Allogeneic stem cell transplantation mitigates the adverse prognostic impact of high diagnostic BAALC and MN1 expression in AML

Acute myeloid leukemia (AML) is a highly heterogeneous disease for which reliable risk stratifications are needed to individualize treatment strategies [1]. Today, potential consolidation therapies for AML patients in remission after successful induction therapy include intensive chemotherapy cycles alone or an allogeneic hematopoietic stem cell transplantation (HSCT). Through immunological graft-versus-leukemia (GvL) effects, where the donor’s immunocompetent cells are believed to eradicate residual disease [2, 3], allogeneic HSCT remains the treatment option with the highest chance of sustained remissions in most AML patients, albeit the associated morbidity and mortality [1].

The AML-associated genes BAALC (brain and acute leukemia, cytoplasmatic) and MN1 (meningioma-1) have been shown to be physiologically expressed at high levels in myeloid progenitor cells and downregulated during maturation and to promote leukemogenesis through blockage of myeloid differentiation [4‐6]. While BAALC maps to chromosome band 8q22.3 and was initially identified in AML patients harboring a trisomy 8 [7], MN1 is located on chromosome 22q12.3 and a transcription coactivator firstly described in meningioma pathogenesis [8]. High expression levels of both genes at AML diagnosis have repeatedly been associated with adverse outcomes in both younger [4, 9] and older AML patients [10, 11], especially in the context of a normal karyotype [12‐14]. Furthermore, the expression levels of both genes have been identified as feasible markers for residual disease in AML patients in complete remission (CR) independent of the applied consolidation therapy [15‐19].

However, the majority of the studies investigating the prognostic impact of diagnostic BAALC and MN1 expression levels focused on patients consolidated with standard cytarabine-based chemotherapies or autologous HSCT in which either none or only a small number of the analyzed individuals received allogeneic HSCT for consolidation. Only one recently published manuscript analyzed the data of 71 AML patients from The Cancer Genome Atlas (TCGA) and suggested no prognostic impact of BAALC expression levels at diagnosis in patients receiving allogeneic HSCT [20]. This study was restricted by patient numbers and limited information on the applied treatments (e.g., intensity of conditioning regimens). Here, we analyzed the prognostic significance of the differential diagnostic BAALC and MN1 expression levels in a well-defined cohort of AML patients who were either treated with chemotherapy alone or received an allogeneic HSCT as consolidation therapy at our institution. For better reproducibility, and to develop a feasible clinical routine assay, we adopted a digital droplet PCR (ddPCR) technology for absolute diagnostic BAALC and MN1 quantification [21].

As a result of the search for better risk stratification in AML patients with normal cytogenetics, high diagnostic expression of the AML-associated genes BAALC and MN1 were shown to have independent adverse prognostic impact on CR achievement, relapse rates, EFS, and OS in younger [4, 9, 12‐14, 27‐29] and older [10‐12] AML patients. Some later investigations also suggested a prognostic impact in AML patients with abnormal cytogenetics [30] or independently from cytogenetic groups [20, 31, 32]. Most of these studies focused on chemotherapy-based consolidation therapies or autologous HSCT with only a very small proportion of patients receiving an allogeneic—and in the majority of cases related donor—HSCT. However, there have already been some indications that the prognostic impact of diagnostic BAALC and MN1 expression may be modulated by the consolidation treatment. Yoon et al. [33] analyzed a cohort of 125 cytogenetically normal AML patients of whom approximately half were consolidated with an allogeneic HSCT and did not observe a prognostic impact of high BAALC expression levels, which might be explained by the mixed consolidation therapies. One recent study suggested comparable EFS and OS for high and low BAALC expressers in the TCGA dataset for patients after allogeneic HSCT, but this analysis was limited by low patient numbers and missing data on the applied chemotherapies and conditioning regimens [20]. In a subanalysis of 48 patients receiving allogeneic HSCT, Baldus et al. [28] observed very low relapse rates irrespective of BAALC expression at diagnosis and suggested that high BAALC expressing patients might benefit from an allogeneic HSCT. With respect to diagnostic MN1 expression, in a donor vs no donor subanalysis by Heuser et al. [4], no benefit of an allogeneic HSCT in high expressers was observed, but also this study was also restricted by low patient numbers (n = 39). Thus, the prognostic significance of BAALC and MN1 expression levels at diagnosis in the context of an allogeneic HSCT remains to be evaluated in a large homogeneously treated and genetically well-defined patient set—which was the main objective of our study.

In contrast to previous reports that used qRT-PCR [4, 9, 13, 14, 27, 28] or microarray-based [12, 32] assays for evaluation of BAALC and MN1 expression levels, we adopted a ddPCR technology. This method allows absolute quantification of gene copy numbers at high sensitivity, specificity, and reproducibility without the need of standard curves [21] and enabled us to establish an assay sufficient for a routine clinical assessment of BAALC and MN1 expression. In a subset of 110 patients, we observed a high correlation between qRT-PCR and ddPCR results for both gene expressions (Fig. 1) underlining the feasibility of our ddPCR assays.

