Dear Editor,
The integration of tyrosine kinase inhibitors (TKIs) into multiagent chemotherapy regimens has markedly improved the prognosis of BCR::ABL1-positive acute lymphoblastic leukemia (BCR::ABL1 + ALL). Allogeneic hematopoietic stem cell transplantation (allo-HSCT) remains a backbone of contemporary curative treatments for adult BCR::ABL1 + ALL.
IKZF1plus is a genotype characterized by the coexistence of IKZF1 deletions with deletions in CDKN2A, CDKN2B, PAX5, or PAR1 in the absence of ERG deletion [1]. In 2023, the National Comprehensive Cancer Network (NCCN) ALL guideline officially stratified BCR::ABL1 + ALL into poor-risk [IKZF1plus or antecedent chronic myeloid leukemia (CML)] or standard-risk (non-IKZF1plus and without antecedent CML) category [2]. Simultaneously, minimal residual disease (MRD) is a well-recognized prognostic factor of ALL. However, there have been no studies on the synergy of the two prognostic factors (IKZF1plus genotyping and MRD assessment) in risk stratification. Particularly, although increasing evidence suggests that allo-HSCT may not benefit all patients, the criteria for determining which patients should undergo or be spared from allo-HSCT remain elusive.
In this study, we aimed to refine the risk stratification by integrating IKZF1plus genotyping and MRD assessment, thus improving the management of allo-HSCT in BCR::ABL1 + ALL therapy. Additionally, we preliminarily explored the molecular characteristics of IKZF1plus ALL concerning its high-risk phenotype through targeted exome sequencing and RNA sequencing (RNA-seq), providing new insights into mechanistic research.
Here, we analyzed 156 adult patients with newly diagnosed BCR::ABL1 + ALL in three clinical trials conducted from 5 June 2014 to 15 November 2022. Till 31 December 2023, the overall median follow-up period was 34.6 months (range, 7.5–116.5). The patients were treated with a TKI-based standardized regimen, including imatinib or flumatinib (a second-generation TKI). In order to reduce high-dose chemotherapy-associated toxicity and early deaths, the relatively low intensity of chemotherapy was applied [3, 4]. There was no significant difference in baseline characteristics and survival outcomes between imatinib and flumatinib cohort, allowing a joint prognostic analysis (Supplemental Table 1, Supplemental Fig. 1A–C). In accordance with the Declaration of Helsinki, the study was approved by the Ethics Committee of Ruijin Hospital. [Clinical Trial Registration Number: ChiCTR-ONRC-14004968 [5], ChiCTR2100042248 [6, 7], and ChiCTR2100044308].
A landscape of gene deletions, mutations, and clinical data of the 156 patients was illustrated in Fig. 1A and Supplemental Fig. 2A, B. The patients were classified into IKZF1plus group (n = 54) or non-IKZF1plus group (n = 102) [composed of IKZF1 deletion alone (n = 65) and no IKZF1 deletion (n = 37)], according to multiplex ligation-dependent probe amplification (MLPA) results (Fig. 1A). Internal validation (Supplemental Table 4) and whole genome sequencing (Supplemental Fig. 2C) were performed to validate the MLPA technique. Clinical information was provided in Supplemental Tables 2 and 3. The IKZF1plus group revealed micro-deletions in CDKN2A/2B (34.6%), PAX5 (31.4%), ERG (0%), and PAR1 region (0%) gene loci.
139 patients (aged 18-64 years) were included in the survival analysis. The OS, EFS, and CIR of IKZF1plus group (n = 48) were markedly worse than those observed in non-IKZF1plus group (n = 91) (Supplemental Fig. 3A–C).
MRD evaluation was performed for 125 patients at 3 months of treatment by RT-qPCR (sensitivity: 0.001%). Outcomes of patients who failed to achieve complete molecular remission (CMR) at 3 months (MRD+, n = 68) were significantly worse than those with CMR at 3 months (MRD−, n = 57) (Supplemental Fig. 3D–F).
