Acute myeloid leukaemia with BCR::ABL1 fusion

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Haematolymphoid Tumours (WHO Classification, 5th ed.)

editContent Update To WHO 5th Edition Classification Is In Process; Content Below is Based on WHO 4th Edition Classification
This page was converted to the new template on 2023-12-07. The original page can be found at HAEM4:Acute Myeloid Leukemia (AML) with BCR-ABL1.

(General Instructions – The focus of these pages is the clinically significant genetic alterations in each disease type. This is based on up-to-date knowledge from multiple resources such as PubMed and the WHO classification books. The CCGA is meant to be a supplemental resource to the WHO classification books; the CCGA captures in a continually updated wiki-stye manner the current genetics/genomics knowledge of each disease, which evolves more rapidly than books can be revised and published. If the same disease is described in multiple WHO classification books, the genetics-related information for that disease will be consolidated into a single main page that has this template (other pages would only contain a link to this main page). Use HUGO-approved gene names and symbols (italicized when appropriate), HGVS-based nomenclature for variants, as well as generic names of drugs and testing platforms or assays if applicable. Please complete tables whenever possible and do not delete them (add N/A if not applicable in the table and delete the examples); to add (or move) a row or column in a table, click nearby within the table and select the > symbol that appears. Please do not delete or alter the section headings. The use of bullet points alongside short blocks of text rather than only large paragraphs is encouraged. Additional instructions below in italicized blue text should not be included in the final page content. Please also see Author_Instructions and FAQs as well as contact your Associate Editor or Technical Support.)

Primary Author(s)*

Xinxiu Xu PhD, PharmB, Vanderbilt University Medical Center

WHO Classification of Disease

Structure Disease
Book Haematolymphoid Tumours (5th ed.)
Category Myeloid proliferations and neoplasms
Family Acute myeloid leukaemia
Type Acute myeloid leukaemia with defining genetic abnormalities
Subtype(s) Acute myeloid leukaemia with BCR::ABL1 fusion

Related Terminology

Acceptable Acute myeloid leukaemia with t(9;22)(q34;q11.2)
Not Recommended N/A

Gene Rearrangements

The t(9:22)(q34.1;q11.2) results in the formation of the Ph chromosome and the chimeric BCR-ABL1 fusion gene. In AML, ~70 - 80% cases with BCR::ABL1 harbor p210 transcripts, and 50-60% cases with additional chromosomal abnormalities[1][2][3][4]. The most common BCR-ABL1 transcripts p190 and p210 have been detected in nearly equal distribution[5]. Since p190 is very rare in CML (p210 transcripts in >99% of cases), the presentation with a p190 transcript is in favor of the diagnosis of AML rather than CML[6].

Driver Gene Fusion(s) and Common Partner Genes Molecular Pathogenesis Typical Chromosomal Alteration(s) Prevalence -Common >20%, Recurrent 5-20% or Rare <5% (Disease) Diagnostic, Prognostic, and Therapeutic Significance - D, P, T Established Clinical Significance Per Guidelines - Yes or No (Source) Clinical Relevance Details/Other Notes
ABL1 BCR::ABL1 The pathogenic derivative is the der(22) resulting in fusion of 5’ BCR and 3’ABL1. t(9;22)(q34;q11.2) Common (CML); Rare (AML). Diagnosis: BCR-ABL1 positive AML is an emerging entity. The proliferation of BCR-ABL1 positive blasts present a diagnostic dilemma. While it may be difficult, it is essential to distinguish between BCR-ABL1 positive AML and Chronic Myeloid Leukemia in Myeloid Blast Crisis (CML-MBC), in order to choose the most appropriate therapy (e.g., intensive induction chemotherapy versus tyrosine kinase inhibitor (TKI) followed by an early allogeneic stem cell transplant). After the exclusion of acute leukemia of ambiguous lineage (a separate entity according to WHO) by flow cytometry, it is helpful to note any past history of antecedent hematological disease. Compared to CML-MBC, a higher percentage of blasts (median: 47% vs 13%), a lower percentage of basophils (median: 0% vs 2.5%) and absolute basophil count, a lower frequency of splenomegaly (25% vs 65%), lower cellularity, fewer dwarf megakaryocytes, and normal M:E ratio favor the diagnosis of BCR-ABL1 positive AML[2][1]. The detection of p190 transcript and the occurrence of any BCR-ABL1 transcript in less than 100% of metaphases supports the diagnosis of AML rather than CML. Persistent CCyR (Complete Cytogenetic Response) after conventional chemotherapy is unusual for CML-MBC and supports the diagnosis of BCR-ABL1 positive AML[5]. Karyotype analysis that identifies the t(9;22)(q34;q11.2) translocation, either alone or in conjunction with additional chromosomal abnormalities, characterizes BCR-ABL1 positive AML[1][2]. In addition, molecular methods including dual-colour dual-fusion FISH, RT-PCR, qPCR, and RNA or DNA sequencing are used to identify all common breakpoint variants when applicable.


