Concurrent ETV6::ABL1 and BCR::ABL1 in a rare case of Chronic Myeloid Leukemia: A paradox of imatinib resistance and indolent clinical course

Concurrent ETV6::ABL1 and BCR::ABL1 in a rare case of Chronic Myeloid Leukemia: A paradox of imatinib resistance and indolent clinical course | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Case Report Concurrent ETV6::ABL1 and BCR::ABL1 in a rare case of Chronic Myeloid Leukemia: A paradox of imatinib resistance and indolent clinical course Purvi Mohanty, Dhanlaxmi Shetty, Pratibha Amare, Nikhil Patkar, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6495243/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 6 You are reading this latest preprint version Abstract Chronic myeloid leukaemia (CML) is characterized by the presence of BCR::ABL1 showing favorable response to imatinib therapy. Complex rearrangements in CML are indicative of clonal evolution and often associated with disease progression and poor response to therapy. Cytogenetically, these cases present with atypical Fluorescence in-situ hybridization signal patterns and additional cytogenetic abnormalities on conventional karyotyping. Current research in CML is primarily focused on discovery of new tyrosine kinase inhibitors (TKIs) and uncovering the underlying causes of resistance to imatinib. In this report, we describe a rare case of Ph-positive CML on imatinib therapy showing atypical FISH signal pattern, harboring concurrent BCR::ABL1 and ETV6::ABL1 fusions characterized by conventional cytogenetics and Fluorescence in-situ hybridization. This is the first report of dual oncogenic fusions in a case CML, showing complex ABL1 rearrangements along with Philadelphia chromosome, demonstrating long term survival on imatinib therapy despite the failure to achieve major molecular response throughout the course of the disease. The key highlight of the study was the pivotal role of cytogenetic analysis in elucidating the underlying cause of imatinib resistance. The systematic documentation of such rare cases is essential for efficient management and evolving our understanding of dual oncogenic drivers in myeloid neoplasms. BCR:ABL1 ETV6:ABL1 CML IMATINIB RESISTANCE ABL1 REARRANGEMENT ETV6 Figures Figure 1 Figure 2 INTRODUCTION Philadelphia (Ph) chromosome is the defining feature of Chronic Myeloid Leukemia (CML), resulting from a reciprocal translocation t(9;22)(q34;q11.2). Conventional cytogenetic analysis confirms the presence of the Ph chromosome and additional cytogenetic abnormalities, while Fluorescence in-situ hybridization (FISH) using dual-color, dual-fusion probe (DCDF) verifies the BCR::ABL1 fusion and can show typical (1G1R2F) or atypical signal patterns indicating 9q deletions on the derivative chromosome 9 (1G1R1F), three way or more variant translocations (2G2R1F), supernumerary Ph (1G1R3F/4F), deletions of sequences proximal to chromosome 9 breakpoint or distal to chromosome 22 breakpoint (1G2R1F/1R2G1F) and other genetic aberrations [ 1 ]. The presence of atypical signal pattern in FISH is often indicative of complex genetic rearrangements and additional cytogenetic abnormalities (ACA) which are likely to be associated with disease progression and resistance to therapy [ 1 , 2 ]. In this report, we describe a unique case of Ph positive CML on treatment with atypical signal pattern (1G2R2F) using DCDF BCR-ABL1 FISH probe which was characterized to reveal a complex rearrangement of ABL1 gene resulting in concurrent BCR::ABL1 and ETV6::ABL1 fusions. ETV6::ABL1 is a rare genetic fusion identified in Myeloproliferative neoplasms (MPNs) including Ph negative CML with t(9;12)(q34;p13), BCR-ABL1 like Acute Lymphoblastic Leukemia (ALL) and Acute Myeloid Leukemia (AML) which leads to constitutive tyrosine kinase activation and oncogenic transformation similar to BCR::ABL1 [ 3 , 4 ]. Owing to the rarity of this fusion, there is inconsistent data on the prognostic significance of this fusion in MPNs/CML and its impact on outcome with tyrosine kinase inhibitor (TKI) therapy [ 5 – 11 ]. To the best of our knowledge, this is the first report of Ph positive CML with concomitant BCR::ABL1 and ETV6::ABL1, demonstrating long term survival on imatinib therapy without achieving a major molecular response (MMR) during the course of the disease. CASE REPORT A 63-year-old male with history of hypertension presented with splenomegaly, low grade fever, pallor and loss of appetite in July 2012. The haematological profile at this time point showed leucocytosis with total leukocyte count of 24.5x10 9 /L (78.7% neutrophils, 8% lymphocytes, 5.4% monocytes, 2.2% eosinophils and 3% basophils), haemoglobin level of 11.2 g/dL, and platelet count of 762x10 9 /L. Bone marrow morphological examination revealed a markedly hypercellular marrow with myeloid-to-erythroid ratio of 50:1 and 5% blasts. Based on the clinical findings the patient was advised cytogenetic and molecular workup for the diagnosis of CML. Conventional cytogenetic analysis of Giemsa-banded metaphases from an unstimulated overnight bone marrow aspirate culture, revealed the karyotype-46,XY,t(9;22)(q34,q11.2)[ 20 ]; while FISH on interphase cells using DCDF BCR-ABL1 probe (ZytoVision, Bremerhaven, Germany) showed typical signal pattern 1G1R2F indicating BCR::ABL1 resulting from balanced translocation in 98% cells analyzed. Reverse transcriptase Polymerase chain reaction (RT-PCR) was positive for the p210 major BCR-ABL1 fusion transcript. He was initiated on Imatinib 400 mg/day and achieved a complete hematological response (CHR) within two months of therapy. Thereafter, he continued treatment in his hometown, in a resource limited setting with no access to molecular monitoring. He then presented two years post therapy with rising basophil and eosinophil counts and no other complaints (supplementary material 1). The patient reported compliance with therapy and laboratory reports during the period showed sustained haematological response. Quantitative real time PCR (RQ-PCR) was subsequently performed out at our Centre, to assess BCR::ABL1 transcript levels; however, he had failed to achieve MMR, two years post initiation of imatinib therapy and thereafter (supplementary material 1). Due to financial constraints, the patient was unable to afford second generation TKI and was started on Imatinib at an escalated dosage of 800mg/day and continued the same throughout the course of the disease. The patient’s