Leukemia-associated Immunophenotypes Research Articles

Impact of hemodilution on flow cytometry based measurable residual disease assessment in acute myeloid leukemia

Measurable residual disease (MRD) measured in the bone marrow (BM) of acute myeloid leukemia (AML) patients after induction chemotherapy is an established prognostic factor. Hemodilution, stemming from peripheral blood (PB) mixing within BM during aspiration, can yield false-negative MRD results. We prospectively examined hemodilution by measuring MRD in BM aspirates obtained from three consecutive 2 mL pulls, along with PB samples. Our results demonstrated a significant decrease in MRD percentages between the first and second pulls (P = 0.025) and between the second and third pulls (P = 0.025), highlighting the impact of hemodilution. Initially, 39% of MRD levels (18/46 leukemia-associated immunophenotypes) exceeded the 0.1% cut-off, decreasing to 30% (14/46) in the third pull. Additionally, we assessed the performance of six published methods and parameters for distinguishing BM from PB samples, addressing or compensating for hemodilution. The most promising results relied on the percentages of CD16dim granulocytic population (scarce in BM) and CD117high mast cells (exclusive to BM). Our findings highlight the importance of estimating hemodilution in MRD assessment to qualify MRD results, particularly near the common 0.1% cut-off. To avoid false-negative results by hemodilution, it is essential to collect high-quality BM aspirations and preferably utilizing the initial pull for MRD testing.

Clinical significance of monitoring NUP98::NSD1 fusion genes before and after allogeneic hematopoietic stem cell transplantation

Objective: This study aimed to observe the dynamic changes of NUP98::NSD1 expression before and after allogeneic hematopoietic stem cell transplantation (allo-HSCT) . Moreover, the clinical value of measurable residual disease (MRD) was analyzed. Methods: Sixteen AML patients who were diagnosed with the NUP98::NSD1 fusion gene and received allo-HSCT at Peking University People's Hospital were included. The NUP98::NSD1 fusion gene and leukemia-associated immunophenotype (LAIP) were monitored before and after transplantation to evaluate their MRD status. Results: The median follow-up time for all patients was 526 days (139-1136 days) , with four patients (25.0%) experiencing hematological recurrence at a median of 474 days (283-607 days) after transplantation. Three patients (18.8%) died, two of whom (12.5%) died of leukemia recurrence. The median expression level of NUP98::NSD1 in newly diagnosed patients with complete data was 78.5% (18.9%-184.4%) at the time of initial diagnosis. The recurrence rate was higher in NUP98::NSD1-positive patients after transplantation, with 44.4% of patients experiencing recurrence, whereas no recurrence occurred in NUP98::NSD1-negative patients after transplantation. The area under the receiver operating characteristic curve predicted by the NUP98::NSD1 level after transplantation was 1.000 (95% confidence interval: 1.000-1.000, P=0.003) . Among the four patients with recurrence, NUP98::NSD1 was more sensitive than flow cytometry residual (FCM) and Wilms' tumor gene 1 (WT1) . Conclusions: The NUP98::NSD1 fusion gene can be used to evaluate the MRD status of allo-HSCT. NUP98::NSD1-positive patients after transplantation have a high relapse rate and poor prognosis. NUP98::NSD1 was more sensitive than FCM and WT1 in predicting posttransplant relapse.

A 19-color single-tube full spectrum flow cytometry assay for the detection of measurable residual disease in acute myeloid leukemia.

Multiparameter flow cytometry (MFC) has emerged as a standard method for quantifying measurable residual disease (MRD) in acute myeloid leukemia. However, the limited number of available channels on conventional flow cytometers requires the division of a diagnostic sample into several tubes, restricting the number of cells and the complexity of immunophenotypes that can be analyzed. Full spectrum flow cytometers overcome this limitation by enabling the simultaneous use of up to 40 fluorescent markers. Here, we used this approach to develop a good laboratory practice-conform single-tube 19-color MRD detection assay that complies with recommendations of the European LeukemiaNet Flow-MRD Working Party. We based our assay on clinically-validated antibody clones and evaluated its performance on an IVD-certified full spectrum flow cytometer. We measured MRD and normal bone marrow samples and compared the MRD data to a widely used reference MRD-MFC panel generating highly concordant results. Using our newly developed single-tube panel, we established reference values in healthy bone marrow for 28 consensus leukemia-associated immunophenotypes and introduced a semi-automated dimensionality-reduction, clustering and cell type identification approach that aids the unbiased detection of aberrant cells. In summary, we provide a comprehensive full spectrum MRD-MFC workflow with the potential for rapid implementation for routine diagnostics due to reduced cell requirements and ease of data analysis with increased reproducibility in comparison to conventional FlowMRD routines.

The Laip-Based-Dfn Approach Is Superior in Terms of Useful MRD Results As Compared to the Laip Approach after Cycle II in Acute Myeloid Leukemia

Clinical decision-making based on measurable residual disease (MRD) in acute myeloid leukemia (AML) is steadily increasing; therefore, accurate MRD results are imperative. Multi-parameter flow cytometry (MFC) is often used due to wide availability, particularly when no suitable mutation is present. Two approaches are most common in MFC-MRD: 1. Leukemia-associated immunophenotype (LAIP) approach, in which the aberrant phenotype is identified at diagnosis and tracked during follow-up. 2. Different-from-Normal (DfN) approach, in which aberrant surface antigen expression patterns not present in normal bone marrow (empty spaces in 2D dot plots) are identified at follow-up. The LAIP approach is sensitive, but does not consider immunophenotypic shifts and cannot be used when no LAIP is identified at diagnosis or when a diagnosis sample is unavailable. The DfN approach can detect these shifts, but ample expertise is needed to determine a malignant population. In the ELN-DAVID AML-MRD guidelines 2022, it is recommended to use the combination of the LAIP approach and the DfN approach to use the advantages of both approaches. In the HOVON-SAKK132 (HO132), the MRD was based on the combination of MFC-MRD and NPM1 RQ-PCR. Initially, the MFC-MRD in this study was based on the LAIP approach. However, the complete MFC panel (four 8-color tubes) published by Cloos et al. (J.Vis.Exp, 2018) was used for measuring MRD during follow-up. Therefore in this study, we had the unique opportunity to retrospectively analyze the samples after induction cycle 2 (C2) of patients in complete remission (CR/CRi) and determine additional MRD results with the LAIP-based-DfN approach. The original LAIP approach encompasses determining the percentages of the LAIPs in the follow-up sample, which were also identified at diagnosis. For the LAIP-based-DfN approach, we followed the same approach, but determined the percentages of all possible LAIPs in the MFC-MRD panel at diagnosis and after C2. An emerging LAIP is defined as a LAIP that is present in the follow-up but was not found at diagnosis. MRD positivity was defined as ≥ 0.1% LAIP cells of white blood cells. Patients with an emerging LAIP < 0.1% or no LAIPs in follow-up would result in MRD negativity for LAIP-based-DfN, but was only possible when at least 500,000 cells were acquired in all four tubes. At diagnosis, we received 884 samples of 905 patients (98%), in which we found a LAIP ≥ 10% of CD45dim blasts in 83% of the samples (Figure 1A). After C2, we received 615 samples, for which we had MFC-MRD results for 79% (487/615) by the LAIP approach. When we applied the LAIP-based-DfN approach, we scored 69 of 615 extra MRD results: an emerging LAIP ≥ 0.1% (MRDpos, N = 14), no LAIPs (MRDneg, N = 25) or an emerging LAIP < 0.1% (MRDneg, N = 30). When including these results in the data of the LAIP approach, the percentage of patients with an MRD result increased from 79% (487/615) to 90% (556/615), and the MRD positive percentage increased from 13% (81/615) to 19% (118/615)(Figure 1B). The LAIPs of emerging clones most often included CD56, CD15, and CD22. To assess the prognostic value in the HO132, we combined the reanalyzed LAIP-based-DfN MFC-MRD with the NPM1-MRD (N = 567). In these analyses, overall survival (OS) hazard ratio (HR) 95% confidence interval (CI) 1.92 (1.44-2.56) and relapse-free survival (RFS) HR 95% CI 1.7 (1.31-2.19) were similar to the original LAIP based/ NPM1 approach: OS HR: 95%CI 2.02 (1.48-2.76) and RFS HR: 95%CI 1.78 (1.34-2.35), respectively. In conclusion, the LAIP-based-DfN approach adds additional MRD results while retaining the prognostic value. Since HOVON-SAKK centers are highly compliant with the protocol and 98% of diagnosis samples were available, the LAIP-based-DfN approach can offer additional value for studies with limited access to diagnosis samples.