The observed associations of diagnostic BAALC and MN1 copy numbers with clinical and genetic parameter stand in line with previously published analyses [4, 9‐14, 20, 27, 31, 32]. As previously reported [13], high BAALC and MN1 expression correlated with each other, as well as with a high expression of immature markers such as CD34 [4, 9, 10, 31] and CD117 [9]. Additionally, we observed an association of high BAALC/ABL1 and MN1/ABL1 copy numbers with the CD34+/CD38− cell burden, and GPR56, which match the suggestions by Liu et al. [34] that MN1 overexpression might contribute to an expansion of the leukemic stem cell population. High BAALC/ABL1 and MN1/ABL1 copy numbers correlated with a specific immunophenotype, including a lower expression of mature myeloid antigens, e.g., CD11b or CD15, which have already been described for BAALC [27], and higher expression of antigens associated with T cell differentiation. Additionally, both high BAALC/ABL1 and MN1/ABL1 expressing patients showed lower CD33 expression, which might have clinical consequences when considering CD33-targeted treatment approaches [35]. We also observed the previously reported association of high BAALC and MN1 levels with lower white blood counts [9, 11, 14], immature FAB types [12, 14], abnormal cytogenetics [20, 32], NPM1 wild-type [9‐13], as well as mutated CEBPA for high MN1 expressers [12]. Within the TCGA data set an association of high BAALC expression levels with mutated RUNX1 was described [20] that we observed for both high BAALC and high MN1 expressing patients. While we did not find an association of high BAALC levels with wild-type PTPN11 [20], there was a not yet reported lower incidence of DNMT3A mutations for high BAALC expressers, as well as a trend for less TET2 mutations in both high BAALC and MN1 expressing patients.

As expected, high BAALC and MN1 copy numbers associated with inferior outcomes in AML patients after chemotherapy-based consolidation. In contrast, within the large group of patients consolidated with an allogeneic HSCT, we observed no prognostic impact of BAALC or MN1 copy numbers at diagnosis, which was also seen in separate analyses for patients with a normal karyotype and patients transplanted in first CR. Noteworthy, also the cumulative incidences of relapse and nonrelapse mortality according to BAALC/ABL1 and MN1/ABL1 copy numbers did not differ after allogeneic HSCT (Supplementary Fig. S6).

This is especially interesting because even though for some prognostic markers allogeneic HSCT has been described to improve outcomes, the prognostic impact of most of these markers retain their prognostic impact in the HSCT context [23, 36, 37]. However, patients with high BAALC or MN1 expression at diagnosis—both markers repeatedly published to confer inferior prognosis in chemotherapy-consolidated AML patients—might benefit from an allogeneic HSCT as consolidation therapy. Noteworthy, genes involved in antigen processing and expression—among those genes encoding for MHC class I and MHC class II molecules—correlate positively with MN1 gene expression signatures [13]. This associated gene expression might support immunologic GvL effects after HSCT to contribute to better outcomes in AML patients with high MN1 expression.

We previously described the prognostic utility of BAALC/ABL1 and MN1/ABL1 copy numbers for risk stratification in remission prior to an allogeneic HSCT—which are likely to reflect residual disease burden at this time point [15, 16]. In the here-presented patient set, we also observed a strong impact on EFS and OS after HSCT according to preHSCT BAALC/ABL1 (Supplementary Fig. S7A, B) and MN1/ABL1 copy numbers (Supplementary Fig. S8A, B). Noteworthy, there was no correlation between BAALC/ABL1 and MN1/ABL1 copy numbers at diagnosis and in peripheral blood remission samples prior to HSCT (Supplementary Fig. S9). The prognostic impact of preHSCT BAALC/ABL1 and MN1/ABL1 copy numbers was independent of the diagnostic BAALC/ABL1 (Supplementary Fig. S7C–F) or MN1/ABL1 copy numbers (Supplementary Fig. S8C–F). PreHSCT BAALC/ABL1 and MN1/ABL1 copy numbers may have the highest prognostic value in patients with low copy numbers at diagnosis as this may result in higher assay sensitivity (indicated in Supplementary Figs. S7C–F and S8C–F), but larger analyses are needed to confirm this assumption. In contrast, also in patients with high or low preHSCT BAALC/ABL1 or MN1/ABL1 copy numbers, diagnostic BAALC/ABL1 or MN1/ABL1 copy numbers did not impact outcome (Supplementary Fig. S10).

Taken together, these data indicate that in the context of an allogeneic HSCT, the diagnostic BAALC or MN1 expression levels do not impact prognosis. However, independent of the diagnostic BAALC or MN1 expression levels, the assessment of both gene copy numbers in remission prior to allogeneic HSCT allow for relevant risk stratification. This further confirms previous data showing that outcomes of AML patients undergoing allogeneic HSCT remain the most favorable if patients are measurable residual disease negative prior to start of conditioning regimens [15, 16, 38‐41].

In conclusion, we show that the adverse prognostic impact of high BAALC and MN1 expression levels at diagnosis is mitigated in AML patients undergoing allogeneic HSCT. In contrast, in patients receiving chemotherapy alone, we could confirm the described inferior outcomes for individuals with high BAALC or MN1 expression at diagnosis. Our data indicate that patients with high BAALC or MN1 expression at diagnosis might benefit from an allogeneic HSCT which would help to individualize treatment of these patients. Prospective analyses would be helpful to further confirm this observation.