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Year : 2019  |  Volume : 8  |  Issue : 2  |  Page : 107-123

Chronic myeloid leukemia with a rare fusion transcript, b2a3 (e13a3) BCR–ABL1: A report of four cases from India

Department of Hematology, All India Institute of Medical Sciences, New Delhi, India

Date of Web Publication15-Apr-2019

Correspondence Address:
Dr. Sudha Sazawal
Department of Hematology, All India Institute of Medical Sciences, New Delhi
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/sajc.sajc_158_18

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How to cite this article:
Sazawal S, Chhikara S, Singh K, Chaubey R, Mahapatra M, Seth T, Saxena R. Chronic myeloid leukemia with a rare fusion transcript, b2a3 (e13a3) BCR–ABL1: A report of four cases from India. South Asian J Cancer 2019;8:107-23

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Sazawal S, Chhikara S, Singh K, Chaubey R, Mahapatra M, Seth T, Saxena R. Chronic myeloid leukemia with a rare fusion transcript, b2a3 (e13a3) BCR–ABL1: A report of four cases from India. South Asian J Cancer [serial online] 2019 [cited 2020 Jul 4];8:107-23. Available from:

Dear Editor,

Chronic myeloid leukemia (CML) is characterized by reciprocal t(9:22) (q34; q11) translocation, leading to the generation of the BCR-ABL1 protein which plays a crucial role in CML pathogenesis. The BCR-ABL1 fusion gene is the molecular hallmark and causative event of CML. More than 95% of CML patients express the transcript e14a2 (b2a2) or e13a2 (b3a2), namely major BCR-ABL1 coding for p210 protein. Approximately 1%–2% of CMLs show e1a2 (minor BCR-ABL1) coding for p190 protein and <1% of cases show e19a2 (micro BCR-ABL1), encoding a 230-kDa protein.

Another rare fusion transcript e13a3 (b2a3) coding for p203 protein is also reported[1],[2] This uncommon fusion transcript, i.e., b2a3, is formed due to the fusion of BCR breakpoint at exon 13 with ABL point of exon 3 instead of more commonly involved exon 2, resulting in the generation of p203 protein, which is rarely seen CML.[3] To date, only nine CML cases with this rare fusion transcript have been reported worldwide.[4],[5],[6],[7],[8],[9],[10] These infrequent fusion transcripts may escape detection or may be misdiagnosed when the commonly used techniques which detect typical fusion transcripts are used.[11]

Here, we describe the clinicohematological profile and treatment response of four cases of Philadelphia (Ph)-positive CML with b2a3 fusion transcript. All the four patients presented to Hematology Outpatient department, AIIMS New Delhi, India, between January 2013 and December 2017, with chief complaints of generalized body weakness, early fatigability, left-sided abdominal mass, and night sweats for 2–4 months. The general characteristics and hematological parameters are summarized in [Table 1]. Based on clinical features and hematological parameters including peripheral smear (PS) findings, provisional diagnosis of CML was made [Table 1]. Three of the cases had CML-CP, and one patient (case 2) had de novo myeloid blast crisis. The patient (case no 2) had de novo myeloid blast crisis and was initially considered acute leukemia with probable diagnosis of CML-BC. This case had organomegaly (splenomegaly and hepatomegaly) at presentation. Our diagnosis was confirmed by multiplex nested reverse transcriptase polymerase chain reaction (MPX-RT PCR) and was later confirmed by bone marrow biopsy study which showed abnormal megakaryocytes (dwarf) in addition to blasts.
Table 1: General characteristics and hematological parameters of patients with b2a3 fusion transcript