Integrated Analysis of KIT Exon 17 Mutations and Flow-MRD Refines Risk Stratification in Pediatric Acute Myeloid Leukemia with RUNX1:: RUNX1T1

INTRODUCTION: Pediatric acute myeloid leukemia (AML) with RUNX1:: RUNX1T1 is considered a favorable risk group, with a high probability of event-free survival (EFS) in recent clinical trials. However, 20-30% of patients still experience relapse within three years and some patients have poor outcome. Several prognostic factors, including secondary genetic abnormalities and treatment response, have been previously reported. Flow cytometry-based measurable residual disease (flow-MRD) has been suggested as a poor prognostic factor in AML with RUNX1:: RUNX1T1. Additionally, KIT mutations, particularly mutations of exon 17, have been associated with poor EFS in both adult and pediatric patients. However, the combined impact of KIT exon 17 mutations and flow-MRD on prognosis has not been thoroughly investigated. This study aims to evaluate the clinical and genetic features of pediatric patients with RUNX1:: RUNX1T1-positive AML enrolled in the Japanese Pediatric Leukemia/Lymphoma Study Group (JPLSG) AML-12 trial and determine if integrated analysis of flow-MRD and KIT exon 17 mutations can improve risk stratification. METHOD: A total of 101 pediatric AML patients with RUNX1:: RUNX1T1 were enrolled in the study. The patients were treated in the JPLSG AML-12 trial, and their clinical and genetic characteristics were analyzed. Targeted capture sequencing was performed on bone marrow samples obtained at diagnosis. The custom gene panel was designed for mutation profiling of pediatric AML, including 504 genes. Flow-MRD was centrally monitored at the end of induction 1 (EOI1) and the end of induction 2 but was not used to guide subsequent therapies. Leukemia-associated immunophenotypes were identified in diagnostic specimens and marker combinations that allowed detection of leukemia with a sensitivity of at least 0.1% were applied to subsequent samples. RESULTS: Patients with KIT exon 17 mutations had a higher white blood cell count at diagnosis and a significantly higher rate of MRD positivity (≥0.1%) at EOI1 compared to patients without KIT exon 17 mutations. Immunophenotypic analysis showed no significant differences in CD117 or CD33 expression between patients with and without KIT exon 17 mutations; whereas CD19 expression was observed less frequently and, although not significantly, CD56 expression was observed more frequently in the patients with KIT exon 17 mutations. The genetic landscape analysis revealed that KIT mutations were the most common and tended to coexist with ARID1B mutations, while NRAS mutations were mutually exclusive. The 5-year EFS and overall survival (OS) for the entire cohort were 67.3% and 82.7%, respectively. Negative MRD at EOI1 was associated with significantly superior 5-year EFS and OS (71.6% and 85.9%) compared to positive MRD (12.5% and 37.5%)(p<0.01). Patients with KIT exon 17 mutations had significantly inferior 5-year EFS and OS (46.9% and 62.2%) compared to those without KIT exon 17 mutations (76.8% and 92.4%) (p<0.01). Furthermore, we evaluated a prognostic impact of MRD within the KIT exon 17 mutated and non-mutated cases. As for the non-mutated cases, the 5-year OS in the patients with negative MRD was 92.2%. Among the KIT-mutated cases, the 5-year OS in the patients with negative and positive MRD was 68.0% and 33.3%, respectively. CONCLUSION: Patients with both non-mutated KIT exon 17 and negative MRD have the best prognosis, while positive MRD and KIT exon 17 mutations are associated with poorer outcomes. These findings indicated that integrated analysis of flow-MRD and KIT exon 17 status enables optimal risk assignment strategies in pediatric AML with RUNX1:: RUNX1T1.

Use of CLL1 and CD45RA As Biomarkers for Leukemia Stem Cells in Acute Myeloid Leukemia Re-Induction Therapy Decision Making

Background: The decision to re-induce patients with newly diagnosed acute myeloid leukemia (AML) currently relies on morphological evaluation of leukemia blasts in post treatment bone marrow, with more than 5% bone marrow blast counts indicating necessity of re-induction therapy. Our previous study showed that changes in Leukemia Stem Cell (LSC) subsets, identified by CLL1 (CD371) or CD45RA as specific markers, are highly correlated with therapeutic outcome. In this study, we focus on newly diagnosed AML patients undergoing induction therapy to determine whether information gained from LSC subset analysis can aid in decision making for re-induction therapy. Methods: We analyzed flow cytometry data from bone marrow aspirate in patients with newly diagnosed AML of all types except acute promyelocytic leukemia (M3) before and after induction therapy from a single institution. “Leukemic blasts” were identified by morphology and leukemia-associated immunophenotype by Multicolor Flow cytometry (MFC). Hematopoietic stem cells (HSCs) gating was based on CD45 dim/SSC and CD34 +CD38 low/- expression. Leukemic stem cells (LSC) subset was analyzed using % of CD371 (CLL-1) or CD45RA positive cells over total HSCs (%CLL1 +/CD34 +CD38 - or %CD45RA +/CD34 +CD38 -). Newly diagnosed AML with >50% (CLL1 +/CD34 +CD38 - or CD45RA +/CD34 +CD38 -) on diagnosis was selected for further study. Fold change of LSC subset was calculated using LSC percentage post-induction divided by LSC percentage on diagnosis. Chart review was conducted to determine correlation between LSC subset change, bone marrow blasts count and clinical course. Mann-Whitney test was used for statistical analysis. Results: Forty-eight newly diagnosed AML (non-M3) cases, who received at least one cycle of induction therapy with both pre- and post-treatment bone marrow biopsy were reviewed. Twenty-seven cases were identified with CLL1 +/CD34 +CD38 - or CD45RA +/CD34 +CD38 - above the 50% threshold on diagnosis. Four cases were later excluded due to inadequate CD34 +CD38 - cellular events on flow cytometry (<20) in post-treatment bone marrow samples. As shown in figure 1, in all the 9 patients with post induction blasts counts of less than 5% (complete remission, CR), post induction LSC subset is reduced to less than 0.5× of LSC subset on diagnosis. Thus, post induction LSC subset less than 0.5× of diagnosis is used as cut off for “adequate reduction”. In 14 patients with residual blasts of more than 5%, there is a wide range of LSC subset change. Interestingly, 6 of them showed adequate reduction of LSC subsets, similar to patients who achieved CR. Among them, one was observed and showed CR on repeat bone marrow biopsy at a later time point without further therapy. The other 5 patients were given re-induction and achieved CR after a second cycle. Eight patients with residual blasts did not achieve adequate reduction of LSC subset (residual LSC subset > 0.5× of diagnosis). Five achieved CR on subsequent re-induction. Three had persistent disease and failed to achieve CR despite 3 cycles of induction therapy. Conclusion: In newly diagnosed AML with high percent of CLL1 +/CD34 +CD38 - or CD45RA +/CD34 +CD38 - LSC subset on diagnosis, monitoring LSC subset offers additional information regarding efficacy of induction therapy. All the patients with CR showed residual LSC subset of 0.5-fold or less compared to LSC subset on diagnosis (defined as “adequate reduction” of LSC subset). For patients who did not achieve remission but adequately reduced LSC subset, which indicates efficacy of induction therapy, observation with repeat bone marrow biopsy, or re-induction with similar regimen can be considered. For patients with no adequate reduction of LSC subset, intensified chemotherapy or alternative therapy with different mechanism of action needs to be considered to maximize the possibility of achieving CR on re-induction. A multi-institutional study with more patients is needed to confirm these findings and validate these LSC biomarkers for this important treatment decision making in AML.

