) 101 (32)
the presence of splenomegaly at the time of initial presentation e14a2 15 (17) 151 (48) 5.85 (3.01-11.37) ,.001
was predictive of inferior EFS (P 5 .03). Similarly, e14a2 and Both 11 (13) 61 (19) 3.18 (1.50-6.74) .003
coexpressed transcripts predicted for significantly improved prob- *White blood cell count, age, Sokal score, hemoglobin, peripheral blood blasts,
ability of TFS compared with e13a2 (supplemental Table 2; e14a2, and serum lactate dehydrogenase are not significant (P 5 not significant; data not
HR 5 0.52, 95% CI 5 0.25-1.07 [P 5 .07]; coexpressed transcripts, shown).
HR 5 0.22, 95% CI 5 0.05–0.94 [P 5 .04]). Treatment with †Imatinib 400 is the reference for comparison with the other 3 TKI modalities.
‡e13a2 is the reference for comparison with e14a2 and both (coexpressed transcripts).
imatinib 800 and dasatinib also predicted for longer TFS (P 5 .02 §Platelet count and spleen size were not significant in multivariate analysis (data
and .04, respectively). Coexpression of both transcripts was marginally not shown).
 From www.bloodjournal.org by guest on March 6, 2019. For personal use only.
1274 JAIN et al
both types of transcripts independently predicted for achievement of
optimal ELN response32 and an improved probability of EFS and
TFS but not OS.
The question of whether the type of transcript has prognostic sig-
nificance for patients with newly diagnosed CML–chronic phase has
been debated for many years.13,33 More than 95% of patients with CML
have e13a2 (b2a2), e14a2 (b3a2), or both transcripts coding for p210
BCR-ABL1 tyrosine kinase, whereas only a minority express rare
variants such as e1a2 transcripts,34 which code for p190 BCR-ABL1,
which is associated with rapid disease progression. Previous reports have
suggested that patients with e14a2 achieve deeper molecular response to
standard dose imatinib23 and have higher platelet counts compared with
patients with e13a2 transcripts.19,21 To our knowledge, no prior analyses
have suggested any influence of transcript type on survival outcomes or
tested whether the type of transcript can predict for an optimal ELN
response. Of further note, we showed that patients expressing the
e13a2 transcript have a significantly lower incidence of sustained
MR4.5 response compared with e14a2 and coexpressed transcripts
(supplemental Figure 4). Our data indicate that the type of transcript
may also increase the probability of reaching end points required
for treatment discontinuation. Unfortunately, too few patients in this
series have elected to discontinue therapy. Thus, we cannot address
whether the probability of recurrence after treatment discontinuation
is affected by the transcript type.
Consistent with previous reports, our analysis shows a higher
platelet count in patients with e14a2 transcripts21,35; however, we did
not detect any difference in white blood cell counts as had been reported
by Hanfstein et al,21 nor did we identify any other significant difference
in the baseline characteristics of patients with different transcripts.
In our analysis, the rates of MCyR and CCyR, as well as MMR and
MR4.5, were lower in patients with e13a2 transcripts at various time
points. However, the median time to achieve CCyR was similar for all
cohorts (3 months in each; supplemental Figure 5A). This is consistent
with what was reported by Hanfstein et al in 1105 imatinib-treated
patients.21
Superior molecular responses in patients with e14a2 transcripts
were reported previously in patients treated with standard-dose
imatinib.21,23 The median time to achieve MMR or MR4.5 was longer
in patients with imatinib 400 compared with the other 3 TKI modalities,
irrespective of the type of transcript. However, patients with e13a2
treated with imatinib 400 had the longest time to achieve MMR
(supplemental Figure 5C-D), again suggesting that these patients have a
worse outcome when treated with this treatment modality.
Because the type of TKI can influence the time and depth of
cytogenetic and molecular response, we analyzed the impact of TKI
type in each transcript for attaining cytogenetic and molecular
responses. Interestingly, there was a suggestion that treatment with
imatinib 400 mg daily was associated with a lower probability of
response only among patients with e13a2. The rates of CCyR and
MMR for patients with e14a2 or with coexpression of e13a2 and
e14a2 treated with imatinib 400 mg daily was similar to that of
patients treated with imatinib 800, dasatinib, or nilotinib. If these
observations were to be confirmed in a prospective study, it would
suggest that transcript type could be a tool to help select the TKI to be
used for patients with newly diagnosed CML. For example, patients
with e14a2 could be offered imatinib 400, whereas those with e13a2
may derive more benefit from the use of 2GTKI as initial therapy.
Although our study does not provide a mechanism with which these
differences between e13a2 vs e14a2 and coexpressed transcripts could
be elucidated, we could hypothesize some biological reasons to explain
these observations. Based on the observed differences in attaining