Next, incorporating the two risk factors, 125 patients (aged 18–64 years) with available data were stratified into four subgroups [non-IKZF1plus/MRD− (n = 37), non-IKZF1plus/MRD+ (n = 43), IKZF1plus/MRD− (n = 20) and IKZF1plus/MRD+ (n = 25)] (Supplemental Fig. 4A–C). The non-IKZF1plus/MRD− patients were classified into the low-risk group, demonstrating the best survival outcomes and the lowest relapse rate. In contrast, IKZF1plus/MRD−, IKZF1plus/MRD+, and IKZF1plus/MRD not available (n = 3) subgroups had the worst outcomes and highest relapse rates, therefore combined into the high-risk group (IKZF1plus, n = 48), indicating MRD assessment did not contribute to the risk stratification of IKZF1plus patients. The remaining non-IKZF1plus/MRD+ subgroup was stratified as an intermediate-risk group (n = 43). Finally, compared to the intermediate-risk or high-risk group, the low-risk group had better OS (P = 0.10 or P < 0.001), EFS (P = 0.005 or P < 0.001), and lower CIR (P = 0.01 or P < 0.001), respectively (Fig. 1B–D, Supplemental Table 5). Overall, the refined risk stratification could better discriminate the prognosis of adult BCR::ABL1 + ALL patients.
Therefore, based on our refined risk stratification system, 128 patients (aged 18-64 years) eligible for transplantation were analyzed. In low-risk group, OS of allo-HSCT subgroup was similar to non-HSCT subgroup (P = 0.74) (Fig. 1E), suggesting that low-risk patients did not benefit from transplantation. Among 23 patients transplanted, three died of infections post allo-HSCT. Among 14 patients without transplantation, one succumbed to heart failure and another due to leukemia progression.
For high-risk patients, OS of allo-HSCT subgroup was significantly higher than non-HSCT subgroup (P < 0.001) (Fig. 1G), confirming the necessity of transplantation in high-risk group. Finally, among intermediate-risk patients, OS of allo-HSCT subgroup showed a more favorable trend (P = 0.08) (Fig. 1F). Without allo-HSCT, OS of low-risk group was significantly superior to intermediate-risk and high-risk groups, respectively (Supplemental Fig. 5E). While after allo-HSCT, OS of three groups reached a comparable level (P = 0.85) (Supplemental Fig. 5F). Overall, our data suggest that allo-HSCT should be spared for low-risk group but is recommended for the other two groups (Supplemental Fig. 6).
Multivariate analysis demonstrated that IKZF1plus genotype (all P < 0.001) and MRD positivity at 3 months (P = 0.01, P < 0.001, P < 0.001) were independent risk factors for OS, EFS, and RFS, while allo-HSCT (all P < 0.001) was an independent protective factor (Supplemental Fig. 7).
Based on RNA-seq data from 137 patients, the developmental stages of all patients were inferenced by using diffusion map-based dimensionality reduction (Supplemental Fig. 8) and lineage signatures (top 100 genes) in Bastian et al. [8]. It is consistent with previous reports, the non-IKZF1plus group and IKZF1plus group enriched in distinct hematopoietic lineage, including B lymphoid/myeloid lineage, early pro-B cells, and pre-B I/II large stages (Fig. 2A–C) [9, 10]. Using multiparameter flow cytometry [11], similar results at the protein expression level were validated (Fig. 2D).
Several unreported signature genes of IKZF1plus group were identified in this work for the first time (Fig. 2E), including upregulated (TUNAR, GPR68, TAFA1, CD24, and TUBB3) or downregulated genes (MARCKS, CDKN2A, and TBL1X) (Supplemental Table 6). IKZF1plus genotype was associated with activation of proliferative pathways [PI3K-Akt and Ras signaling pathways] and inhibition of hematopoietic/immune functions [T cell activation and other immune system process] (Fig. 2F). The above findings then were validated by additional gene sets [12] and immunocyte deconvolution (xCell algorithm) (Fig. 2G, Supplemental Fig. 9A) [13]. Consistently, peripheral blood samples of IKZF1plus group showed significantly lower expression of a T cell antigen CD3 (P = 0.04) (Supplemental Fig. 9B). Therefore, better immune function may be a positive factor contributing to the improved prognosis of non-IKZF1plus group.
