Secondary acquisition of the Philadelphia chromosome in acute lymphoblastic leukemia
Authors: Qiudan Shen, Elias J. Jabbour, Guilin Tang, Hong Fang, Wei Wang, Nicholas J. Short, M. James You, L. Jeffrey Medeiros, Shimin Hu
Journal: American Journal of Hematology (2024)

The Philadelphia chromosome (Ph), resulting from the t(9;22)(q34;q11), is the defining cytogenetic abnormality in chronic myeloid leukemia (CML).1 This chromosomal aberration harbors the BCR::ABL1 fusion gene, which encodes a constitutively active tyrosine kinase that initiates downstream signaling pathways crucial for leukemogenesis. Beyond CML, the Ph is also observed in other hematologic malignancies, including acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), and mixed-phenotype acute leukemia. Ph-positive B-ALL (Ph+ B-ALL) is the most common subtype of B-ALL in adults, accounting for approximately 25% of cases. While the Ph is typically detected at the initial diagnosis of CML and Ph+ acute leukemia, its secondary acquisition during treatment of Ph-negative leukemia has been reported, predominantly in refractory AML and myelodysplastic syndrome (MDS) in progression. The secondary acquisition of the Ph during treatment of patients with Ph-negative ALL is uncommon, and its emergence as a subclone at the time of initial diagnosis of ALL is exceedingly rare.2 The clinical characteristics, management, and outcomes in these scenarios remain unclear. Here we report eight such cases identified through a retrospective review of 732 cases of ALL (B-ALL 727, T-ALL 5) diagnosed between 2000 and 2023. In these cases, the Ph was detected at initial diagnosis or at relapse using fluorescence in situ hybridization (FISH), with or without karyotyping. The study group consisted of three men and five women, with a median age of 38 years (range, 14–66) at the time of emergence of the Ph (Table 1). Seven patients were initially diagnosed with B-ALL, and one with T-ALL (#6). Six patients (#1–6) acquired the Ph secondarily during treatment of ALL at a median of 37.5 months (range, 19–192) from initial diagnosis of ALL. Two patients (#7 and 8) presented with the Ph as a subclone at the time of initial diagnosis of ALL. Among the six patients who acquired the Ph during treatment for ALL, four did so during the first to third relapse of B-ALL (patients #1–4), whereas two acquired the Ph during the refractory stage of B-ALL (#5) and T-ALL (#6), respectively (Table 1). For patients #1–4, the absence of the Ph and BCR::ABL1 fusion at the time of the initial B-ALL diagnosis was confirmed by karyotyping, FISH, and/or quantitative reverse transcription polymerase chain reaction (RT-qPCR) (Table 2). Interestingly, patient #4 developed therapy-related AML (t-AML) with monosomy 7 approximately 32 months after the initial diagnosis of B-ALL. Seven months after the t-AML diagnosis, a dominant population of B-ALL cells, along with a small myeloid population, was detected by flow cytometric immunophenotyping. Karyotype analysis revealed two separate subclones: a Ph+ clone without monosomy 7 and Ph-negative clone with monosomy 7, indicating a secondary acquisition of the Ph in B-ALL but not in AML cells. Karyotype: NA FISH: negative RT-qPCR: negative 46,XY[20] FISH: negative RT-qPCR: NA ABL1 p.E255V NGS 81-gene panel: DNMT3A p.F752L (3.9%), JAK3 p.M902V (14.9%) Karyotype: NA FISH: negative RT-qPCR: negative ABL1 p.E255Va NGS 81-gene panel: None Karyotype: 46,XX[18] FISH: NA RT-qPCR: NA Seven months before Ph emergence 45,XX,-7[16]/46,XX[5] therapy-related AML No Ph in next two BMs NGS 28-gene panel: TP53 p.P278S (63.9%) NGS 28-gene panel: JAK2 p.L884P (3.4%) JAK2 p.R683G (2.4%) JAK2 p.R867Q (2.3%) NGS 81-gene panel: CRLF2 p.F232C (15.6%) PTPN11 p.E76K (19.5%) IL7R p.N232S (50.7%) For patients #5 and 6, information regarding the Ph and BCR::ABL1 was unavailable at the initial diagnosis of ALL (Table 2). However, both patients developed refractory disease before the Ph was detected by FISH. In patient #5, BCR::ABL1 was initially negative during follow-up and subsequently consistently low by FISH (0–5.5%) and by RT-qPCR (<0.01% to 11.77%), despite persistently high blast counts (median 91%, range 38%–94%) throughout the disease course. These data suggest the absence of the Ph and BCR::ABL1 at the initial diagnosis of B-ALL and support a sub-clonal nature of the Ph during follow-up. For patients #6, BCR::ABL1 levels were high when first detected approximately 19 months after the initial diagnosis of T-ALL. However, the Ph and BCR::ABL1 were consistently not detected by karyotyping, FISH, and RT-qPCR, despite high blast counts before the initial detection of the Ph, indicating a secondary nature of the Ph and BCR::ABL1 acquisition. In patients #7 and #8, the presence of a Ph+ subclone at initial diagnosis was characterized by the high blast count, 82% and 76%, respectively, but low levels of Ph/BCR::ABL1 as determined by FISH (20.5% and 9.0%, respectively) and RT-qPCR (48.20% and 6.67%, respectively). Additionally, in patient #8, flow cytometric immunophenotyping detected low-level residual ALL at 18 and 22 months after the initial diagnosis (0.03% and 1.15%, respectively), whereas RT-qPCR was negative for BCR::ABL1 during the same period. At the initial detection of the Ph by FISH analysis, none of