Jain P et al BCR-ABL transcripts and TKI in CML 1 Original Article Impact of BCR-ABL transcript ...

31 Pages·2015·0.9 MB·English

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Blood First Edition Paper, prepublished online January 4, 2016; DOI 10.1182/blood-2015-10-674242
Jain P et al BCR-ABL transcripts and TKI in CML
Original Article
Impact of BCR-ABL transcript type on response and survival in patients with
chronic phase chronic myeloid leukemia treated with tyrosine kinase inhibitors
Preetesh Jain1,2, Hagop Kantarjian1, Keyur P. Patel3, Graciela Nogueras
Gonzalez4,Rajyalakshmi Luthra3, Rashmi Kanagal Shamanna3, Koji Sasaki1, Elias
Jabbour1, Carlos Guillermo Romo1, Tapan M. Kadia1, Naveen Pemmaraju1, Naval
Daver1, Gautam Borthakur1, Zeev Estrov1, Farhad Ravandi1, Susan O’Brien1 and Jorge
Cortes1
Affiliations: 1Department of Leukemia, The University of Texas MD Anderson Cancer
Center, Houston, Texas , 2Department of Internal Medicine, University of Texas Medical
School at Houston, 3Department of Hematopathology, 4Department of Biostatistics, The
University of Texas MD Anderson Cancer Center, Houston, Texas
Corresponding Author: Jorge Cortes MD, Professor and Deputy Chairman, Department
of Leukemia, Unit 428, 1515 Holcombe Boulevard, Houston, TX 77030; Phone: 713-
794-5783; Fax: [phone]; E-mail: [email protected]

Abstract (223 and 3741 Words)
Figures and Tables – Main – (2 figures and 4 tables), Supplemental – (5 tables and 6
figures)
References – (36)

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Copyright © 2016 American Society of Hematology
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Jain P et al BCR-ABL transcripts and TKI in CML
Key Words – Chronic myeloid leukemia in chronic phase, CML, CML-CP, Tyrosine
kinase inhibitors (TKI), imatinib, nilotinib, dasatinib, BCR-ABL transcripts
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Jain P et al BCR-ABL transcripts and TKI in CML
Key Points
1. Patients with e13a2 transcripts have inferior outcomes with imatinib 400; e14a2
have favorable outcomes regardless of treatment modality.
2. Multivariate analysis showing that the expression of e14a2 or both e14a2 and
e13a2 predicts optimal ELN responses and longer EFS and TFS.

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Jain P et al BCR-ABL transcripts and TKI in CML
Abstract
The most common BCR-ABL transcripts in chronic myeloid leukemia (CML) are e13a2
(b2a2) or e14a2 (b3a2). The impact of the type of transcript on response and survival
after initial treatment with different tyrosine kinase inhibitors (TKI) is unknown. This
study involved 481 patients with chronic phase CML expressing various BCR-ABL
transcripts. Two hundred patients expressed e13a2 (42%), 196 (41%) e14a2 and 85
(18%) both transcripts. The proportion of patients with e13a2, e14a2 and both achieving
CCyR at 3 and 6 months was 59%, 67% and 63%, and 73%, 81% and 82%, respectively,
while MMR rates were 27%, 49% and 50% at 3 months, 42%, 67% and 70% at 6 months,
and 55%, 83% and 76% at 12 months, respectively. Median (IS) levels of transcripts
e13a2, e14a2 and both at 3 months were 0.2004, 0.056 and 0.0612, and at 6 months
0.091, 0.0109 and 0.0130, respectively. In multivariate analysis (MVA), e14a2 and both
predicted for optimal responses at 3, 6 and 12 months. The type of transcript also
predicted for improved probability of event-free (p=0.043; e14a2) and transformation-
free survival (p=0.04 for both). Patients with e14a2 (whether alone or concomitant with
e13a2 achieved earlier and deeper responses compared to those with only e13a2
transcripts and predicted for optimal ELN responses at 3, 6 and at 12 months and longer
event free and transformation free survival.

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Jain P et al BCR-ABL transcripts and TKI in CML
Introduction
The Philadelphia (Ph) chromosome resulting from the balanced reciprocal 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 two 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 co-expressed 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 which
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 mg19. Improved response has been
reported in patients carrying the e14a2 (b3a2) transcript compared to 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
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Jain P et al BCR-ABL transcripts and TKI in CML
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 2nd generation tyrosine kinase inhibitors (2GTKI) dasatinib
and nilotinib have improved the responses in patients when used either as front-line
therapy or as second-line treatment after imatinib failure.27-29 To our knowledge, none of
the previously published studies have systematically analyzed the responses and survival
outcomes in patients treated with imatinib 400, imatinib 800 and 2GTKI as initial therapy
for CML according to the type of BCR-ABL1 transcripts.
In this analysis we have evaluated the prognostic relevance of commonly expressed
BCR-ABL1 transcripts in patients with chronic phase CML treated with 4 different
frontline TKI modalities. The objective of this analysis was to determine the prognostic
significance of transcript types across patients with CML-CP treated with different TKI
modalities.