basophil count normalized soon after, however, his eosinophil count gradually decreased after two years. The patient was in haematological remission and continued treatment at his hometown. During this entire period cytogenetic re-evaluation was not performed despite failure to achieve MMR. Following seven years on treatment with imatinib at a dosage of 800mg/day, cytogenetic re-evaluation was done in 2021. Chromosomal analysis of bone marrow aspirate cells revealed the karyotype-46,XY,ins(3; 9 )(p21;q22q34),t(9;22)(q34;q11.2)[ 20 ] showing the presence of a balanced t(9;22)(q35;q11.2) with derivative chromosome 9, Ph chromosome and a derivative chromosome 3 resulting from insertion of long arm of homologous chromosome 9 (breakpoint q22 to q34) into the short arm of chromosome 3 in all metaphases analyzed, indicating clonal evolution (Fig. 1). Interphase FISH using DCDF BCR-ABL1 probe (ZytoVision, Bremerhaven, Germany) showed an atypical signal pattern (1G2R2F) in 95% cells analyzed. FISH was performed on metaphase cells to characterize the signal pattern which showed the presence of BCR::ABL1 fusion signal on derivative chromosome 9 and Philadelphia chromosome, green signal corresponding to BCR on normal chromosome 22 while one red signal corresponding to ABL1 , likely derived from homologous chromosome 9 inserted in the short arm of chromosome 3 and the second red signal localized on the p arm of chromosome 12 (Fig. 2 a). Whole chromosome painting probes (WCP) specific to chromosomes 3 and 9 were used to confirm the insertion of chromosome 9 in the p arm of chromosome 3 and rule out complex rearrangements involving either chromosome (Fig. 2 b). We suspected ETV6::ABL1 fusion resulting from cryptic insertion of ABL1 at 12p13 loci. This was confirmed using ETV6 breakapart probe (Empire Genomics, Buffalo, NY) which showed a split signal indicating ETV6 rearrangement in 95% interphase cells analyzed (Fig. 2 c). Concurrent BCR::ABL1 and ETV6::ABL1 was confirmed in the patient indicating clonal evolution in a case of Ph positive CML on treatment likely associated with imatinib resistance. Bone marrow morphological examination and immunophenotyping at this time point showed normocellular bone marrow with 4% blasts in a known case of chronic myeloid leukemia- chronic phase on therapy with no evidence of disease progression. Although, independent immunophenotypic analysis revealed 0.59% abnormal myeloid blasts with abnormal downregulation of CD13, CD15 and CD117, and overexpression of HLADR also, granulocytes gated at 60.63% of all viable cells showed abnormal downregulation of CD13 and CD15. Next generation sequencing to determine kinase domain mutation status of BCR::ABL1 fusion transcript was negative. ETV6::ABL1, identified later in disease course was the most probable factor contributing to imatinib resistance in this case. Owing to the indolent course of the disease, age of the patient, the patient was continued on Imatinib 800 mg/day as he remained in hematological remission, showed no evidence of splenomegaly, and tolerated the treatment without any adverse effects. The patient visited regularly for follow-up, molecular monitoring during the course of treatment revealed reduction in BCR-ABL1 fusion transcript levels from 49–14% on the International Scale (IS) after more than a decade of treatment with imatinib. Although, the patient failed to achieve a MMR, he survived for twelve years on Imatinib therapy with concurrent BCR::ABL1 and ETV6::ABL1 fusions, succumbing to disease in the year 2024 with no evidence of relapse or progression. Discussion We present a rare case of Ph-positive CML on treatment with imatinib, harboring concurrent BCR::ABL1 and ETV6::ABL1 fusions characterized by conventional cytogenetics and FISH. This is the first report of dual oncogenic fusions in a case of Ph positive CML, showing a durable response to first line imatinib therapy despite the failure to achieve MMR throughout the course of the disease. ETV6::ABL1 fusion is a rare genetic fusion reported in over 80 cases of myeloid/lymphoid neoplasms and in less than 30 cases of Ph negative CML/atypical CML [ 3 , 12 ]. Previously a single case of CML with ETV6::ABL1 fusion has been reported with ambigous information, likely representing atypical CML as FISH and conventional cytogenetics did not show the presence of BCR::ABL1 or Ph chromosome and the fusion transcript was only detected by RT-PCR, also there was no information pertaining to treatment and molecular profiling [ 5 ]. BCR::ABL1 is the defining molecular hallmark of CML, the presence of an additional ETV6::ABL1 fusion, resulting from a cryptic insertion event, is exceptionally rare and presents diagnostic, prognostic, and therapeutic challenges. The rarity of this fusion in haematological malignancies could be attributed to the opposite transcriptional orientation of both the genes [ 3 ]. ETV6::ABL1 fusion requires the occurrence of complex genetic rearrangements with multiple breaks for translocations or insertion of ABL1 at 12p13 loci or insertion of ETV6 at 9q34 loci [ 4 , 5 ]. In our case, the fusion resulted from a cryptic insertion of ABL1 from homologous chromosome 9 at 12p13 loci, resulting in ETV6::ABL1 fusion which was detected by FISH on metaphase cells. The case study highlights the continued importance of cytogenetic response assessment at regular intervals despite growing reliance on high-sensitivity molecular monitoring modalities. Although molecular monitoring was performed regular intervals, cytogenetic response was not evaluated at the appropriate time. The emergence of eosinophilia in the second year of diagnosis combined with lack of molecular response should have prompted cytogenetic evaluation in the patient. Moreover, if conventional karyotyping would have been performed solely the cryptic ABL1 rearrangement involving both the chromosome 9s would have been missed. This case emphasis the importance of FISH when clonal evolution is suspected as atypical signal patterns in FISH are often indicative of complex genetic abnormalities that could affect disease progression and therapeutic response [ 1 , 2 ]. It is therefore, important to integrate FISH results with molecular and clinical findings to gain a more comprehensive understanding of the patient's condition. The therapeutic efficacy of imatinib is well established in BCR::ABL1-positive CML however, there is limited data on response to Imatinib