Prognosis: The overall prognosis of BCR-ABL1 positive AML is poor, with a median survival time of <9 months[7][1]. The National Comprehensive Cancer Network (NCCN) Clinical Practice Guidelines in Oncology for AML categorize this entity into the poor-risk group, comparable with complex aberrant karyotype AML[8]. It appears that the prognosis of BCR-ABL1 positive AML depends more on the genetic background (concurrent aberrations) than on BCR-ABL1 itself. Unlike in CML, BCR-ABL1 does not appear to be the key driver in AML though may provide a proliferative advantage to a particular BCR-ABL1 positive subclone.


Therapeutics: There is currently no standardized treatment approach for BCR-ABL1 positive AML. Therapy with TKI alone does not produce sustained responses in BCR-ABL1 positive AML[1]. This may be due to a very rapid clonal evolution, resulting in resistance in a much higher proportion of patients and in a significantly shorter time than in CML[5].Venetoclax and TKI combination regimens have shown good response in some studies[9].

Yes (WHO, NCCN) The t(9;22) is diagnostic of CML in the appropriate morphology and clinical context[10][11]. The prevalence of BCR"" ABL1 in CML is common ~90-95%[12]. This fusion is responsive to targeted therapy such as Imatinib (Gleevec)[13].


BCR::ABL1 is generally favorable in CML[14][15].

Three BCR-ABL chimeric proteins result from varying mRNA fusions of the ABL and BCR genes. The most common breakpoint occurs in BCR intron 13 or 14, fusing to ABL1 exon a2 (e13a2, e14a2), yielding a 210 kilodalton protein (p210 BCR-ABL1) found in 95% of CML cases. A rare alternative (<1%) is the e19a2 fusion, producing a 230 kilodalton protein (p230 BCR-ABL1), a marker for neutrophilic-chronic myeloid leukemia. The e1a2 fusion results in the p190 BCR-ABL1 protein, prevalent in B cell ALL, less common in AML, and rare in CML[16].


The prevalence of BCR::ABL1 in AML is rare (~0.5 - 3%)[16], per 5th WHO guideline the prevalence is <0.5%[17].

There is a single case report of an AML patient with BCR::ABL1 achieving molecular remission with dasatinib and chemotherapy[18].


Outcome of patients < 50 years of age with TKI pretreated BCR::ABL1 positive AML receiving allogeneic stem cell transplant is relatively favorable[19].


Survival status postallogeneic transplantation appears similar to intermediate risk AML, with one report demonstrating 3 year overall survival of 73%[20].

Individual Region Genomic Gain/Loss/LOH

AML with BCR-ABL1 carries unique genome imbalances. Nacheva et al., used array comparative genomic hybridization (CGH) to perform a comparative study between several BCR-ABL1 positive entities. BCR-ABL1 positive AML displays characteristic of lymphoid disease (found in BCR-ABL1 positive ALL and CML): deletions of IKZF1 and/or CDKN2A/B genes were recurrent findings in BCR-ABL1 positive AML as well as cryptic deletions within the immunoglobulin IGH and T cell receptor gene (TRG alpha) complexes[21]. Importantly, these aberrations were found to be absent in CML-MBC and hence they are potentially a helpful diagnostic tool for difficult cases.

Most cases will have monosomy 7/Del(7q), trisomy 8 or complex karyotypes in addition to the t(9;22)(q34.1;q11.2)[22].

Chr # Gain, Loss, Amp, LOH Minimal Region Cytoband and/or Genomic Coordinates [Genome Build; Size] Relevant Gene(s) Diagnostic, Prognostic, and Therapeutic Significance - D, P, T Established Clinical Significance Per Guidelines - Yes or No (Source) Clinical Relevance Details/Other Notes
7 Loss chr7 IKZF1, TR Beta Chain (TRB) genes D,P No Presence of monosomy 7 (or 7q deletion) is sufficient for a diagnosis of AML with MDS-related changes when there is ≥20% blasts and no prior therapy (add reference).  Monosomy 7/7q deletion is associated with a poor prognosis in AML[8].
8 Gain chr8 Unknown D,P No Common recurrent secondary finding for t(8;21)[23][24].


Characteristic Chromosomal or Other Global Mutational Patterns

Additional chromosomal aberrations are infrequently seen in BCR-ABL AML, it has been described together with different class II aberrations such as CBFB-MYH11, RUNX1- RUNX1T1 and PML-RARA[25][5]. In AML, BCR-ABL1 seems to cooperate with several AML-specific aberrations such as inv(16), t(8;21) and myelodysplasia-related cytogenetic aberrations[5][25]. (For diagnostic purpose, note that inv(16) is not restricted to AML and can also be found in CML-MBC). Additional chromosomal aberrations, such as an additional Ph chromosome, trisomy 19 and isochromosome 17q seen in CML MBP are infrequently seen in AML with BCR::ABL1.