One Tube 23 Color Full Spectral Flow Cytometry Panel in Detecting Minimal Residual Disease in Pediatric B-Cell Acute Lymphoblastic Leukemia

Introduction Minimal residual disease (MRD) is a normalized tool for risk stratification in the treatment of pediatric acute lymphoblastic leukemia (ALL) and has been introduced into many standardized chemotherapy regimens. Flow cytometry (FC) plays an important role in the monitoring of MRD. However, FC-MRD can't reliably detect residual leukemic cells below level of 0.01% in real clinical scenarios and some patients with negative MRD relapsed, suggesting the current used set of markers are not sensitive enough or specific enough. Published studies has shown that more markers with more reliable combination of antibodies may help improve the sensitivity and specificity of FC-MRD. Spectral multicolor flow cytometry (SMFC) has shown an advantage over traditional FC that more fluorescent markers could be applied simultaneously and more complex marker combinations could be exploited to distinguish leukemic blasts from normal B cell precursors with high specificity. Here we designed a SMFC-based panel of 26 markers with 23 fluorescent colors in one tube to monitor B-ALL MRD. Method The one-tube 23-color panels was designed according to previously published studies and our clinical experience based on standardized EuroFlow 8-color MRD panel. All the leukemia-associated immunophenotypes (LAIPs) were defined based on its deviation from hematogones. For CD10, CD19, CD22, CD34, CD58, CD73, CD86, CD123, CD200and CD304, the overexpression was considered as LAIP, while the under-expression was considered as LAIP for CD24, CD38, CD45 and CD81. Asynchronous co-expression of CD34 and CD20, CD34 and CD21 were also included. The aberrant cross-lineage expression was taken as LAIP for CD2, CD56, CD65, CD15, CD13, CD33, CD66c, NG2 and CD133. For CD44, under-expression or overexpression can both be considered as LAIP. To verify the effectiveness of the panel, 317 bone marrow samples from 317 patients with B-ALL diagnosed between 2009 to 2014 at the Shanghai Children's Medical Center (SCMC) were included. These samples were collected at day 19 to 283 (median: day 35), with 213 (67.19%) collected at around day 35, which was a regular time point to monitor MRD and to readjust the risk stratification. The results were compared with those of conventional 8-color FC-MRD. Results The limit of blank (LOB), limit of detection (LOD), and lower limit of quantitation (LLOQ) were firstly determined, the results showed reproducible sensitivity up to 0.001% (1-in-10 5) after acquisition of 4.8 million cells for 23-color panel. The 8-color and 23-color MRD panels showed high correlation of the quantitation of MRD (r 2=0.80, p<0.0001). Among cases of discordant between 8-color MRD negative (with cutoff <0.01%) and 23-color MRD negative (with cutoff <0.001%), relapse only occurred in patients with 23-color MRD positive and 8-color MRD negative, rather than patients with 23-color MRD negative and 8-color MRD positive, suggesting a higher sensitivity and specificity for 23-color MRD assay (See Figure). Patients with detectable MRD by either 8-color or 23-color had a significantly higher incidence of relapse (CIR, p<0.05) and shorter event free survival (EFS, p<0.05). Positive 23-color MRD seemed to be an even stronger factor impacting CIR and EFS. Compared to patients with 8-color MRD negative and 23-color MRD positive, patients with 8-color MRD positive and 23-color MRD negative had a significantly lower CIR (p<0.05) and a better EFS (p=0.068). Patients with positive 23-color MRD lower than 0.01% showed a trend towards poorer EFS and OS (p=0.083% and p=0.061%, respectively) compared to patients with 23-color MRD negative. Conclusion Based on these evidences, SMFC-based one-tube 23-color MRD panel for B-ALL was convenient and maneuverable with higher sensitivity and specificity compared to conventional 8-color FC-MRD panel. It would be a promising method to improve the risk stratification.

Impact of Hemodilution on Measurable Residual Disease Measured Via Flow-Cytometry in Acute Myeloid Leukemia Analyzed Using Subsequent Pulls

Background: Measurable residual disease (MRD) detection plays a crucial role in assessing remission status and prognosis for acute myeloid leukemia (AML) patients. Multiparameter flow cytometry (MFC) and NPM1 gene mutations reverse transcriptase polymerase chain reaction (RT-PCR) are validated and recommended used methods for MRD measurement after two cycles of high-dose induction chemotherapy. However, the accuracy of MRD assessment can be compromised by hemodilution, a phenomenon that occurs during bone marrow (BM) aspiration when peripheral blood (PB) mixes with the BM sample. Due to the lower presence of MRD in PB, this may lead to false-negative results. Although formulas to quantify hemodilution exist, their validation and adoption remain limited, and the exact impact of hemodilution remains unclear. Aim: This prospective study aimed to investigate the impact of hemodilution on MFC-MRD assessment by aspirating three sequential pulls of 2 ml each, instead of the standard 6 ml BM sample, and comparing them with a PB sample collected on the same day. Additionally, we evaluated the performance of different hemodilution formulas and analyzed changes in ratios/percentages of cell populations across the BM pulls and PB samples. Methods: We included 30 AML patients in complete remission, resulting in 40 samples measured after one or two cycles of induction chemotherapy with 46 leukemia-associated immunophenotypes (LAIPs). The first 2 ml of BM were collected as the “first pull”, followed by a second aspirate of another 2 ml to form the “second pull”. This process was repeated to obtain the “third pull”. Precautions were taken during BM aspiration to prevent aspirate loss between pulls, and the aspiration needle remained stationary throughout the procedure. All samples from one time point were analyzed on the same machine by the same operator. The formulas proposed for hemodilution assessment were evaluated using a newly developed tube containing additional markers (CD10, CD16, CD38, and CD138) not present in the standard MFC-MRD assay. Differences in outcomes from the formulas and cell populations across the specimens were analyzed using the non-parametric Friedman's ANOVA test. Moreover, the ability of individual populations or formulas to differentiate between BM and PB samples was assessed using the area under the receiver operating characteristic curve (ROC-AUC) in a binary classification task. Results: Significant decreases in blasts and median MRD% were observed between different pulls and PB samples. The median MRD% in pull 1 (0.06%) was significantly higher than in pull 2 (0.05%), pull 3 (0.04%), and PB (0.01%) ( P<0.001). Pairwise comparisons, adjusted for multiple testing, revealed significant differences between pull 1 and pull 2 ( P=0.025), and between pull 2 to pull 3 ( P=0.025), indicating the effect of hemodilution ( Figure 1A). In the first pull 18/46 LAIPs were above the 0.1% cut-off, compared to 14/46 in the third pull. This resulted in 9 patients being MRD-positive in the first/second pull, compared to 8 patients in the third pull. The evaluated formulas demonstrated progressively higher quantities of diluted samples from pull 1 to PB. Five parameters exhibited an AUC above 0.9, indicating their ability to differentiate between BM and PB samples. These parameters are CD10 (AUC: 0.956), plasma cells (AUC: 0.949), CD16 dim cells (AUC: 0.940), mast cells (AUC: 0.924), and the PB contamination index formula (AUC: 0.905) ( Figure 1B). Conclusion: Hemodilution occurs even after aspirating the initial milliliters of BM, emphasizing the need to consider hemodilution when assessing MRD in AML to avoid false-negative results. We recommend incorporating a hemodilution detection formula into routine practice for AML patients to further evaluate the effect on clinical choices. The results of this study support the examination of the CD16 dim population or mast cell population (CD117hi) for this purpose. Furthermore, we suggest implementing a practical approach that involves numbering each pull of BM during aspiration and taking this into account when giving the final MRD result, thus providing clarity regarding the specific pull being measured. In cases of doubt (e.g., MFC-MRD between 0.07% and 0.09% in a later pull), repeating the BM aspiration is recommended to ensure reliability.