in ETV6::ABL1 positive cases, which can be heterogeneous with slight differences from the classic BCR-ABL1-positive CML [ 8 – 13 ]. The ETV6-ABL1 fusion protein, results in constitutive ABL1 kinase activation like BCR-ABL1 but the structural variability in the fusion product may alter the imatinib binding affinity and therapeutic responsiveness [ 11 ]. Some reports suggest early response to imatinib therapy in CML-like chronic phase with resistance to imatinib developing over time potentially driven by acquisition of secondary mutations in the kinase domain or activation of alternate pathways capable of bypassing imatinib inhibition as observed in our case [ 11 – 13 ]. In others, the imatinib response may be partial, with patients show a more aggressive discourse, progressing to blastic phase while on therapy after initial response. In these cases that are resistant or refractory to imatinib, second-generation TKIs, including dasatinib and nilotinib and stem cell transplantation, have shown superior response [ 14 – 16 ]. In our case, the patient exhibited classical features of CML in the chronic phase, initiation of standard-dose Imatinib (400 mg/day) led to a rapid complete hematologic response (CHR), indicating early treatment effectiveness. However, lack of access to molecular monitoring in a resource-limited setting hindered timely detection of suboptimal molecular response and imatinib resistance. The complex ABL1 rearrangement resulting in ETV6::ABL1 fusion, was the most likely factor contributing to imatinib resistance in our patient. The mechanisms for TKI resistance in ETV6::ABL1 positive cases remain unclear in vitro studies have shown that an activating mutation in the GNB1 gene could result in a resistance to TKI through restoration of signaling via the phosphoinositide-3-kinase (PI3K)/Akt/mTOR and mitogen-activated protein kinase (MAPK) pathways [ 17 ]. In other cases, other factors have been postulated, such as the activation of alternative signaling pathways, including the RAS/MAPK and JAK/STAT pathways, or changes in epigenetic regulation (termed BCR-ABL1 independent resistance) [ 17 – 19 , 20 ]. The variable response to imatinib and eventual development of resistance reinstates the need for comprehensive molecular testing for identification of the rare fusions such as ETV6::ABL1 in this case, after exclusion of other common causes of imatinib resistance. The patient exhibited a notably indolent disease course maintaining hematological remission for 12 years on Imatinib despite the presence of dual oncogenic fusions. This outcome could be due to several factors including indolent disease biology, the limited dominance of aggressive clones, partial TKI sensitivity to high dose imatinib of both BCR::ABL1 and ETV6::ABL1-driven pathways or host-related factors including immune surveillance [ 18 , 19 ]. This case demonstrates that long-term response to treatment can be achieved with escalated dose of imatinib and that transcript levels do not always correlate directly with clinical progression, particularly when atypical fusions or complex karyotypic rearrangements are present [ 15 ]. In conclusion, this unique case with long term follow-up data emphasizes the importance of integrating cytogenetics in the era of next generation sequencing to tailor therapy based on individual genetic profile especially when resistance to therapy and clonal evolution is suspected. Further studies are warranted to accurately predict outcome in such unique cases and documentation of these rare cases is essential to refine management strategies and enhance our understanding of biological and clinical implications of dual oncogenic drivers in myeloid neoplasms. Declarations Acknowledgments We thank the staff and students at the Cancer Cytogenetic Dept., Dept. of Haematopathology and Tata Hospital for their technical support. Funding information There was no funding received for conducting this study. Conflict of interest The authors declare no conflict of interest. Data availability No datasets were generated or analysed during the current study. Financial or non-financial interests The authors have no relevant financial or non-financial interests to disclose. Competing Interests The authors have no competing interests to declare that are relevant to the content of this article. Patients consent statement Informed consent was obtained from the patient for participating in the study and publish the results. Ethical Approval The study was approved by the Institutional Ethics Committee and performed in accordance with the ethical standards as laid down in the 1964 Declaration of Helsinki and its later amendments or comparable ethical standards. Authors’ contribution P.M, D.S-Conceptualized and designed the study, carried out follow-up cytogenetic and FISH analysis P.M-Wrote the manuscript. P.A conducted preliminary cytogenetics and FISH investigations. N.P performed molecular analyses. P.T and P.G.S conducted bone marrow morphology and immunophenotyping. S.P, A.G, N.J and N.K treated the patient and conducted clinical evaluations. References Zhang Z, Chen Z, Jiang M et al (2019) Heterogeneous BCR-ABL1 signal patterns identified by fluorescence in situ hybridization are associated with leukemic clonal evolution and poorer prognosis in BCR-ABL1 positive leukemia. BMC Cancer 19:935 Bakshi SR, Brahmbhatt MM, Trivedi PJ et al (2006) Atypical D-FISH patterns of BCR/ABL gene rearrangements in 169 chronic myeloid leukemia patients. J Assoc Genet Technol 32:164–167 Zaliova M, Moorman AV, Cazzaniga G et al (2016) Characterization of leukemias with ETV6-ABL1 fusion. Haematologica 101(9):1082–1093 Xie W, Wang SA, Hu S et al (2018) Myeloproliferative neoplasm with ABL1/ETV6 rearrangement mimics chronic myeloid leukemia and responds to tyrosine kinase inhibitors. Cancer Gen 228–229:41–46 Choi SI, Jang MA, Jeong WJ et al (2017) A case of chronic myeloid leukemia with rare variant ETV6/ABL1 rearrangement. Ann Lab Med 37(1):77–80 Keung YK, Beaty M, Steward W et al (2002) Chronic myelocytic leukemia with eosinophilia, t(9;12)(q34;p13), and ETV6-ABL gene rearrangement: case report and review of the literature. Cancer Genet Cytogenet 138:139–142 Yao J, Xu L, Aypar U et al (2021) Myeloid/lymphoid neoplasms with eosinophilia/basophilia and ETV6-ABL1 fusion: cell-of-origin and response to tyrosine kinase inhibition. Haematologica 106(2):614–618 O'Brien SG, Vieira SA, Connors S et al (2002) Transient response to imatinib mesylate (STI571) in a patient with the ETV6-ABL t(9;12) translocation. Blood 99:3465–3467 Kakadia PM, Schmidmaier R, Volkl A et al (2016) An ETV6-ABL1 fusion in a patient with chronic myeloproliferative neoplasm: initial response to imatinib followed by rapid transformation into ALL. Leuk Res Rep 6:50–54 Barbouti A, Ahlgren T, Johansson B et al (2003) Clinical and genetic studies of ETV6/ABL1-positive chronic myeloid leukaemia in blast crisis treated with imatinib mesylate. Br J Haematol 122(1):85–93 Renzi S, Algawahmed F, Davidson S et al (2023) Myeloproliferative neoplasm driven by ETV6 ABL1 in an adolescent with recent history of Burkitt leukemia. Curr Oncol 30(7):5946–5952 Bochicchio MT, Marconi G, Baldazzi C et al (2023) ETV6::ABL1-positive myeloid neoplasm: a case of a durable response to imatinib mesylate without additional or previous treatment. Int J Mol Sci 25(1):118 Kawamata N, Dashti A, Lu D et al (2008) Chronic phase of ETV6-ABL1 positive CML responds to imatinib. Genes Chromosomes Cancer 47:919–921 Nand R, Bryke C, Kroft SH et al (2009) Myeloproliferative disorder with eosinophilia and ETV6-ABL gene rearrangement: efficacy of second-generation tyrosine kinase inhibitors. Leuk Res 33:1144–1146 Tiribelli M, Barraco D, Medeot M et al (2015) Long-term efficacy and safety of nilotinib therapy after imatinib failure in eosinophilic myeloproliferative neoplasm and ETV6-ABL rearrangement. Ann Hematol 94:1423–1424 Zhang Y, Nguyen L, Lu CM et al (2023) Clinical response to upfront targeted tyrosine kinase inhibitors among patients with myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusions. Clin Lymphoma Myeloma Leuk 23:e150–e163 Zimmermannova O, Doktorova E, Stuchly J, et al (2017) An activating mutation of GNB1 is associated with resistance to tyrosine kinase inhibitors in ETV6-ABL1-positive leukemia. Oncogene 36:5985–5994 Steelman LS, Pohnert SC, Shelton JG et al (2004) JAK/STAT, Raf/MEK/ERK, PI3K/Akt and BCR-ABL in cell cycle progression and leukemogenesis. Leukemia 18:189–218 Amarante-Mendes GP, Rana A, Datoguia TS, et al (2022) BCR-ABL1 tyrosine kinase complex signaling transduction: challenges to overcome resistance in chronic myeloid leukemia. Pharmaceutics 14:215 Perna F, Abdel-Wahab O, Levine RL, et al (2011) ETV6-ABL1-positive "chronic myeloid leukemia": clinical and molecular response to tyrosine kinase inhibition. Haematologica 96:342–343 Additional Declarations No competing interests reported. Supplementary Files supplementary1.docx Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 23 Mar, 2026 Reviewers agreed at journal 23 Mar, 2026 Reviewers invited by journal 10 Jun, 2025 Editor assigned by journal 25 Apr, 2025 Submission checks completed at journal 25 Apr, 2025 First submitted to journal 21 Apr, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6495243","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Case Report","associatedPublications":[],"authors":[{"id":469283419,"identity":"2b1d0219-f83b-4a1f-8a0e-858fd87e64f7","order_by":0,"name":"Purvi Mohanty","email":"","orcid":"","institution":"Tata Memorial Centre","correspondingAuthor":false,"prefix":"","firstName":"Purvi","middleName":"","lastName":"Mohanty","suffix":""},{"id":469283420,"identity":"1a636702-f920-43f7-ac16-ff43e4aa4807","order_by":1,"name":"Dhanlaxmi Shetty","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAz0lEQVRIiWNgGAWjYDACCTDJLMMPF2EmrIWx4QADM49kG8laDI4R6y752c3HH39ss+Yxvt+d+IHhl01iAzvvAbxaDO4cS2w42JbOY3aMd7MEY19aYgMzXwJ+LRI5hkAth0FatjEw9hw2BjkSv8Nm5H8EazFuI1YLw40cRrAWAzagFoYfh+UIajG4kWY448y5dB6JY7mbJRIb0uTYCDss+cGHijJrOf7msxs/fPhjw8PPf4aAw0CAkQ3KSATGJxtepXDwB4MxCkbBKBgFowABAJ/SQvo0+o9BAAAAAElFTkSuQmCC","orcid":"","institution":"Tata Memorial Centre","correspondingAuthor":true,"prefix":"","firstName":"Dhanlaxmi","middleName":"","lastName":"Shetty","suffix":""},{"id":469283428,"identity":"cc0ee0e4-7a61-4a93-8051-fe4c69945f81","order_by":2,"name":"Pratibha Amare","email":"","orcid":"","institution":"Lilac Insights Pvt. 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karyotype-46,XY,ins(3;\u003cu\u003e9\u003c/u\u003e)(p21;q22q34),t(9;22)(q34;q11.2) showing major clonal abnormality t(9;22)(q34;q11.2) resulting in derivative chromosome 9 and Philadelphia chromosome along with insertion of long arm of homologous chromosome 9 from q22 loci into the short arm of chromosome 3 as indicated by arrows\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-6495243/v1/73d9ee4ca7e458caf7f43f14.png"},{"id":84665632,"identity":"83effe6e-6581-4f84-bec9-817b78b3a6dc","added_by":"auto","created_at":"2025-06-16 05:38:36","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":162314,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003ea)\u003c/strong\u003e Metaphase FISH using DCDF BCR-ABL1 probe revealed an atypical signal pattern (1G2R2F), \u0026nbsp;with green signal from \u003cem\u003eBCR\u003c/em\u003e on normal chromosome 22 and a complex \u003cem\u003eABL1\u003c/em\u003erearrangement with two extra red signals showing insertion of \u003cem\u003eABL1 \u003c/em\u003efrom homologous chromosome 9\u003cem\u003e \u003c/em\u003einto the short arm of chromosome 3 and a second cryptic insertion into the short arm of chromosome 12 along with a \u0026nbsp;concurrent BCR::ABL1 fusion present on derivative chromosome 9 and Philadelphia chromosome from balanced translocation t(9;22)(q34;q11.2) as seen in respective grayscale and coloured images \u003cstrong\u003eb)\u003c/strong\u003e Metaphase FISH using whole chromosome painting (WCP) probes for chromosome 3 (green) and chromosome 9 (red) confirmed insertion of chromosome 9 into the short arm of chromosome 3 \u003cstrong\u003ec)\u003c/strong\u003e FISH on interphase cells using dual color ETV6 breakapart probe showing break in signal indicating \u003cem\u003eETV6\u003c/em\u003e rearrangement\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-6495243/v1/99b4e351438dfaa9713bb8f0.png"},{"id":84665840,"identity":"d4583699-3c69-4601-8a40-8b32d7babad0","added_by":"auto","created_at":"2025-06-16 05:39:00","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":754521,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6495243/v1/356ca6e1-6418-4c19-b325-039fdcac6122.pdf"},{"id":84664448,"identity":"95d74da9-dee4-4b2a-9df9-a31fb026f5fe","added_by":"auto","created_at":"2025-06-16 05:30:36","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":75854,"visible":true,"origin":"","legend":"","description":"","filename":"supplementary1.docx","url":"https://assets-eu.researchsquare.com/files/rs-6495243/v1/c73d23f2acd9c83c1dff6eac.