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Fluorescence in situ hybridization (FISH) for cytogenetics and MPX-RT PCR for BCR-ABL fusion transcript was advised. Cytogenetic analysis by FISH revealed t(9:22) (q34; q11.2), and no other chromosomal abnormality was detected. Using MPX-RT PCR fusion transcript b3a2 (472 bp), b2a2 (397 bp), e19a2 (808 bp), and e1a2 (310 bp) was negative, but it showed unexpected band at 230 bp [Figure 1]. Real-time quantitative PCR was also negative for b3a2, b2a2, e19a2, and e1a2 fusion transcript. On the basis of these findings, CML with atypical fusion transcript was suspected, and DNA sample of the patients was further processed for DNA sequencing. Sequencing of the amplified product was performed as per the instructions of The BigDye® Terminator v3.1 Cycle Sequencing Kit (ABI, USA) on an ABI Genetic Analyzer 3730 (ABI , Japan) reagents (Applied Biosystems). The samples were placed in autosampler tray, and the purified reaction product was electrophoresed at 50°C in ABI 310 genetic analyzer. At the end of the run, the sequence was analyzed with sequence analysis software which confirmed b2a3 fusion transcript [Figure 2]. The patients were started on imatinib 400 mg/day as first-line treatment. Written informed consent was obtained from all the patients.
Figure 1: 3% Agarose gel electrophoresis of multiplex reverse transcriptase polymerase chain reaction product, Lane M: 100 bp marker; Lane1: positive control for b3a2 (472 bp), Lane 3,6,8,9: positive for b3a2 (472 bp), Lane 5: positive for b2a2 (397 bp), Lane 4 , 11 : positive for b2a3 (230 bp), Lane 2,7,10: negative for chronic myeloid leukemia and Lane B: negative control

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Figure 2: DNA sequencing showing the presence of BCR-ABL b2a3 fusion transcript

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  Results and Discussion Top

In all the four cases, CML was suspected on the basis of complete history, general physical examination, and characteristic PS findings. Using multiplex RT-PCR, an unexpected band at 230 bp was observed and hence impression of atypical fusion transcript was made [Figure 1]. Our findings were later confirmed by DNA sequencing which revealed b2a3 fusion transcript [Figure 2]. The final diagnosis of CML with atypical fusion transcript b2a3 was reported.

In a total of 1350 BCR-ABL-positive CML patients, 4 (0.01%) cases showed this rare b2a3 fusion transcript encoding a 203-kDa protein. The other rare fusion transcript e19a2 encoding a 230-kDa protein has also been reported in 0.30% of cases of CML patients who presented to the Department of Haematology, AIIMS, New Delhi, India, between January 2013 and December 2017.[12]

Snyder et al. in the year 2004 observed that the estimated frequency of b2a3 variant transcript was 0.9% among all of the BCR-ABL-positive patients.[2] Biologically, BCR/ABL a3 type transcripts lack part of the ABL SH3 domain, which is believed to contribute leukemogenesis by negatively regulating the kinase domain (SH1) and activating STAT5 signaling. CML with BCR/ABL a3 type transcripts may have a better prognosis because of lacking part of ABL SH3.[5],[13]

Multiplex RT-PCR may fail to detect certain rare BCR-ABL1 fusion transcript type, as many commercially available and laboratory-developed primer sets do not cover such rare fusions.[14] One of the modifications of RT-PCR is nested multiplex RT-PCR which is used in our laboratory for the detection of various BCR-ABL transcripts and to differentiate between these BCR-ABL breakpoints in CML patients. This method allowed us a reliable detection of typical BCR-ABL transcripts, such as b2a2 and b3a2, and also the atypical types, such as transcripts lacking ABL exon a2 (b2a3 and e19a2). Hence, for diagnostic samples, the use of multiplex PCR may be recommended so that several kinds of BCR-ABL and BCR transcripts can be detected simultaneously.

All the patients with fusion transcript b2a3 coding for p203 protein achieved complete hematological remission within 3 months of imatinib therapy (400 mg/day) which was similar to the patients having p210 transcript. No chemotherapy was given as the patients achieved complete hematological response within 3 months of imatinib therapy. All the patients showed improvement in clinical features, reduction in organomegaly, and normalization of white cell count.

At present, all the patients are on regular follow-up and in hematological remission till date [Table 1]. Our findings are in line with Pienkowska-Grela et al. who reported a case of 39-year-old male with e13a3 variant CML who reached a complete molecular remission after 8 months of imatinib treatment.[6] Other studies have also reported a favorable response of patients with b2a3 fusion transcript on imatinib treatment.[4],[5],[6],[7],[8],[9],[10] Furthermore, Jinawath et al. reported that CML with BCR/ABL a3 fusion transcripts might have a different response to tyrosine kinase inhibitors compared to CML with BCR/ABL a2 fusion transcripts because of the alterations of tertiary structure.[14]

  Conclusion Top

Reporting of the patients with this rare b2a3 fusion transcript will provide better insight into understanding the clinicopathological profile and treatment response of these patients. Furthermore, the importance of multiplex nested PCR in combination with sequencing can be helpful for detecting rare BCR/ABL fusion transcripts such as b2a3 fusion transcript. Hence, reporting of more such cases is required to understand the relation between this transcript and treatment outcome.