Blast Clearance after High Dose-Melphalan Conditioning for Allogeneic Stem Cell Transplantation in Relapsed and Refractory Acute Myeloid Leukemia

Introduction: For patients (pts) with relapsed or refractory acute myeloid leukemia (r/r AML) allogeneic stem cell transplantation (ASCT) has become an established highly effective and potential curative treatment option. Even for pts with active disease, direct ASCT using sequential conditioning regimens has shown promising outcomes. In this retrospective study, we examined prognostic factors for long-term survival in r/r AML pts with active disease with special focus to the prognostic value of blast clearance during condition therapy. Patients and Methods: 186 r/r AML pts treated with sequential conditioning regimens at our center between 2014-2023 were included in our analysis. Patients underwent high-dose melphalan (100 - 140 mg/m 2, day -11 prior ASCT) followed by either fractionated total body irradiation with 8 Gy (TBI, n = 71) or non-TBI regimens (busulfan, n = 101, or treosulfan, n = 14) in combination with fludarabin (120 - 150 mg/m 2) from day -6 before ASCT. TBI-based conditioning was applied almost exclusively in patients aged < 60 years. Graft versus host-disease (GvHD) prophylaxis consisted of calcineurin inhibitors, mycophenolate and anti-T-lymphocyte globulin. In 180 out of 186 patients, blast clearance was assessed by cytologic and flow cytometric blast count via bone marrow (BM) aspirate in median 5 days after Melphalan and prior to continuation of the sequential conditioning therapy. Blast clearance was defined as cytologic BM blast count < 5% and < 0.1% BM cells with leukemia-associated immunophenotype in flow cytometry. Results: Median pts age was 67 years (range 45 - 76 years) in the non-TBI group and 51 years (range 19 - 71 years) in the TBI group, respectively. Median follow up of surviving patients was 46 months. As expected, comorbidities and disease-specific factors varied between these groups. HCTCI scores > 3 points were observed in 14% of TBI pts compared to 32% in non-TBI pts ( p .01) and 45% versus 54% harbored adverse risk genetics according to European Leukemia Net (ELN) 2017 classification ( p .41), respectively. In the non-TBI group, 38% of the pts had a secondary or therapy-related AML compared to 20% of pts in the TBI group ( p .03). HLA-mismatched (<10/10 matched) donor grafts were transplanted in 21% (TBI) vs. 20% (non-TBI) of the pts. 185 of 188 pts received GCS-F mobilized stem cell grafts; 3 pts received a bone marrow graft. Kaplan-Meier estimates for overall survival (OS) with and without blast clearance at 2 years were 69.6% (95% CI 60.1-80.6%) vs. 58% (95% CI 48.8-69.1%, p .33), for event free survival (EFS, event defined as death or overt relapse) 58.9% (95% CI 49-70.8%) vs. 46.1% (95% CI 36.7-58.1%, p .2), respectively. We included the re-occurrence / persistence of defined molecular and cytogenetic markers or decreasing CD34 + bone marrow chimerism (< 95%) after transplant as measures for impending relapse as a modified EFS. The EFS including impending relapse was 49.8% (95% CI 40-62%) vs. 36.4% (27.7-47.8%) after 2 years. A non-significant trend with reduced relapse risk for those patients who achieved blast clearance after Melphalan ( p .1, HR 0.73) was observed. Most patients with impending relapse showed similar survival as patients without evidence of relapse after ASCT. In multivariate cox regression, age, HCTCI scores > 3 points, adverse risk according to ELN 2017 definitions and donor mismatch < 10/10 resulted in adverse prognosis. Especially, patients with mismatched donors displayed highly significant inferior outcomes. Both leukemic burden prior to ASCT as well as blast clearance after melphalan showed no significant correlation with clinical outcome parameters. Conclusion: Sequential conditioning regimens followed by ASCT offer long-term survival for more than 50% of pts with active relapsed or refractory AML. Patients who did not achieve complete blast clearance during conditioning therapy showed a trend towards higher relapse risk after ASCT which did not result in inferior survival. This underscores the importance of close monitoring and early interventions such as accelerated immunosuppression tapering, preemptive donor lymphocyte infusions and targeted therapies in case of impending relapse after ASCT.

Measurable Residual Disease Assessment in Patients with Acute Myeloid Leukemia Aged ≥60 Years Treated with a 10-Day Decitabine Schedule Versus Intensive Chemotherapy in the AML21 Study (NCT02172872)

Introduction Several studies have demonstrated that patients with acute myeloid leukemia (AML) who test measurable residual disease (MRD) positive during or after treatment have a higher probability of relapse and a shorter duration of survival, as compared to those who are persistently MRD negative. Indeed, a status of MRD positivity reflects a condition of resistant disease, existing below the threshold of the morphologic evaluation of complete remission (CR). The bulk of our knowledge in terms of MRD assessment has been generated in the setting of intensive chemotherapy; much less is known for older patients receiving less intensive treatments, such as decitabine (DEC) using a 10-day schedule. Methods The AML21 study was a randomized open-label phase 3 clinical trial conducted by the EORTC Leukemia Group, GIMEMA, and GMDS-SG. Patients with a newly diagnosed AML, aged ≥60 years and eligible for intensive chemotherapy were randomized 1:1 to receive DEC (20mg/m2 a day) using a 10-day schedule or intensive chemotherapy regimen consisting of daunorubicin 60 mg/m2 x 3 days and cytarabine 200 mg/m2 x 7 days (3+7), followed by 1-4 additional chemotherapy cycles. Patients who had an HLA-matched donor and at least stable disease were encouraged to undergo HSCT after >1 treatment cycle. Patients from the DEC arm not receiving HSCT could continue DEC treatment. A subset of patients treated in GIMEMA sites underwent a prospectively planned MRD evaluation post cycle 3 (DEC arm)/post consolidation (3+7 arm), and at 6, 12 and 18 months after the randomization, in case they were in a first CR and had not been allografted. MRD was studied by multiparameter flow cytometry. Based on several retrospective validations in the context of former EORTC/GIMEMA protocols, the threshold for discriminating MRD negative from MRD positive cases was set at 3.5x10-4 (0.035%) residual leukemic cells, upon full blood count recovery. Results In total, 130 out of 154 patients treated in GIMEMA centers provided consent for participation in translational research, had leukemia associated immunophenotype suitable for MRD monitoring, and initiated the protocol treatment, DEC (N=66) or 3+7 (N=64). Median age was 68 years (range 60-78), 33% of patients were ≥70 years old, 54% were male, and 31% and 30% had good and adverse European LeukemiaNet 2017 risk profile, respectively. At the MRD evaluation post cycle 3/consolidation, 9 out of 66 (14%) patients from the DEC and 12 out of 64 (19%) patients from the 3+7 arm had documented MRD negativity. The number of patients who either had documented MRD negativity or had undergone allografting and were alive and progression-free was 12 (18%) and 17 (27%) at 6 months, 14 (21%) and 13 (20%) at 12 months, and 14 (21%) and 7 (11%) at 18 months in the DEC and 3+7 arms, respectively. The inspection of individual profiles of patients who underwent the first MRD evaluation (and were at remission at that time) indicated that all MRD-positive patients from the DEC arm who were not allografted eventually relapsed, which often occurred just after the discontinuation of DEC maintenance. Conclusions 10-day DEC treatment can induce MRD-negativity. However, early MRD-negativity appeared more difficult to achieve with 10-day DEC than with 3+7. Among patients in whom 10-day DEC did not induce MRD-negativity, allografting or DEC maintenance appeared necessary to avoid a disease relapse.