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Concurrent ETV6::ABL1 and BCR::ABL1 in a rare case of Chronic Myeloid Leukemia: A paradox of imatinib resistance and indolent clinical course","fulltext":[{"header":"INTRODUCTION","content":"\u003cp\u003ePhiladelphia (Ph) chromosome is the defining feature of Chronic Myeloid Leukemia (CML), resulting from a reciprocal translocation t(9;22)(q34;q11.2). Conventional cytogenetic analysis confirms the presence of the Ph chromosome and additional cytogenetic abnormalities, while Fluorescence in-situ hybridization (FISH) using dual-color, dual-fusion probe (DCDF) verifies the BCR::ABL1 fusion and can show typical (1G1R2F) or atypical signal patterns indicating 9q deletions on the derivative chromosome 9 (1G1R1F), three way or more variant translocations (2G2R1F), supernumerary Ph (1G1R3F/4F), deletions of sequences proximal to chromosome 9 breakpoint or distal to chromosome 22 breakpoint (1G2R1F/1R2G1F) and other genetic aberrations [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. The presence of atypical signal pattern in FISH is often indicative of complex genetic rearrangements and additional cytogenetic abnormalities (ACA) which are likely to be associated with disease progression and resistance to therapy [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn this report, we describe a unique case of Ph positive CML on treatment with atypical signal pattern (1G2R2F) using DCDF BCR-ABL1 FISH probe which was characterized to reveal a complex rearrangement of \u003cem\u003eABL1\u003c/em\u003e gene resulting in concurrent BCR::ABL1 and ETV6::ABL1 fusions. ETV6::ABL1 is a rare genetic fusion identified in Myeloproliferative neoplasms (MPNs) including Ph negative CML with t(9;12)(q34;p13), BCR-ABL1 like Acute Lymphoblastic Leukemia (ALL) and Acute Myeloid Leukemia (AML) which leads to constitutive tyrosine kinase activation and oncogenic transformation similar to BCR::ABL1 [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Owing to the rarity of this fusion, there is inconsistent data on the prognostic significance of this fusion in MPNs/CML and its impact on outcome with tyrosine kinase inhibitor (TKI) therapy [\u003cspan additionalcitationids=\"CR6 CR7 CR8 CR9 CR10\" citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. To the best of our knowledge, this is the first report of Ph positive CML with concomitant BCR::ABL1 and ETV6::ABL1, demonstrating long term survival on imatinib therapy without achieving a major molecular response (MMR) during the course of the disease.\u003c/p\u003e"},{"header":"CASE REPORT","content":"\u003cp\u003eA 63-year-old male with history of hypertension presented with splenomegaly, low grade fever, pallor and loss of appetite in July 2012. The haematological profile at this time point showed leucocytosis with total leukocyte count of 24.5x10\u003csup\u003e9\u003c/sup\u003e/L (78.7% neutrophils, 8% lymphocytes, 5.4% monocytes, 2.2% eosinophils and 3% basophils), haemoglobin level of 11.2 g/dL, and platelet count of 762x10\u003csup\u003e9\u003c/sup\u003e/L. Bone marrow morphological examination revealed a markedly hypercellular marrow with myeloid-to-erythroid ratio of 50:1 and 5% blasts. Based on the clinical findings the patient was advised cytogenetic and molecular workup for the diagnosis of CML. Conventional cytogenetic analysis of Giemsa-banded metaphases from an unstimulated overnight bone marrow aspirate culture, revealed the karyotype-46,XY,t(9;22)(q34,q11.2)[\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e]; while FISH on interphase cells using DCDF BCR-ABL1 probe (ZytoVision, Bremerhaven, Germany) showed typical signal pattern 1G1R2F indicating BCR::ABL1 resulting from balanced translocation in 98% cells analyzed. Reverse transcriptase Polymerase chain reaction (RT-PCR) was positive for the p210 major BCR-ABL1 fusion transcript. He was initiated on Imatinib 400 mg/day and achieved a complete hematological response (CHR) within two months of therapy. Thereafter, he continued treatment in his hometown, in a resource limited setting with no access to molecular monitoring.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eHe then presented two years post therapy with rising basophil and eosinophil counts and no other complaints (supplementary material 1). The patient reported compliance with therapy and laboratory reports during the period showed sustained haematological response. Quantitative real time PCR (RQ-PCR) was subsequently performed out at our Centre, to assess BCR::ABL1 transcript levels; however, he had failed to achieve MMR, two years post initiation of imatinib therapy and thereafter (supplementary material 1). Due to financial constraints, the patient was unable to afford second generation TKI and was started on Imatinib at an escalated dosage of 800mg/day and continued the same throughout the course of the disease. The patient\u0026rsquo;s basophil count normalized soon after, however, his eosinophil count gradually decreased after two years. The patient was in haematological remission and continued treatment at his hometown. During this entire period cytogenetic re-evaluation was not performed despite failure to achieve MMR. Following seven years on treatment with imatinib at a dosage of 800mg/day, cytogenetic re-evaluation was done in 2021. Chromosomal analysis of bone marrow aspirate cells revealed the karyotype-46,XY,ins(3;\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e9\u003c/span\u003e)(p21;q22q34),t(9;22)(q34;q11.2)[\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e] showing the presence of a balanced t(9;22)(q35;q11.2) with derivative chromosome 9, Ph chromosome and a derivative chromosome 3 resulting from insertion of long arm of homologous chromosome 9 (breakpoint q22 to q34) into the short arm of chromosome 3 in all metaphases analyzed, indicating clonal evolution (Fig.\u0026nbsp;1).