Chromosomal Pattern Molecular Pathogenesis Prevalence -

Common >20%, Recurrent 5-20% or Rare <5% (Disease)

Diagnostic, Prognostic, and Therapeutic Significance - D, P, T Established Clinical Significance Per Guidelines - Yes or No (Source) Clinical Relevance Details/Other Notes
inv(16)(p13.1q22) or t(16;16)(p13.1;q22) CBFB::MYH11 fusion Rare (BCR-ABL1 AML) D,P No The rarity of Philadelphia-positive subclones in AML patients with specific genetic lesions requires more cases for conclusive prognosis and therapeutic insights[25].
t(8;21)(q22;q22.1) RUNX1- RUNX1T1 Rare (BCR-ABL1 AML) D,P No The rarity of Philadelphia-positive subclones in AML patients with specific genetic lesions requires more cases for conclusive prognosis and therapeutic insights[25].
t(15;17)(q13.4;q21.2) PML-RARA Rare (BCR-ABL1 AML) D,P No The rarity of Philadelphia-positive subclones in AML patients with specific genetic lesions requires more cases for conclusive prognosis and therapeutic insights[25].
AML-myelodysplasia-related (AML-MR) cytogenetic aberrations:

• del(5q), t(5q)

• inv(3)(q21q26)

• ‐7, del(7q)

Unknown Rare (BCR-ABL1 AML) D,P No The rarity of Philadelphia-positive subclones in AML patients with specific genetic lesions requires more cases for conclusive prognosis and therapeutic insights[25].

In AML, BCR-ABL appears to interact with specific aberrations like inv(16) and myelodysplasia-related cytogenetic changes, like del(5q), t(5q)[25], inv(3)(q21q26)[25], ‐7, del(7q)[26], but the mechanisms of disease initiation and cooperation remain unclear[5].


Gene Mutations (SNV/INDEL)

RUNX1 mutation is common in AML with BCR::ABL1 and occurs in ~40% of cases[4]. Other mutated genes include ASXL1, BCOR, IDH1 / IDH2 and SRSF2; each of these occur in 10 - 15% of cases[27][28][4].Coinciding molecular events such as NPM1 mutations have been reported[25]. Mutations of FLT3 or DNMT3A are not commonly detected[4].

Gene Genetic Alteration Tumor Suppressor Gene, Oncogene, Other Prevalence -

Common >20%, Recurrent 5-20% or Rare <5% (Disease)

Diagnostic, Prognostic, and Therapeutic Significance - D, P, T   Established Clinical Significance Per Guidelines - Yes or No (Source) Clinical Relevance Details/Other Notes
RUNX1


Variable LOF and missense mutations Tumor Suppressor Gene Common (BCR-ABL1 AML) D,P No AML with RUNX1 mutation is associated with a poorer prognosis[8]. RUNX1 was the most commonly mutated gene, altered in eight of 21 BCR-ABL1 AML cases (38%)[4].

Mutations in five genes (BCOR, BCORL1, SF3B1, SRSF2, and STAG2), along with ASXL1 and RUNX1 mutations, are linked to the proposed high-risk AML chromatin-spliceosome group[4].

ASXL1 Variable LOF and missense mutations Tumor Suppressor Gene Recurrent (BCR-ABL1 AML) D,P No Mutations in five genes (BCOR, BCORL1, SF3B1, SRSF2, and STAG2), along with ASXL1 and RUNX1 mutations, are linked to the proposed high-risk AML chromatin-spliceosome group[4].
BCOR Variable LOF and missense mutations Tumor Suppressor Gene Recurrent (BCR-ABL1 AML) D,P No Mutations in five genes (BCOR, BCORL1, SF3B1, SRSF2, and STAG2), along with ASXL1 and RUNX1 mutations, are linked to the proposed high-risk AML chromatin-spliceosome group[4].
IDH1 / IDH2 Missense Oncogene Recurrent (BCR-ABL1 AML) D,P No Other mutated genes include ASXL1, BCOR, IDH1 / IDH2 and SRSF2; each of these occur in 10 - 15% of cases[27][28][4].
SRSF2 Missense and in frame del Tumor Suppressor Gene Recurrent (BCR-ABL1 AML) D,P No Mutations in five genes (BCOR, BCORL1, SF3B1, SRSF2, and STAG2), along with ASXL1 and RUNX1 mutations, are linked to the proposed high-risk AML chromatin-spliceosome group[4].
NPM1 Variable LOF Tumor Suppressor Gene and Oncogene Rare (BCR-ABL1 AML) D,P No Philadelphia-positive subclones can emerge in NPM1-mutated AML at diagnosis or during follow-up, and may cooperate with the NPM1 mutation like other class I mutations, such as FLT3-ITD or MLL-PTD[25].