This study is the largest cohort to date focusing on IKZF1plus aberration and MRD simultaneously in adult BCR::ABL1 + ALL. Integrating both IKZF1 genotype and MRD status at 3 months, BCR::ABL1 + ALL could be further classified into three distinct risk groups: low-risk, intermediate-risk, and high-risk. The refined stratification system not only essentially meets the criterion for 2023 NCCN’s poor-risk category, but also allows for a subdivision of NCCN’s standard-risk category into two separate entities: low-risk and intermediate-risk.
Low-risk group (non-IKZF1plus/MRD−), for the first time, was identified in adult BCR::ABL1 + ALL. Prior studies indicated that BCR::ABL1 + ALL patients attaining CMR at 3 months had favorable survival and did not benefit from transplantation [14, 15]. In contrast, the scenario for IKZF1plus/MRD− patients was distinct: despite achieving 3-month CMR, prognosis of these high-risk patients was still significantly worse than non-IKZF1plus patients, and transplantation remarkably improved their OS (Supplemental Fig. 5G). This underscored that for IKZF1plus genotype with an inherent propensity for relapse, achieving MRD negativity may not be sufficient to mitigate the adverse impact of a poor genetic profile. The classification of low-risk group was only restricted to non-IKZF1plus patients who were MRD negative at 3 months, which did not benefit from allo-HSCT and should avoid it.
Within intermediate-risk group (non-IKZF1plus/MRD+), compared to non-HSCT subgroup, there was a promising trend towards better OS in allo-HSCT subgroup. It is advisable to employ targeted immunotherapies to eradicate MRD, and subsequently bridge allo-HSCT. To more comprehensively elucidate the role of allo-HSCT in this group, further studies with larger sample size and extended follow-up are warranted.
High-risk group actually consisted of all IKZF1plus patients, irrespective of MRD at 3 months. Allo-HSCT subgroup consistently exhibited significantly better OS than non-HSCT counterparts, therefore allo-HSCT was crucial for high-risk patients by reducing relapse risk (Supplemental Fig. 5H).
In conclusion, the refined risk stratification based on IKZF1plus genotyping and MRD assessment helps to guide transplantation decisions for adult BCR::ABL1 + ALL patients. Allo-HSCT should be spared for the low-risk group, but is recommended for intermediate-risk and high-risk groups (Supplemental Fig. 6). More comprehensive clinical studies are warranted for further validation of our findings.
Data availability
Anonymized RNAseq data have been deposited in the Genome Sequence Archive for Humans (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human) (accession number: HRA005804). For other data, please contact jinwang@shsmu.edu.cn.
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Acknowledgements
This study was funded by National Natural Science Foundation of China (82270187, 82070227, and M-0337), National Key R&D Program of China (2023YFC2508900), Science and Technology Commission of Shanghai Municipality (21430711800, and 23141903000), National Natural Science Foundation of China for Young Scholars (82300168), Shanghai Sailing Program (23YF1424400), and Shanghai Municipal Education Commission-Major Project for Scientific Research and Innovation Plan of Natural Science (2021-01-07-00-02-E00091).
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JW, JQM, and DHJ designed research, led the research team, and supervised the manuscript; JW and JQM funded the study; YFL, JJZ, WYL, JYR, and LJP collected samples and provided treatment for patients; CW, JFL, WYL, and YCY collected clinical data; CW, YMZ, LLZ, and HY performed molecular experiments, targeted exome sequencing, and RNAseq; XQW performed multiparameter flow cytometry; CW and JFL analyzed clinical data, performed bioinformatic analysis, and wrote the paper; and all authors approved the final version of the manuscript.
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Wang, C., Li, J., Liu, W. et al. Refined risk stratification helps guiding transplantation choice in adult BCR::ABL1-positive acute lymphoblastic leukemia. Blood Cancer J. 14, 71 (2024). https://doi.org/10.1038/s41408-024-01055-1
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DOI: https://doi.org/10.1038/s41408-024-01055-1