\u003c/p\u003e \u003cp\u003eInterphase FISH using DCDF BCR-ABL1 probe (ZytoVision, Bremerhaven, Germany) showed an atypical signal pattern (1G2R2F) in 95% cells analyzed. FISH was performed on metaphase cells to characterize the signal pattern which showed the presence of BCR::ABL1 fusion signal on derivative chromosome 9 and Philadelphia chromosome, green signal corresponding to \u003cem\u003eBCR\u003c/em\u003e on normal chromosome 22 while one red signal corresponding to \u003cem\u003eABL1\u003c/em\u003e, likely derived from homologous chromosome 9 inserted in the short arm of chromosome 3 and the second red signal localized on the p arm of chromosome 12 (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e2\u003c/span\u003ea). Whole chromosome painting probes (WCP) specific to chromosomes\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e3 and 9 were used to confirm the insertion of chromosome 9 in the p arm of chromosome 3 and rule out complex rearrangements involving either chromosome (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e2\u003c/span\u003eb). We suspected ETV6::ABL1 fusion resulting from cryptic insertion of \u003cem\u003eABL1\u003c/em\u003e at 12p13 loci. This was confirmed using ETV6 breakapart probe (Empire Genomics, Buffalo, NY) which showed a split signal indicating \u003cem\u003eETV6\u003c/em\u003e rearrangement in 95% interphase cells analyzed (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e2\u003c/span\u003ec). Concurrent BCR::ABL1 and ETV6::ABL1 was confirmed in the patient indicating clonal evolution in a case of Ph positive CML on treatment likely associated with imatinib resistance. Bone marrow morphological examination and immunophenotyping at this time point showed normocellular bone marrow with 4% blasts in a known case of chronic myeloid leukemia- chronic phase on therapy with no evidence of disease progression. Although, independent immunophenotypic analysis revealed 0.59% abnormal myeloid blasts with abnormal downregulation of CD13, CD15 and CD117, and overexpression of HLADR also, granulocytes gated at 60.63% of all viable cells showed abnormal downregulation of CD13 and CD15.\u003c/p\u003e \u003cp\u003eNext generation sequencing to determine kinase domain mutation status of BCR::ABL1 fusion transcript was negative. ETV6::ABL1, identified later in disease course was the most probable factor contributing to imatinib resistance in this case. Owing to the indolent course of the disease, age of the patient, the patient was continued on Imatinib 800 mg/day as he remained in hematological remission, showed no evidence of splenomegaly, and tolerated the treatment without any adverse effects. The patient visited regularly for follow-up, molecular monitoring during the course of treatment revealed reduction in BCR-ABL1 fusion transcript levels from 49\u0026ndash;14% on the International Scale (IS) after more than a decade of treatment with imatinib. Although, the patient failed to achieve a MMR, he survived for twelve years on Imatinib therapy with concurrent BCR::ABL1 and ETV6::ABL1 fusions, succumbing to disease in the year 2024 with no evidence of relapse or progression.\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eWe present a rare case of Ph-positive CML on treatment with imatinib, harboring concurrent BCR::ABL1 and ETV6::ABL1 fusions characterized by conventional cytogenetics and FISH. This is the first report of dual oncogenic fusions in a case of Ph positive CML, showing a durable response to first line imatinib therapy despite the failure to achieve MMR throughout the course of the disease. ETV6::ABL1 fusion is a rare genetic fusion reported in over 80 cases of myeloid/lymphoid neoplasms and in less than 30 cases of Ph negative CML/atypical CML [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. Previously a single case of CML with ETV6::ABL1 fusion has been reported with ambigous information, likely representing atypical CML as FISH and conventional cytogenetics did not show the presence of BCR::ABL1 or Ph chromosome and the fusion transcript was only detected by RT-PCR, also there was no information pertaining to treatment and molecular profiling [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. BCR::ABL1 is the defining molecular hallmark of CML, the presence of an additional ETV6::ABL1 fusion, resulting from a cryptic insertion event, is exceptionally rare and presents diagnostic, prognostic, and therapeutic challenges. The rarity of this fusion in haematological malignancies could be attributed to the opposite transcriptional orientation of both the genes [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eETV6::ABL1 fusion requires the occurrence of complex genetic rearrangements with multiple breaks for translocations or insertion of \u003cem\u003eABL1\u003c/em\u003e at 12p13 loci or insertion of \u003cem\u003eETV6\u003c/em\u003e at 9q34 loci [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e, \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. In our case, the fusion resulted from a cryptic insertion of \u003cem\u003eABL1\u003c/em\u003e from homologous chromosome 9 at 12p13 loci, resulting in ETV6::ABL1 fusion which was detected by FISH on metaphase cells. The case study highlights the continued importance of cytogenetic response assessment at regular intervals despite growing reliance on high-sensitivity molecular monitoring modalities. Although molecular monitoring was performed regular intervals, cytogenetic response was not evaluated at the appropriate time. The emergence of eosinophilia in the second year of diagnosis combined with lack of molecular response should have prompted cytogenetic evaluation in the patient. Moreover, if conventional karyotyping would have been performed solely the cryptic \u003cem\u003eABL1\u003c/em\u003e rearrangement involving both the chromosome 9s would have been missed. This case emphasis the importance of FISH when clonal evolution is suspected as atypical signal patterns in FISH are often indicative of complex genetic abnormalities that could affect disease progression and therapeutic response [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. It is therefore, important to integrate FISH results with molecular and clinical findings to gain a more comprehensive understanding of the patient's condition.