response, higher platelet counts, trend for better survival, and lower
BLOOD, 10 MARCH 2016 x VOLUME 127, NUMBER 10
occurrence of disease transformation in patients with e14a2, it could
be hypothesized that disease with e13a2 and e14a2 or coexpressed
transcripts have different biological features that may participate
differently in the pathogenesis of CML. One possible explanation
for inferior outcome for patients with e13a2 is the reported higher
tyrosine kinase activity reflected by higher pCrKL levels with e13a2
transcripts.19 This could result in a given TKI being able to more
effectively suppress the kinase activity associated with the less active
e14a2 transcripts. Because imatinib 400 has the weakest inhibitory
activity, this could also explain the possible inferior outcome for
patients with the e13a2 when treated with standard dose imatinib. It has
also been described that the presence of an extra 25 amino acids in the
e14a2 transcripts leads to changes in the structure of the binding domain
of BCR-ABL kinase leading to reduced tyrosine kinase activity thereby
causing better responses in e14a2 transcripts.7,19,36 Hai et al26 reported
that the presence of the additional 25 amino acids encoded by the e14
exon not present in e13a2 lead to differences in SRC homology domain
(SH1-SH3) and DNA binding domains, which regulate the tyrosine
kinase activity in p210 BCR-ABL protein isoform. Interestingly, this
difference was shown to influence difference in platelet counts in the 2
transcripts.36 Overall, this variability in the structure of the 2 isoforms has
the potential to differentially influence signal transduction in CML cells.
The transcript type not only influenced response outcomes, but also
long-term survival outcomes. Previous studies21 have not shown any
difference in EFS or TFS according to transcript types among patients
treated with imatinib. In our analysis, we showed that patients with
e13a2 transcripts show a trend for inferior EFS and TFS compared with
e14a2 and/or both transcripts among patients treated with various TKI
modalities. By multivariate analysis, transcript type remained statisti-
cally significant and an independent variable affecting long-term EFS
and TFS. One possible explanation for these results could be due to
differences in treatments because our study population included a mix
of 4 TKI modalities, whereas previous studies included only patients
treated with imatinib. Finally, overall results were similar in patients
with e14a2 and those who expressed both e13a2 and e14a2. This
equivalence in outcome is expected because at the genomic level, these
patients have an e14a2 rearrangement with an alternative splicing that
gives rise to the coexpression of e13a2.
In summary, we showed that type of transcript may impact the
probability of response to TKI among patients with CML treated with
various TKI regimens. The difference in response translates in inferior
probability of EFS and TFS for patients with e13a2 transcripts. The
inferior outcome appears to be more evident for patients treated with
imatinib 400, whereas patients with e14a2 treated with imatinib 400
may have a similarly favorable outcome as those treated with dasatinib
or nilotinib. If confirmed, transcript type could be used to select TKI
regimen for patients with CML. The biological mechanism behind this
effect and the possible modulating effect of treatment modality in this
possible differential outcome by transcript type deserves further study.
Acknowledgments
Funding for these studies was provided in part by the MD Anderson
Cancer Center support grant CA016672 (principal investigator [PI]:
Dr Ronald DePinho) and award P01 CA049639 (PI: Dr Richard
Champlin) from the National Institutes of Health, National Cancer
Institute (NCI). None of the authors are employed by the National
Institutes of Health. J.C. is the recipient of a grant from the NCI (PI of
project 1 of P01 CA049639).
 From www.bloodjournal.org by guest on March 6, 2019. For personal use only.
BLOOD, 10 MARCH 2016 x VOLUME 127, NUMBER 10
Authorship
Contribution: P.J. and J.C. designed the study; G.N.G., P.J., H.K.,
and J.C. analyzed results; P.J., G.N.G., K.S., C.G.R., and J.C. wrote
the paper; P.J., G.N.G., R.L., K.P.P., R.K.S., H.K., and J.C. did the
clinical correlation; H.K., S.O., F.R., E.J., Z.E., N.P., N.D., T.M.K.,
G.B., and J.C. contributed patient samples; and all authors reviewed
and gave the final approval for the paper.
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 From www.bloodjournal.org by guest on March 6, 2019. For personal use only.

2016 127: 1269-1275

doi:10.1182/blood-2015-10-674242 originally published
online January 4, 2016

Impact of BCR-ABL transcript type on outcome in patients with

chronic-phase CML treated with tyrosine kinase inhibitors
Preetesh Jain, Hagop Kantarjian, Keyur P. Patel, Graciela Nogueras Gonzalez, Rajyalakshmi Luthra,
Rashmi Kanagal Shamanna, Koji Sasaki, Elias Jabbour, Carlos Guillermo Romo, Tapan M. Kadia,
Naveen Pemmaraju, Naval Daver, Gautam Borthakur, Zeev Estrov, Farhad Ravandi, Susan O'Brien
and Jorge Cortes

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