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Conflicts of interest

There are no conflicts of interest.

  References Top

Verma D, Kantarjian HM, Jones D, Luthra R, Borthakur G, Verstovsek S, et al. Chronic myeloid leukemia (CML) with P190 BCR-ABL: Analysis of characteristics, outcomes, and prognostic significance. Blood 2009;114:2232-5.  Back to cited text no. 1
Snyder DS, McMahon R, Cohen SR, Slovak ML. Chronic myeloid leukemia with an e13a3 BCR-ABL fusion: Benign course responsive to imatinib with an RT-PCR advisory. Am J Hematol 2004;75:92-5.  Back to cited text no. 2
Liu B, Zhang W, Ma H. Complete cytogenetic response to nilotinib in a chronic myeloid leukemia case with a rare e13a3(b2a3) BCR-ABL fusion transcript: A case report. Mol Med Rep 2016;13:2635-8.  Back to cited text no. 3
Liu LG, Tanaka H, Ito K, Kyo T, Ito T, Kimura A, et al. Chronic myelogenous leukemia with e13a3 (b2a3) type of BCR-ABL transcript having a DNA breakpoint between ABL exons a2 and a3. Am J Hematol 2003;74:268-72.  Back to cited text no. 4
Moravcová J, Rulcová J, Polák J, Zemanová Z, Klamová H, Haskovec C, et al. CML patient with rare b 2 a 3 (e 13 a 3) variant of BCR-ABL transcript: Complete molecular response to imatinib. Leuk Res 2005;29:1365-6.  Back to cited text no. 5
Pienkowska-Grela B, Woroniecka R, Solarska I, Kos K, Pastwińska A, Konopka L, et al. Complete cytogenetic and molecular response after imatinib treatment for chronic myeloid leukemia in a patient with atypical karyotype and BCR-ABL b2a3 transcript. Cancer Genet Cytogenet 2007;174:111-5.  Back to cited text no. 6
Masuko M, Furukawa T, Abe T, Wada R, Maruyama S, Kitajima T, et al. A chronic myeloid leukemia patient with atypical karyotype and BCR-ABL e13a3 transcript caused by complex chromosome rearrangement. Int J Hematol 2009;90:230-4.  Back to cited text no. 7
Achkar WA, Wafa A, Ali BY, Manvelyan M, Liehr T. A rare chronic myeloid leukemia case with Philadelphia chromosome, BCR-ABL e13a3 transcript and complex translocation involving four different chromosomes. Oncol Lett 2010;1:797-800.  Back to cited text no. 8
McCarron SL, Langabeer SE, Bolger K, Haslam K, Crampe M, Kelly J, et al. Molecular response to imatinib in chronic myeloid leukaemia with a variant e13a3 BCR-ABL1 fusion. Med Oncol 2015;32:452.  Back to cited text no. 9
Ha J, Cheong JW, Shin S, Lee ST, Choi JR. Chronic myeloid leukemia with rare variant b2a3 (e13a3) BCR-ABL1 fusion. Ann Lab Med 2016;36:287-9.  Back to cited text no. 10
Melo JV. BCR-ABL gene variants. Baillieres Clin Haematol 1997;10:203-22.  Back to cited text no. 11
Sazawal S, Chikkara S, Singh K, Chaubey R, Chandra D, Mishra P, et al. Chronic myeloid leukemia with a rare fusion transcript, e19a2 BCR-ABL1: A report of three cases from India. Ann Diagn Pathol 2017;27:24-7.  Back to cited text no. 12
Nieborowska-Skorska M, Wasik MA, Slupianek A, Salomoni P, Kitamura T, Calabretta B, et al. Signal transducer and activator of transcription (STAT) 5 activation by BCR/ABL is dependent on intact Src homology (SH) 3 and SH2 domains of BCR/ABL and is required for leukemogenesis. J Exp Med 1999;189:1229-42.  Back to cited text no. 13
Jinawath N, Norris-Kirby A, Smith BD, Gocke CD, Batista DA, Griffin CA, et al. A rare e14a3 (b3a3) BCR-ABL fusion transcript in chronic myeloid leukemia: Diagnostic challenges in clinical laboratory practice. J Mol Diagn 2009;11:359-63.  Back to cited text no. 14


  [Figure 1], [Figure 2]

  [Table 1]


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