\u003c/p\u003e \u003cp\u003eThe therapeutic efficacy of imatinib is well established in BCR::ABL1-positive CML however, there is limited data on response to Imatinib in ETV6::ABL1 positive cases, which can be heterogeneous with slight differences from the classic BCR-ABL1-positive CML [\u003cspan additionalcitationids=\"CR9 CR10 CR11 CR12\" citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. The ETV6-ABL1 fusion protein, results in constitutive ABL1 kinase activation like BCR-ABL1 but the structural variability in the fusion product may alter the imatinib binding affinity and therapeutic responsiveness [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. Some reports suggest early response to imatinib therapy in CML-like chronic phase with resistance to imatinib developing over time potentially driven by acquisition of secondary mutations in the kinase domain or activation of alternate pathways capable of bypassing imatinib inhibition as observed in our case [\u003cspan additionalcitationids=\"CR12\" citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. In others, the imatinib response may be partial, with patients show a more aggressive discourse, progressing to blastic phase while on therapy after initial response. In these cases that are resistant or refractory to imatinib, second-generation TKIs, including dasatinib and nilotinib and stem cell transplantation, have shown superior response [\u003cspan additionalcitationids=\"CR15\" citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn our case, the patient exhibited classical features of CML in the chronic phase, initiation of standard-dose Imatinib (400 mg/day) led to a rapid complete hematologic response (CHR), indicating early treatment effectiveness. However, lack of access to molecular monitoring in a resource-limited setting hindered timely detection of suboptimal molecular response and imatinib resistance. The complex \u003cem\u003eABL1\u003c/em\u003e rearrangement resulting in ETV6::ABL1 fusion, was the most likely factor contributing to imatinib resistance in our patient. The mechanisms for TKI resistance in ETV6::ABL1 positive cases remain unclear in vitro studies have shown that an activating mutation in the \u003cem\u003eGNB1\u003c/em\u003e gene could result in a resistance to TKI through restoration of signaling via the phosphoinositide-3-kinase (PI3K)/Akt/mTOR and mitogen-activated protein kinase (MAPK) pathways [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. In other cases, other factors have been postulated, such as the activation of alternative signaling pathways, including the RAS/MAPK and JAK/STAT pathways, or changes in epigenetic regulation (termed BCR-ABL1 independent resistance) [\u003cspan additionalcitationids=\"CR18\" citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e, \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e]. The variable response to imatinib and eventual development of resistance reinstates the need for comprehensive molecular testing for identification of the rare fusions such as ETV6::ABL1 in this case, after exclusion of other common causes of imatinib resistance.\u003c/p\u003e \u003cp\u003eThe patient exhibited a notably indolent disease course maintaining hematological remission for 12 years on Imatinib despite the presence of dual oncogenic fusions. This outcome could be due to several factors including indolent disease biology, the limited dominance of aggressive clones, partial TKI sensitivity to high dose imatinib of both BCR::ABL1 and ETV6::ABL1-driven pathways or host-related factors including immune surveillance [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e, \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e]. This case demonstrates that long-term response to treatment can be achieved with escalated dose of imatinib and that transcript levels do not always correlate directly with clinical progression, particularly when atypical fusions or complex karyotypic rearrangements are present [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. In conclusion, this unique case with long term follow-up data emphasizes the importance of integrating cytogenetics in the era of next generation sequencing to tailor therapy based on individual genetic profile especially when resistance to therapy and clonal evolution is suspected. Further studies are warranted to accurately predict outcome in such unique cases and documentation of these rare cases is essential to refine management strategies and enhance our understanding of biological and clinical implications of dual oncogenic drivers in myeloid neoplasms.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe thank the staff and students at the Cancer Cytogenetic Dept., Dept. of Haematopathology and Tata Hospital for their technical support.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding information\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThere was no funding received for conducting this study.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflict of interest\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare no conflict of interest.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData availability\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNo datasets were generated or analysed during the current study.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFinancial or non-financial interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors have no relevant financial or non-financial interests to disclose.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting Interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors have no competing interests to declare that are relevant to the content of this article.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003ePatients consent statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eInformed consent was obtained from the patient for participating in the study and publish the results.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthical Approval\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe study was approved by the Institutional Ethics Committee and performed in accordance with the ethical standards as laid down in the 1964 Declaration of Helsinki and its later amendments or comparable ethical standards.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors\u0026rsquo; contribution\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eP.M, D.S-Conceptualized and designed the study, carried out follow-up cytogenetic and FISH analysis P.M-Wrote the manuscript. P.A conducted preliminary cytogenetics and FISH investigations. N.P performed molecular analyses. P.T and P.G.S conducted bone marrow morphology and immunophenotyping. S.P, A.G, N.J and N.K treated the patient and conducted clinical evaluations.