Note: A more extensive list of mutations can be found in cBioportal, COSMIC, and/or other databases. When applicable, gene-specific pages within the CCGA site directly link to pertinent external content.

Epigenomic Alterations

Not applicable

Genes and Main Pathways Involved

The BCR gene product has serine/threonine kinase activity and is a GTPase-activating protein for p21rac[29]. The ABL1 gene is a proto-oncogene that encodes a protein tyrosine kinase involved in a variety of cellular processes, including cell division, adhesion, differentiation, and response to stress. The activity of this protein is negatively regulated by its SH3 domain, whereby deletion of the region encoding this domain results in an oncogene[30]. The t(9,22)(q34;q11) leads to the formation of a Philadelphia chromosome and generates an active chimeric BCR-ABL1 tyrosine kinase. The fusion gene is created by juxtaposing the ABL1 gene on chromosome 9 (region q34) to a part of BCR (breakpoint cluster region) gene on chromosome 22 (region q11). This is a reciprocal translocation, creating an elongated chromosome 9 (der 9), and a truncated chromosome 22 (the Philadelphia chromosome, 22q-), the oncogenic BCR-ABL1 being found on the shorter derivative 22 chromosome[31][32]. This gene encodes for a BCR-ABL1 fusion protein, a tyrosine kinase. Tyrosine kinase activities are typically regulated in an auto-inhibitory manner, but the BCR-ABL1 fusion gene codes for a protein that is continuously activated, causing unregulated cell division. This is a result of the replacement of the myristoylated cap region which causes a conformational change rendering the kinase domain inactive, with a truncated portion of the BCR protein[33]. The enzyme is responsible for the uncontrolled growth of leukemic cells which survive better than normal blood cells. As a result of BCR/ABL1 variable splicing (fusion RNA and hybrid proteins), two transcripts p190 and p210 are found for BCR-ABL1 positive AML.

Gene; Genetic Alteration Pathway Pathophysiologic Outcome
BCR and ABL1; Activating mutations Ras/MAPK, PI3K/AKT, JAK/STAT and NF-kappaB pathways The BCR-ABL fusion protein is an constitutively active tyrosine kinase that triggers multiple pathways, promoting unchecked cell proliferation and survival.


Figure 1. Philadelphia chromosome. A piece of chromosome 9 and a piece of chrosomome 22 break off and trade places. The BCR-ABL1 gene is formed on chromosome 22 where the piece of chromosome 9 attaches. The changed chromosome 22 is called Philadelphia chromosome. Image from National Cancer Institute website https://www.cancer.gov/publications/dictionaries/cancer-terms/def/bcr-abl-fusion-gene
Figure 2. Signal transduction pathway of the BCR-ABL fusion gene

Genetic Diagnostic Testing Methods

Bone marrow with myeloid blasts >20% combined with detection of t(9,22) by karyotype analysis or BCR-ABL1 using FISH or reverse transcriptase-quantitative PCR (RT-qPCR) and RNA or DNA seq[5]. A graphic of the clinical path for the differential diagnosis of BCR-ABL1 positive acute myeloid leukemia and chronic myeloid leukemia-myeloid blast crisis (CML-MBC) is presented[5].

Familial Forms

Not applicable

Additional Information

Not applicable

Links

ABL1

BCR

Vogel A, et al. Acute Myeloid Leukemia with BCR-ABL1. SH2017-0299. Presentation at Society for Hematopathology / European Association for Haematopathology (SH/EAHP) 2017 Workshop. https://www.sh-eahp.org/images/2017_Workshop/3_3SH-EAHP%202017_AML%20with%20BCR-ABL1_%20AV%20FINAL.pdf (accessed 29th June 2018)

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Notes

*Primary authors will typically be those that initially create and complete the content of a page.  If a subsequent user modifies the content and feels the effort put forth is of high enough significance to warrant listing in the authorship section, please contact the Associate Editor or other CCGA representative.  When pages have a major update, the new author will be acknowledged at the beginning of the page, and those who contributed previously will be acknowledged below as a prior author.

Prior Author(s):

Kay Weng Choy MBBS, Monash Medical Centre


*Citation of this Page: “Acute myeloid leukaemia with BCR::ABL1 fusion”. Compendium of Cancer Genome Aberrations (CCGA), Cancer Genomics Consortium (CGC), updated 07/3/2025, https://ccga.io/index.php/HAEM5:Acute_myeloid_leukaemia_with_BCR::ABL1_fusion.