Single-Cell Transcriptomics Points to a Role of Stemness and Bone Marrow Niche Interactions in the Poor Response to Induction Therapy in T-Cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia (T-ALL) has a poor prognosis with a 15-20% relapse rate. The induction therapy response is the strongest predictor of relapse and shows great variation between patients. However, whether intra-patient leukemic cell heterogeneity plays a role for the induction therapy response has not yet been investigated. We studied 13 patients with T-ALL (11 pediatric and 2 young adult, median follow-up 37 months). Of these, three were good responders (end of induction (EOI) minimal residual disease (MRD) undetectable/non-quantifiable by flowcytometry and PCR), while ten had a poor response (EOI MRD>0.01%, (range 0.05-97%). Of the ten poor responders, three experienced relapse and one died from resistant disease. Bone marrow samples from diagnosis (n=13) and paired samples from relapse (n=3) or MRD (n=4, MRD >5%) were subjected to combined single-cell RNA sequencing, single-cell surface marker profiling by antibody-derived tag (ADT)-sequencing, and single-cell TCR sequencing, using the 10X Genomics platform. A published healthy bone marrow dataset was used for cell annotation and clear distinction was observed between healthy cell subsets and leukemic blasts. TCR sequencing data revealed a hyperexpanded clone in six patients, with identical clonal sequences at diagnosis and relapse(n=2)/MRD(n=1). Surface marker profiling using a panel of 134 surface antigens showed good correspondence between leukemia-associated immunophenotypes found by ADT-sequencing and by flow cytometry for 16 common clinically used markers. To examine factors associated with a poor therapy response, we compared average gene expression of leukemic cells in poor and good responders at diagnosis using differential gene expression (DGE) and gene set enrichment analysis (GSEA). At diagnosis, poor responders showed upregulation of genes involved in extracellular matrix (ECM) degradation/organization, including the adhesion molecules ITGA5 and PECAM1, and MMP11, while showing downregulation of cell cycle genes. Accordingly, the fraction of cells predicted to be in G0/G1 phase at diagnosis of poor responders positively correlated with EOI MRD (r=0.52, p=0.07, Spearman's rank correlation). To investigate if this high fraction of quiescent cells in poor responders was associated with a more stem-like cell state, we examined the expression of a published hematopoietic stem cell (HSC) signature (Forsberg et al, 2010) that we previously selected for investigation in BCP-ALL (Modvig et al, Molecular Oncology, 2022). Indeed, patients with a poor response had a higher percentage of leukemic blasts with an HSC signature module score above zero (p=0.028, Kolmogorov-Smirnov, distribution in Figure 1), suggestive of stemness as a contributing factor to therapy resistance. To define molecular changes in leukemic blasts during therapy, we compared the leukemic blast gene expression profiles in matched diagnostic and MRD samples using DGE and GSEA. This revealed that the leukemic blasts within the first month of therapy downregulated cell cycle genes, while upregulating chemokine receptors, such as CXCR4. To identify specific genes associated with high MRD, we combined genes upregulated in poor responders (n=314, p<0.01, DGE) with genes associated with EOI MRD levels (n=98, r>0.8 and p<0.001, rank regression). This resulted in a 30-gene signature, comprising several genes previously associated with cancer stem cells, such as MICAL3, ELF4, and NLRP3, and genes encoding proteins involved in cancer drug resistance. These included sialyl transferases, acid ceramidase ( ASAH1) and zyxin ( ZYX). ZYX silencing was previously shown to downregulate the anti-apoptotic protein BCL-2 in leukemia. Accordingly, the percentage of cells with detectable BCL2 expression at diagnosis correlated with EOI MRD (r=0.58, p=0.04), supporting a role of BCL-2 inhibitor therapy in T-ALL. In conclusion, our data suggest that therapy-resistant cells are more stem-like and quiescent at diagnosis, display upregulation of genes involved in bone marrow niche ECM organization and adhesion, and genes related to drug resistance. Likewise, residual leukemic blast following therapy show less proliferation and CXCR4 upregulation. Thus, single-cell transcriptomics provides important molecular insights into therapy-resistant leukemic cells and could comprise a valuable prognostic tool in T-ALL.

Minimal Infiltrative Disease Identification in Cryopreserved Ovarian Tissue of Girls with Cancer for Future Use: A Systematic Review.

Ovarian tissue cryopreservation and transplantation are the only available fertility techniques for prepubertal girls with cancer. Though autotransplantation carries a risk of reintroducing malignant cells, it can be avoided by identifying minimal infiltrative disease (MID) within ovarian tissue. A broad search for peer-reviewed articles in the PubMed database was conducted in accordance with PRISMA guidelines up to March 2023. Search terms included 'minimal residual disease', 'cryopreservation', 'ovarian', 'cancer' and synonyms. Out of 542 identified records, 17 were included. Ovarian tissues of at least 115 girls were evaluated and categorized as: hematological malignancies (n = 56; 48.7%), solid tumors (n = 42; 36.5%) and tumors of the central nervous system (n = 17; 14.8%). In ovarian tissue of 25 patients (21.7%), MID was detected using RT-qPCR, FISH or multicolor flow cytometry: 16 of them (64%) being ALL (IgH rearrangements with/without TRG, BCL-ABL1, EA2-PBX1, TEL-AML1 fusion transcripts), 3 (12%) Ewing sarcoma (EWS-FLI1 fusion transcript, EWSR1 rearrangements), 3 (12%) CML (BCR-ABL1 fusion transcript, FLT3) and 3 (12%) AML (leukemia-associated immunophenotypes, BCR-ABL1 fusion transcript) patients. While the majority of malignancies were found to have a low risk of containing malignant cells in ovarian tissue, further studies are needed to ensure safe implementation of future fertility restoration in clinical practice.

Validation of a 12-color flow cytometry assay for acute myeloid leukemia minimal/measurable residual disease detection.

Acute myeloid leukemia (AML) minimal/measurable residual disease (MRD) by multicolor flow cytometry is a complex laboratory developed test (LDT), challenging for implementation. We share our experience in the validation of a 12-color AML MRD flow cytometry assay to meet stringent regulatory requirements. We worked under the guidelines of the CLSI HL62 publication, illustrated the details of the validation process that was tailored to uniqueness of AML MRD, and tested its clinical validity in 61 patients. The "trueness" was determined by correlating with concurrent molecular genetic testing and follow-up bone marrow examinations. Under assay specificity, we shared the details of panel design, analysis, and criteria for interpretation and reporting. The assay accuracy was assessed by testing known positive and negative samples and correlating with molecular genetic testing and follow-up bone marrow examination. The limit of detection (LOD) and limit of quantification (LOQ) were validated to a level between 0.01% and 0.1%, varied from the leukemia-associated immunophenotypes (LAIP) and the numbers of events obtained for analysis. Assay linearity, precision and carry over studies all met acceptable criteria. In the clinical validity test, the concordance was 93%, specificity 98% and sensitivity 83%. The most challenging aspects of the assay were the discrimination of pre-leukemic cells (persistent clonal hematopoiesis) or underlying myelodysplastic clones from AML MRD with immunophenotypic switch or subclone selection. The validation met all criteria and obtained FDA IDE (investigational device exemption) approval. This study provides ample technical and professional details in setting up the AML MRD flow cytometry assay and illustrates through the example of the "fit for purpose" validation process. We also highlight the need for further characterization of abnormal blasts bearing the potential for AML relapse.