Patients and Methods
All patients with chronic phase CML enrolled in consecutive or parallel clinical trials at
MD Anderson Cancer Center using TKI as frontline therapy from July 31st 2000 to
September 10th 2013 were included in this analysis. Patients were treated on protocols
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Jain P et al BCR-ABL transcripts and TKI in CML
approved by the institutional review board (IRB) 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 2-3 years, then every 1-2 years. Real time
polymerase chain reaction (RT-PCR) was generally assessed every 3 months for the first
year, then every 6 months. Response criteria were as previously described.30 Only
patients with BCR-ABL transcripts e13a2 (previously b2a2), e14a2 (previously b3a2)
and co-expressed e13a2 (b2a2) with e14a2 (b3a2) were included in the analyses.
Demographic and baseline disease characteristics were collected at baseline. The
χ
differences between variables were analyzed by the 2 test and the Kruskal-Wallis test for
categorical and continuous variables. Of note, patients treated with imatinib 400 all
initiated therapy between May 2001 and June 2001 when molecular analysis was not
routinely done before achievement of 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 IRIS study)31 while on therapy: loss of complete
hematologic remission (CHR), loss of major cytogenetic response (MCyR), progression
≥ ≥ ≥
to accelerated (defined as blasts 15%, blasts + promyelocytes 30%, basophils 20%,
platelets <100 x109/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.
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Jain P et al BCR-ABL transcripts and TKI in CML
Transformation-free survival (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 (i.e.
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-value 0.10 in the univariate
analysis were entered into a multivariate model and analyzed using the Cox proportional
hazard regression. A p-value of <0.05 was considered significant. Survival endpoints
were analyzed using the Kaplan-Meier method and differences calculated by the log-rank
test. Statistical analyses were carried out using STATA/SE version 13.1 statistical
software (Stata Corp. LP, College Station, Texas).

Results
Patients
Overall, 487 patients with previously untreated chronic phase CML were treated with
different TKI modalities of which 481 patients expressing e13a2, e14a2 and/or co-
expression of e13a2 with e14a2 transcripts (both) were included in this analysis. Six
patients with variant transcripts (e1a2; n=4, b3a3; n=2) were excluded from this analysis.
Patients were treated with 4 different frontline TKI modalities - imatinib 400 mg daily
(n=69), imatinib 800 mg daily (n=199), dasatinib 50 mg twice daily or 100 mg daily
(n=105), or nilotinib 400 mg twice daily (n=108). The baseline characteristics of the
patients are summarized in Table-1. Two hundred patients (42%) expressed e13a2, 196
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Jain P et al BCR-ABL transcripts and TKI in CML
(41%) e14a2 and 85 (18%) expressed both transcripts. Patients with e13a2 had
significantly lower platelets (median 288 K/µL; range 15-1906) compared to e14a2 or
both (median 405; range 77-1476 and 358 K/µL; range 100-2928, respectively)
(p<0.001). 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=7,
accelerated phase n=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 co-
expressed both transcripts (p=0.04). The distribution of patients who transformed to
accelerated or blast phase (n=21) by Sokal risk categories were low risk 13 (62 %),
intermediate 6 (28%), and high risk 2 (9%). A total of 52 (11%) patients died (n=26
e13a2, n=20 e14a2 and n=6 in 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:
CCyR - e13a2 (89%), e14a2 (94%) and both (94%) P=NS; MMR - e13a2 (79%), e14a2
(91%) and both (95%) P=0.0001; and MR4.5 - e13a2 (57%), e14a2 (79%) and both
(80%) P=0.00001 (See supplemental Figure 1A). We then assessed the response rates by
TKI modality for each transcript cohort (See supplemental Figure 1B-D). For CCyR,
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Jain P et al BCR-ABL transcripts and TKI in CML
patients with e13a2 who received imatinib 400 had an inferior response rate (77%)
compared to 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%). Similarly, for MMR and MR4.5, patients with e13a2
treated with imatinib 400 had a trend for an inferior response rate compared to 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 to patients treated with imatinib 800 or dasatinib (Supplemental Figure
1D).
We then analyzed response rates at different time points. For e13a2, e14a2 and co-
expression 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 to the e14a2
cohort persisted even at 60 months.
Rates of MMR for the e13a2, e14a2 and co-expression 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 ELN response32), respectively (Supplemental Figure 2B).
Similarly, rates of MR4.5 were lower for the e13a2 cohort over time compared to the
e14a2 and co-expression cohorts (Supplemental Figure 2C). Patients with e13a2
transcripts achieved lower rates of MMR or MR4.5 at all-time points compared to those
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