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n \u003cli\u003eZhang Z, Chen Z, Jiang M et al (2019) Heterogeneous BCR-ABL1 signal patterns identified by fluorescence in situ hybridization are associated with leukemic clonal evolution and poorer prognosis in BCR-ABL1 positive leukemia. BMC Cancer 19:935\u003c/li\u003e\n \u003cli\u003eBakshi SR, Brahmbhatt MM, Trivedi PJ et al (2006) Atypical D-FISH patterns of BCR/ABL gene rearrangements in 169 chronic myeloid leukemia patients. J Assoc Genet Technol 32:164\u0026ndash;167\u003c/li\u003e\n \u003cli\u003eZaliova M, Moorman AV, Cazzaniga G et al (2016) Characterization of leukemias with ETV6-ABL1 fusion. Haematologica 101(9):1082\u0026ndash;1093\u003c/li\u003e\n \u003cli\u003eXie W, Wang SA, Hu S et al (2018) Myeloproliferative neoplasm with ABL1/ETV6 rearrangement mimics chronic myeloid leukemia and responds to tyrosine kinase inhibitors. Cancer Gen 228\u0026ndash;229:41\u0026ndash;46\u003c/li\u003e\n \u003cli\u003eChoi SI, Jang MA, Jeong WJ et al (2017) A case of chronic myeloid leukemia with rare variant ETV6/ABL1 rearrangement. Ann Lab Med 37(1):77\u0026ndash;80\u003c/li\u003e\n \u003cli\u003eKeung YK, Beaty M, Steward W et al (2002) Chronic myelocytic leukemia with eosinophilia, t(9;12)(q34;p13), and ETV6-ABL gene rearrangement: case report and review of the literature. Cancer Genet Cytogenet 138:139\u0026ndash;142\u003c/li\u003e\n \u003cli\u003eYao J, Xu L, Aypar U et al (2021) Myeloid/lymphoid neoplasms with eosinophilia/basophilia and ETV6-ABL1 fusion: cell-of-origin and response to tyrosine kinase inhibition. 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Ann Hematol 94:1423\u0026ndash;1424\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eZhang Y, Nguyen L, Lu CM et al (2023) Clinical response to upfront targeted tyrosine kinase inhibitors among patients with myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusions. Clin Lymphoma Myeloma Leuk 23:e150\u0026ndash;e163\u003c/li\u003e\n \u003cli\u003eZimmermannova O, Doktorova E, Stuchly J, et al (2017) An activating mutation of GNB1 is associated with resistance to tyrosine kinase inhibitors in ETV6-ABL1-positive leukemia. Oncogene 36:5985\u0026ndash;5994\u003c/li\u003e\n \u003cli\u003eSteelman LS, Pohnert SC, Shelton JG et al (2004) JAK/STAT, Raf/MEK/ERK, PI3K/Akt and BCR-ABL in cell cycle progression and leukemogenesis. Leukemia 18:189\u0026ndash;218\u003c/li\u003e\n \u003cli\u003eAmarante-Mendes GP, Rana A, Datoguia TS, et al (2022) BCR-ABL1 tyrosine kinase complex signaling transduction: challenges to overcome resistance in chronic myeloid leukemia. Pharmaceutics 14:215\u003c/li\u003e\n \u003cli\u003ePerna F, Abdel-Wahab O, Levine RL, et al (2011) ETV6-ABL1-positive \u0026quot;chronic myeloid leukemia\u0026quot;: clinical and molecular response to tyrosine kinase inhibition. Haematologica 96:342\u0026ndash;343\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"annals-of-hematology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"aohe","sideBox":"Learn more about [Annals of Hematology](http://link.springer.com/journal/277)","snPcode":"277","submissionUrl":"https://submission.nature.com/new-submission/277/3","title":"Annals of Hematology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"BCR:ABL1, ETV6:ABL1, CML, IMATINIB RESISTANCE, ABL1 REARRANGEMENT, ETV6","lastPublishedDoi":"10.21203/rs.3.rs-6495243/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6495243/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eChronic myeloid leukaemia (CML) is characterized by the presence of BCR::ABL1 showing favorable response to imatinib therapy. Complex rearrangements in CML are indicative of clonal evolution and often associated with disease progression and poor response to therapy. Cytogenetically, these cases present with atypical Fluorescence in-situ hybridization signal patterns and additional cytogenetic abnormalities on conventional karyotyping. Current research in CML is primarily focused on discovery of new tyrosine kinase inhibitors (TKIs) and uncovering the underlying causes of resistance to imatinib. In this report, we describe a rare case of Ph-positive CML on imatinib therapy showing atypical FISH signal pattern, harboring concurrent BCR::ABL1 and ETV6::ABL1 fusions characterized by conventional cytogenetics and Fluorescence in-situ hybridization. This is the first report of dual oncogenic fusions in a case CML, showing complex ABL1 rearrangements along with Philadelphia chromosome, demonstrating long term survival on imatinib therapy despite the failure to achieve major molecular response throughout the course of the disease. The key highlight of the study was the pivotal role of cytogenetic analysis in elucidating the underlying cause of imatinib resistance. The systematic documentation of such rare cases is essential for efficient management and evolving our understanding of dual oncogenic drivers in myeloid neoplasms.\u003c/p\u003e","manuscriptTitle":"Concurrent ETV6::ABL1 and BCR::ABL1 in a rare case of Chronic Myeloid Leukemia: A paradox of imatinib resistance and indolent clinical course","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-06-16 05:30:31","doi":"10.21203/rs.3.rs-6495243/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"editorInvitedReview","content":"","date":"2026-03-23T22:25:31+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"155626840017424450398291080135701923820","date":"2026-03-23T20:30:23+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-06-10T14:01:04+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-04-25T12:39:45+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-04-25T12:35:02+00:00","index":"","fulltext":""},{"type":"submitted","content":"Annals of Hematology","date":"2025-04-21T10:31:58+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"annals-of-hematology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"aohe","sideBox":"Learn more about [Annals of Hematology](http://link.springer.com/journal/277)","snPcode":"277","submissionUrl":"https://submission.nature.com/new-submission/277/3","title":"Annals of Hematology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"8249b193-91a8-42f3-a666-4e055ca7a1f3","owner":[],"postedDate":"June 16th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2025-06-16T05:30:31+00:00","versionOfRecord":[],"versionCreatedAt":"2025-06-16 05:30:31","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-6495243","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6495243","identity":"rs-6495243","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}