Minimal residual disease in acute leukemia based on the insight of molecular genetics monitoring

Patients with acute leukemia port 10 malignant cells at presentation. Following chemotherapy or stem cell transplant, patients in complete remission by conventional analyses may still harbor 106/108 malignant cells below the detection limit of standard clinical assessment. Minimal residual disease (MRD) monitoring is one of the most powerful predictors of disease-free and overall survival, particularly for children with acute lymphoblastic leukemia (cALL), the percent annual of cALL increase in the incidence of cALL in Saudi Arabia. Breakpoint fusion regions of chromosomal aberrations can be used as tumor-specific targets for MRD detection by polymerase chain reaction. Levels of MRD, measured at critical time points, significantly correlate with clinical outcomes. Previous works investigated the prognostic significance of leukemia-associated immunophenotypes (LAIPs) as an assessment of the index of MRD in 125 adult B-ALL patients by eight-colour flow cytometry. More advanced molecular and genetics studies are so necessary to identify the mechanisms and cellular structure of the minimal-level disease. Selecting molecular methods for minimal residual disease detection have a much higher sensitivity and precision (100-fold or more) than others. This review highlights the minimal residual disease molecular detection to demonstrate the characterization of the lymphoblastic leukemia gene. Precise MRD monitoring predicts disease relapse after chemotherapy or SCT, provides early intervention, and may result in the rescue of many patients and improvement in the probability of long-term disease-free survival.

Clinical Significance of Flow Cytometry Findings in Brazilian Patients with De Novo Acute Myeloid Leukemia

Introduction: Immunophenotyping by flow cytometry (FC) is an essential method for diagnosis and classification of acute myeloid leukemias (AML), and its extensive use could identify blast cell subpopulations with phenotypes rarely seen in normal myelopoiesis, correlating with clinical, morphological and prognostic characteristics. Methods: In this study we analyzed 143 cases of AML, examining them for leukemia-associated immunophenotype (LAIP) by FC immunophenotyping in leukemic cells using a panel of monoclonal antibodies (MoAb) for diagnosis and classification of acute leukemia (AL). At the same time, clinical, demographic and hematological data of these patients were also investigated. Most patients were male adults and splenomegaly and hepatomegaly were present in most cases. Results: Immunophenotyping showed a characteristic profile of AML with expression of pan-myeloid antigens CD13, CD33 and myeloperoxidase (MPO), combined with CD34 and CD117 in most cases. Expression of CD14 and CD64 were observed in AML with monocytic component (AML-M4/M5), CD235a, CD36 and CD71 in cases of erythroleukemia (AML-M6) and platelet glycoproteins CD41, CD42b and CD61 in acute megakaryocytic leukemia (AML-M7). Regarding the aberrant phenotype, higher levels of expression of CD4, CD7 and CD56 were observed, corresponding to 24.5%, 22.4%, and 16.1% of the cases, respectively. Conclusion: We conclude that LAIP, as they are described here, were present in the vast majority of cases of investigated AML, with a relevant association with prognostic factors, clinical data and cytomorphological classification.

Fast-Track Measurable Residual Disease Detection By Multiparametric Flow Cytometry in Acute Myeloid Leukemia before Allogeneic Hematopoietic Cell Transplantation

Introduction In acute myeloid leukemia (AML), measurable residual disease (MRD) becomes more and more important for individualized treatment decisions. The MRD status at the time of allogeneic hematopoietic cell transplantation (alloHCT) provides prognostic information beyond baseline risk features. Peri-transplant treatment strategies and conditioning intensity can be stratified according MRD-levels. However, therapeutic interventions (e.g. conditioning intensity) usually require the prompt availability of reliable information on the MRD status. We assessed the prognostic value of a standardized, reproducible, and fast turnover multiparametric flow cytometry (MFC) approach that has been validated at the end of intensive induction therapy to monitor MRD before alloHCT (Röhnert, Leukemia 2022). This approach allows for the simultaneous detection of MRD by the leukemia-associated immunophenotype (LAIP) and the different from normal (DfN) method. Methods Between October 2016 and March 2020, bone marrow (BM) aspirates of patients (pts) with AML were analyzed for the presence of MRD immediately before the start of conditioning. therapy with the aim of analyzing to predictive value of this fast-track parameter. Pts receiving sequential regimens (re-induction chemotherapy followed by reduced-intensity conditioning) were excluded. Briefly, the LAIP-based DfN analysis is based on a hierarchical gating strategy with fixed gates and encompasses the antigens CD34, CD117, HLA-DR (backbone markers), CD13, CD33 (myeloid markers), CD7 and CD56 (lymphoid markers). Within less than 5 minutes, the analysis checks for the presence of the aberrant categories i) deficiency of myeloid markers and ii) cross-lineage expression of lymphoid markers. Reference values for 32 immunophenotypically defined populations were established on BM aspirates of 90 leukemia free controls. An aberrant category already detectable at diagnosis on ≥10% of myeloid progenitors/ monocytes was termed aberrant LAIP (aLAIP) and a de-novo appearance (after chemotherapy) post-treatment DfN (ptDfN). In conclusion this approach is very fast and provides high reproducibility. Results We identified 58 pts with a median follow-up of 33.3 months after alloHCT (Table 1 with pts characteristics). Response assessment was performed in median 8 days before alloHCT. Most of the patients were in morphologic complete remission (CR n=37). A subset of 21 patients had refractory disease with a median BM blast count of 6.5%. Samples at AML diagnosis were available for 48/58 (83%) pts, of whom 34/48 (71%) showed at least one aLAIP at initial diagnosis. Before start of conditioning, 44/58 (76%) patients were MRDpos. The proportion of MRDpos in responders was lower compared to non-responders: 24/37 (65%) vs. 20/21 (95%) (p=0.0106). MRDpos was designated by aLAIPonly, ptDfNonly and aLAIP+ptDfN in 18%, 48% and 34% of cases, respectively. Noteworthy, 8 of 21 pts classified MRDpos by ptDfNonly had no sample available at diagnosis and therefore could not be assessed for aLAIP persistence. Amongst 37 pts in CR before alloHCT, 12/24 (50%) of MRDpos pts relapsed compared to 3/13 (23%) of MRDneg pts. TRM in these patients did not differ (13% vs. 8%). In a univariable Cox regression analysis, the 1-year Overall survival (OS) rate of MRDpos cohort was significantly shorter compared to MRDneg pts (64% vs. 93%, Hazard ratio (HR) 10.5, p=0.004). MRD was detected by ptDfNonly in 23/44 (52%) of MRDpos pts. The OS of these pts was comparable to MRDpos by aLAIP with or without ptDfN (Figure 1). As expected, the MRDpos cohort was enriched for non-responders. However, when the analysis was restricted to pts in CR (n=37), MRD status preserved its prognostic significance (HR 7.9, p=0.019). And even in the subpopulation of pts in first CR, MRDpos was associated with a significantly reduced OS compared to MRDneg (HR 6.3, p=0.043). Interestingly, a single non-responder was classified as MRDneg and showed a long-term OS. Conclusions Our fast-track LAIP-based DfN approach provides relevant prognostic information prior to conditioning for allo HCT. On top of the classical LAIP approach, the ptDfN analysis gives additional prognostic information. The LAIP-based DfN approach might be a suitable tool for fast-track and reliable MRD assessment before starting the preparative regimen for alloHCT and might help to guide potential treatment modifications. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Prospective Validation of CD34+CD38- Leukemic Stem Cell Frequency in the HOVON-SAKK 132 Trial: Perspectives for Future Improvements