the patients exhibited features of CML in the peripheral blood or bone marrow. Seven patients had an e1a2 (P190) BCR::ABL1 fusion transcript and patient #1 had a variant BCR::ABL1 transcript subtype (not e1a2, e13a2, or e14a2) (Table 2). Among the six patients who acquired the Ph during therapy, all exhibited a complex karyotype. However, among the five patients with an available karyotype at initial diagnosis or during the refractory stage of ALL before acquiring the Ph, only two (#5 and 6) had a complex karyotype at some timepoint before the acquisition of the Ph. Patient #6 exhibited a persistently complex karyotype across 10 karyotype analyses, whereas patient #5 developed a complex karyotype 2 months prior to detection of BCR::ABL1 by FISH (data not shown). Following the initial detection of the Ph, next-generation sequencing using a 28 or 81-gene panel was performed in six patients; mutations were detected in four patients (Table 2). ABL1 mutation analysis was performed in two patients (#2 and 3) at relapse 3 years after the acquisition of the Ph, and both harbored the ABL1 p.E255V mutation. Following the emergence of the Ph, patients were treated as follows (Table 1): five received chemotherapy combined with tyrosine kinase inhibitors (TKIs), one (patient #4) received TKI monotherapy, one (patient #5) received blinatumomab monotherapy, and one (patient #6) did not receive any treatment due to rapid disease deterioration (Table 1). In addition, three patients (#2, 3, and 8) underwent hematopoietic stem cell transplantation. After these treatments, six patients initially achieved complete remission (CR) of ALL by flow cytometric immunophenotyping and RT-qPCR; two (#2 and 3) of whom developed Ph+ relapse later. At the last follow-up, five patients were in CR of ALL, including one who developed relapsed t-AML. Two patients (#5 and 6) had refractory disease and deteriorated rapidly, and one patient's disease status was unknown. After a median follow-up of 43.7 months (range, 20.1–222.7), six patients had died: two due to refractory ALL, two from infections, one from t-AML, and one for unknown reasons (lost to follow-up) (Table 1). The median overall survival (OS) was 43.7 months from initial diagnosis of ALL (range, 20.1–222.7) and 28.8 months from the emergence of the Ph (range, 0.7–89.5). In this study, we investigated the clinical features of eight ALL patients in whom the Ph emerged as a secondary event. The emergence of the Ph during therapy in ALL is rare, with only six cases reported in the English literature since 2000, including three cases from our institution.2, 3 Reports of the Ph as a minor clone in ALL at initial diagnosis are even more rare, with only two cases of T-ALL and one case of B-ALL documented.4-6 Similar to the secondary acquisition of the Ph in AML and MDS,2 the emergence of a secondary Ph in ALL patients was associated with an advanced stage of disease. The transcript subtype was predominantly of e1a2 (P190). However, there are notable differences between the secondary acquisition of the Ph in ALL versus in AML and MDS. Firstly, the interval from initial diagnosis to the emergence of the Ph in ALL is longer, with a median time of 37.5 months in ALL versus 14 months in AML patients. Secondly, the secondary acquisition of the Ph appeared to be present in most of ALL cells in five out of six patients, whereas in AML and MDS, the Ph is commonly seen as part of a minor clone, possibly reflecting differences in the growth kinetics of leukemic cells between ALL versus AML or MDS. In two patients (#5 and 8) who showed a low-level Ph by FISH analysis and a low-level BCR::ABL1 fusion by RT-qPCR despite presence of a high blast count, the possibility that the Ph+ cells are not part of the ALL clone cannot be completely excluded. Finally, despite the complexity of the karyotypes, presence of the Ph in a dominant clone, and multiple relapses, chemotherapy combined with TKIs resulted in sustained CR in most patients. However, one patient (#8) had persistent low-level of residual B-ALL by flow cytometric immunophenotyping, despite the eradication of the Ph+ clone. In contrast, all AML and MDS patients with secondarily acquired Ph had persistent disease despite the eradication of Ph+ clones,2 underscoring the difference between true de novo Ph+ diseases and diseases with late acquisition of the Ph. The outcome for these patients is extremely poor, with a median OS of only 3 months after the emergence of the Ph. In summary, we present eight patients with ALL in whom the Ph chromosome emerged secondarily during therapy or was present as a subclone at initial diagnosis. Although chemotherapy combined with TKIs generally leads to favorable responses in this subgroup of ALL patients, it is crucial to distinguish between true de novo Ph+ diseases and those with secondary acquisition of the Ph or its presence in a subclone at initial diagnosis. Eradicating the Ph may not always guarantee complete eradication of the leukemia in every patient. The authors declare no conflicts of interest. Obtaining individual informed consent is not required for this type of observational studies containing no directly identifiable data. The data supporting the findings in this study are available from the corresponding author upon reasonable request.