Clinical implementation of measurable residual disease (MRD) requires accurate MRD detection to assess relapse risk for acute myeloid leukemia (AML) patients. One possibility to further improve the prognostic ability of the current MRD assay is to include the quantification of relapse initiating cells such as the CD34+CD38- leukemic stem cells (LSC) in the assay. In the HOVON-SAKK 102 trial, detection of LSC by multiparameter (MFC) flow MRD at diagnosis and after 2nd chemotherapy cycle (C2) has shown prognostic value (Zeijlemaker et al. Leukemia 2019). In addition, together with MRD detection, LSC could identify a category of patients with very high risk of relapse. Based on those data, improvements for LSC assessment measurements have been suggested, such as measuring more white blood cells (WBC) with the purpose of enhancing the sensitivity for the low frequency of CD34+CD38- cells. In the HOVON-SAKK 132 trial (Lowenberg et al. Blood Adv 2021), the one tube LSC assay was used that included LSC markers CD45RA, CD123, CD33, CD44, CLL-1, TIM-3, CD56, CD7, CD22 and CD11b (Zeijlemaker et al. Leukemia 2016). The one tube approach allows acquiring the suggested 4 million WBC for LSC-load estimation. In the current study, we prospectively validated the prognostic value of LSC burden at the following time points, i.e. at diagnosis (764/905 patients) and after two cycles of chemotherapy (C2; 357/706 patients). The median WBC acquired was 2x106 (range: 3x104- 6x106) at diagnosis and 3x106 (range: 4x105-5x106) after C2. Median percentages of LSC at diagnosis and after C2 were respectively 0.004% (range: 0.0000%-26.85%) and 0.00002% (range: 0.0000%-1.36%). Similar to the HOVON-SAKK102 study, three prognostic groups based on the presence or absence of CD34 and/or LSC, showed significant associations between LSC burden at diagnosis and overall survival (OS) or relapse- free survival (RFS) (Figure 1A): 1. CD34negative patients without any measurable LSCs and Leukemia Associated Immunophenotypes on the CD34+ blasts fraction (CD34negLSC=0 3 years (yrs) OS: 76.4% standard error (SE) 5; median OS not reached). 2. Patients with low percentages of CD34+CD38-LSCs < 0.03% (LSClow; 3 yrs OS 62.8% SE 2; median OS not reached) 3. Patients with high percentages of CD34+CD38-LSCs ≥0.03% (LSChigh, 3 yrs OS 44.5% SE 3; median 25.6 months; 95% confidence interval (CI): 18.7-49.1). Multivariate analysis adjusted for age, WBC at diagnosis, AML type, ELN2017 risk group and -only for RFS- the number of chemotherapy cycles to attain complete remission, showed that LSC burden at diagnosis is a strong independent prognostic factor for OS and RFS (Figure 1B). After C2, before the consolidation treatment, a cut-off value of 0.000075% of LSC showed the best prognostic value of LSC (univariate, LSCneg versus LSCpos: OS, HR 1.79 95% CI: 1.25-2.56, P < 0.01; RFS, HR 1.55, 95% CI: 1.12-2.13, P < 0.01). This cut-off appeared also highly significant as a prognostic factor in former trials (Terwijn et al. PLoS One 2014; Zeijlemaker et al. Leukemia 2018). Multivariate analysis showed that also LSC status after C2 was an independent prognostic factor for OS and RFS (Figure 1B). By combining the LSC status after C2 (≥0.000075%) together with the MRD status as used in the HOVON-SAKK 132 (based on ≥0.1% MFC-MRD and/or NPM1-MRD), MRDpos patients who are LSCpos have worse prognosis in OS and RFS (univariate: MRDnegLSCneg vs MRDposLSCpos; OS HR 3.2, 95% CI: 1.94-5.28, P < 0.01, RFS: HR 2.61 95% CI: 1.65-4.12, P < 0.01, multivariate: Figure 1B). Further analyses of the data are now directed towards potential influences of the cell amount of acquisition, ELN risk groups and MRD guidance in this trial. In conclusion, this prospective validation confirmed that assessing LSC burden, at diagnosis and after C2, remains to have additional prognostic value to MRD. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Utilizing CLL-1 Positive Leukemia Stem Cells As a Marker of Early Treatment Response in Acute Myeloid Leukemia

Background: Current methods to evaluate therapeutic response in Acute Myeloid leukemia (AML) rely primarily on morphological evaluation of leukemia blasts in bone marrow at end of treatment cycles, with complete remission (CR) defined as less than 5% bone marrow blast counts without leukemic phenotype. Measurable residual disease (MRD) has been shown highly prognostic for outcome. MRD by molecular methods is limited to subgroup of patients with defined genetic mutations. MRD detection by Multicolor Flow Cytometry (MFC) is still being standardized. Leukemia stem cells (LSC) has been established as source of treatment resistance and disease recurrence in AML. In this study, we aim to analyze change in LSC during treatment using immunophenotypically defined markers and examine whether information gained from LSC analysis could provide additional insights into disease course and assist management of AML under routine clinical practice setting. Methods: We analyzed flow cytometry data from bone marrow aspirate (BMA) and/or peripheral blood (PB) in patients with AML (excluding acute promyelocytic leukemia) before and after treatment. "Leukemic blasts” were identified by morphology and Leukemia-associated Immunophenotype by MFC. Hematopoietic stem cells (HSCs) gating was based on CD45dim/SSC and CD34+CD38low/- expression. Leukemic stem cells (LSC) fractional change was analyzed using CD371 (CLL-1), CD366 (TIM3), and CD45RA percent of positive over HSCs. A chart review was conducted to determine correlation between LSC fractional change and clinical outcome. Statistical analysis was performed using GraphPad Prism version 9. Results: Fifty AML cases with both pre- and post-treatment data from a single institution in the past 3 years were included in this study. Consistent with published literature, patients with significant reduction in LSC subsets was associated with longer remission, while patients with no significant decrease in the LSC subsets demonstrated no or only a temporary remission. Intriguingly, several patients with drastic reduction in LSC after induction chemotherapy achieved complete remission, despite initial post-treatment bone marrow showing persistence of ">5% leukemia blasts” indicating possibly failed induction therapy. In contrast, in patients with persistently high or increased LSC fraction post-treatment, overt clinical relapse occurred quickly despite "absence” or <1% of leukemia blast differential counts in initial bone marrow. In a series of patients who received allogeneic stem cell transplant (Allo-SCT), rise of LSC fraction post Allo-SCT was associated with early AML relapse (within 6 months), while the decrease of LSC fraction was associated with prolonged remission (Representative patient cases shown in Figure 1). Lastly, among the three LSC-specific markers analyzed, the changes in LSC characterized by CLL-1 expression showed the best correlation with clinical course. In addition, the LSC fraction measured by CLL-1 in the peripheral blood is highly correlated with that of the bone marrow (R2=0.93, P<0.0001). Conclusion: This retrospective study explored the value and applicability of LSC detection in routine clinical practice. Importantly, conventional methods relying on evaluating leukemic blast counts in post-treatment bone marrow can sometimes over- or under- estimate the benefit of certain treatment regimen, leading to inappropriate continuation of the same treatment or switch of a potentially effective treatment regimen. In those groups of patients, the change in LSC fraction provides additional information for early treatment response evaluation, refines outcome prediction, and helps with treatment regimen selection. Trending LSC fractional change identifies impending relapse in post Allo-SCT. LSC fractional change determined by CLL-1 showed the best clinical correlation and should be incorporated into routine evaluation for AML patient in clinical practice, and possibly for those participating in investigational trials. Future studies will focus on collecting more data to validate above findings, determining the thresholds of LSC fractional change which constitute potential treatment response vs failure and testing the feasibility of tracking LSC subsets non-invasively in peripheral blood during treatment to predict therapeutic outcome and potentially guide treatment decisions. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

From Generic RNA-Based MRD Assessment Towards Patient-Specific Genomic (DNA-based) MRD in AML and Other Non-B Cell Acute Leukemia

Pediatric acute myeloid (AML) is considered as a heterogeneous disease affecting 15% of children with acute leukemia. Outcome is still unsatisfactory with an overall survival around 70-80% and a relapse rate of 30-40% after primary treatment. The most important factors determining clinical outcome are genetic aberrations, and early response to treatment. Many studies have demonstrated the prognostic significance of minimal residual disease (MRD) monitoring. Although MRD monitoring is now an integral part in the management (including MRD-guided stratification) of Acute Lymphoblastic Leukemia (ALL) in children (generally done by ASO-qPCR on tumor specific IG/TCR targets), its clinical utility in childhood non-lymphoblastic leukemia (such as AML) is currently unknown/not used. Contemporary approaches to MRD detection in AML rely on PCR amplification of usually fixed genetic abnormalities (MRD-PCR) or on flowcytometric profiling of leukemia-associated immunophenotypes (LAIP). Molecular MRD detection is in general more sensitive than flow-based MRD, but the applicability is lower since recurrent mutational targets (e.g. fusion genes) using conventional technology, are present in only 40-50% of pediatric AML patients. This RNA-based MRD is common practice for CBFb-MYH11, RUNX1-RUNXT1, KMT2A-AFF1, -MLLT1, -MLLT3, and NPM1 exon 12 mutations and standard curves necessary for MRD quantification are available for all mentioned genes. Since the introduction of Whole Transcriptome Sequencing (WTS; RNAseq) as standard diagnostics in our laboratory, we identified various additional fusion genes in AML (increasing available molecular targets up to 75%), but also in other non-B cell malignancies such as SCLL, CEL, HES and BPDCN. By designing patient specific primers/probe sets surrounding the breakpoint sequences, we were able to generate 36 RNA-based MRD assays (including FOP-FGFR1, RANBP2-ALK, DEK-NUP214, ETV6-PDGFRB, KMT2A-AFDN) and monitor MRD during/after therapy. Although RNA-based MRD approach allows additional molecular monitoring in these patients, this type of MRD displays several disadvantages: sensitivity of a certain MRD assay can be low due to low expression levels of the fusion gene or low RNA yield and/or quality. Furthermore, quantification can be hampered by lack of available standard curves. Therefore DNA-based MRD is favorable over RNA-based MRD and Whole Exome Sequencing (WES) or Whole Genomic Sequencing (WGS) can identify the genomic breakpoint sequence in respectively genomic exons or introns. In addition, other genomic aberrations (such as insertions, deletions and point mutations) can be identified by these techniques and used for development of DNA-based MRD. By using this approach we were able to generate 17 additional DNA-based MRD assays (including FOP-FGFR1, RANBP2-ALK, RUNX1-CBFA2T3 NPM1-MLF1 UBTF-TD, p53 deletion), all with very high sensitivity (e.g. around 10-4 to 5x10-5) and patient-derived standard curves to quantify MRD. Figure 1 shows an example for DNA-based MRD monitoring of 3 AML patients harboring the recently described poor-outcome UBTF-TD aberration showing no/slow decrease of MRD in all patients. In conclusion, we show that fusion gene detection by WTS, preferably in combination with mutation analysis by WES/WGS, is providing comprehensive diagnostic results to improve the development of highly sensitive patient specific MRD targets to allow better molecular monitoring (and prediction of relapse), eventually leading to treatment stratification of patients in the future. We will present an update of our results and interesting cases at the upcoming conference. Figure 1: By WES, 3 patients with tandem duplications (TD) in exon 13 of the UBTF gene were identified, and patient specific primers and probes were designed for MRD on follow-up DNA samples. MRD was quantified by using a standard curve derived from serial dilutions from the diagnostic DNA. Quantitative range, sensitivity and background were determined according to the ESG-MRD-ALL guidelines. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Prognostic Impact of Persistent Measurable Residual Disease in Patients with Acute Myeloid Leukemia FLT3+ Treated with Intensive Chemotherapy Plus Midostaurin - a Retrospective Study of the Polish Adult Leukemia Group (PALG)

Background: Measurable residual disease (MRD) is detected during morphological remission after standard chemotherapy in acute myeloid leukemia (AML) patients (pts). It is a strong prognostic factor for relapse and shorter overall survival (OS). Immunophenotyping by multiparameter flow cytometry (MFC) is currently the most commonly used method in AML pts. There is still a lack of studies evaluating MRD in specific AML populations in the era of targeted therapies, including thyrosine kinase inhibitors. A retrospective study in adult pts with a newly diagnosed AML FLT3+ treated with intensive chemotherapy plus midostaurin has been performed to evaluate the prognostic impact of positive MRD (MRD+) on RFS and OS. Objectives: To assess the prognostic impact of MRD status during the clinical course of AML FLT3+ on RFS and OS. Patients and methods: Seventy three pts with AML FLT3 were treated in Polish hematological centers between 2018 and 2021. Bone marrow aspiration was performed after induction and consolidation treatment to assess response and MRD by MFC. MRD+ was defined as ≥ 0.1% abnormal cells within mononucleated cells by MFC with diagnostic leukemia-associated immunophenotype (LAIP) and different from normal (DfN) aberrant immunophenotype approaches. Results: The median age of the pts was 55 (range: 18-74). Induction regimen was DA "3+7" in 50 (70%), DA-90 in 8 (11%), DAC in 11 (15%), other in 2 (4%) pts. Fifty seven (78%) pts achieved first composite complete remission (CRc=CR+CRi) after 1 or 2 courses of induction, 12 (17%) had primary refractory disease (PRD) and 2 (3%) pts died in aplasia. Median number of consolidation courses was 2 (range: 1-4). Fifty one (89%) pts with CR1 fulfill the criteria for MRD analysis after 1 or 2 courses of induction and 34 (48%) pts after consolidations. Thirty four pts had 2 timepoints evaluation: after induction and at the end of consolidation courses. MRD+ was reported in 35 (68%) of pts after induction (median 0.5; IQR 0.25-0.85) and in 19 (52%) of pts at the end of consolidations (median 0.64; IQR 0.22-1.99). Analysis of 4 pts groups was performed: Group 1.: MRD+ after induction and at the end of consolidations (persistent MRD+)(n=16; 47%); Group 2.: MRD+ after induction with conversion to MRD- at the end of consolidations (n=6; 18%); Group 3.: MRD- after induction with conversion to MRD+ at the end of consolidations (n=2; 6%); Group 4.: MRD- after induction and at the end of consolidations (persistent MRD-)(n=10; 29%); Baseline clinical characteristics were similar between 4 groups regarding age, FLT3-ITD and FLT3-TKD frequency, FLT3-ITD allelic ratio (AR), WBC, PLT, peripheral blood and bone marrow blast percentage, AML type: de novovs sAML vs tAML (p-values > 0.05). The probability of 1- year RFS was significantly lower in pts with persistent MRD+ (group 1.) vs group 2. vs 3. vs 4. (27% vs 83% vs 50% vs 78%; p=0.034, respectively). Relapse rate after 1 year was in group 1. vs 2. vs 3. vs 4.: 73% vs 16% vs 50% vs 20% (p=0.015), respectively. The shorter OS, but insignificant, was noted in group 1. vs 2. vs 3. vs 4. (p=0.49). A univariate analysis revealed that allo-HSCT (hazard ratio [HR] 0.345; 95% confidence interval (CI), 0.152-0.784; p=0.011) and male sex (HR, 0.433; 95% CI, 0.217-0.861; p=0.017) are predictors for longer OS. MRD- at the end of consolidations (HR, 0.211; 95% CI, 0.066-0.669; p=0.008), persistent MRD- (HR, 0.252; 95% CI, 0.070-0.909; p=0.035), allo-HSCT (HR, 0.416; 95% CI, 0.183-0.947; p=0.0368) are predictors for longer RFS. However, older age (HR, 1.049; 95% CI, 1.018-1.081; p=0.0017) and higher WBC (HR, 1.005; 95% CI, 1.002-1.008; p=0.0022) are predictors for shorter RFS. Conclusions: We observed high rate of CR1 MRD+ AML FLT3 pts after induction (68%) and at the end of consolidations (52%). Significantly lower RFS and higher relapse rate, but not OS, were noted in pts with persistent MRD+ in comparison to pts in other MRD groups. Longer follow-up period and larger studies are necessary to confirm our preliminary findings.