Distinct outcomes, ABL1 mutation profile, and transcriptome features between p190 and p210 transcripts in adult Philadelphia-positive acute lymphoblastic leukemia in the TKI era

A multi-modal molecular characterization of the Philadelphia translocation featuring long read sequencing

OBJECTIVE

Clinically significant structural variation (SV), notably chromosomal translocation, results in the formation of fusion genes that drive leukaemogenesis. Detection of SVs is vital in clinical diagnosis, prognosis and therapy of haematological malignancies. Current methods for SV identification are low in sensitivity for cryptic cases and time-consuming for complex cases. This study investigated the feasibility of long read sequencing as an approach for SV detection and precise breakpoint characterization.

METHODS

Six archival samples, including 4 bone marrow blood samples (F/66 B-ALL, F/25 B-ALL, M/53 CML, F/34 B-ALL) and 1 cytogenetic cell pellet each in cell culture medium (M/52 CML) or Carnoy's fixative (M/44 CML) with known and previously characterized BCR::ABL1 fusion transcript were selected for study. The genomic DNA was extracted from each case for further breakpoint characterization by long read sequencing (MinION R9.4.1 flow cell, Oxford Nanopore Technologies, UK).

RESULTS

All the genomic breakpoints were concordant with the RNA fusion transcript breakpoints. Three typical (e1a2, e13a2, and e14a2) and 3 variant (e23a2Ins52, e8a2, and e13a2ins74) BCR breakpoints were identified.

CONCLUSION

Using the Ph translocation as an example, long read sequencing is a promising alternative method to detect SV, revolutionizing detection of chromosomal translocation to a higher precision. A more comprehensive spectrum of SV can be resolved along with cytogenetic results, enabling precise diagnosis and personalized monitoring of haematological malignancies.

Effect of TKI Maintenance Therapy After Allogeneic Hematopoietic Stem Cell Transplantation on Recurrence of Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia p190 and p210 Transcripts: A Multicentre Study

OBJECTIVE

To analyze the impact of tyrosine kinase inhibitor (TKI) maintenance therapy following allogeneic hematopoietic stem cell transplantation (HSCT) in patients with Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph + ALL) on recurrence rates and prognosis for the 2 transcripts, p190 and p210.

METHODS

We conducted a retrospective analysis of clinical data from 58 patients diagnosed with Ph + ALL who underwent HSCT. All patients received TKI maintenance therapy following hematopoietic reconstruction post-transplantation. We compared the clinical characteristics and prognostic differences between 2 transcript types: p190 (n = 43) and p210 (n = 15).

RESULT

In terms of clinical characteristics, no significant differences were observed between patients with the 2 transcripts. Multivariate analysis revealed that the T3151 mutation (HR = 5.021, 95% CI [1.129-22.3], P = .034) was an independent risk factor for relapse-free survival (RFS) post-transplantation. Additionally, TKI maintenance therapy for over 1 year was identified as a protective factor for RFS (HR = 0.315, 95% CI [0.115-0.86], P = .025). The median RFS was 89.4 months for the p190 group compared to 59.1 months for the p210 group, which was statistically significant (P = .031). In the subgroup with more than 1 year of TKI maintenance therapy, the median RFS times for p190 and p210 were 95.3 and 90.5 months, respectively, with no statistically significant difference in RFS (P = .080).

CONCLUSION

The p190 group demonstrated longer RFS compared to the p210 group. However, with early HSCT following induction remission and long-term TKI maintenance therapy post-transplant, the poor prognosis associated with p210 could be mitigated, leading to a trend towards equivalence in outcomes between the 2 transcripts.

Comprehensive Analysis of High-Sensitive Flow Cytometry and Molecular Mensurable Residual Disease in Philadelphia Chromosome-Positive Acute Leukemia

Monitoring measurable residual disease (MRD) is critical for the management of B-cell acute lymphoblastic leukemia (B-ALL). While a quantitative assessment of BCR::ABL1 transcripts is standard for Philadelphia chromosome-positive cases (Ph+ ALL), a multiparameter flow cytometry (FCM) is commonly used for MRD detection in other genetic subtypes. A total of 106 B-ALL patients underwent genetic and phenotypic analyses. Among them, 27 patients (20 adults and 7 children) harbored the t(9;22)(q34.1;q11.2) translocation and/or the BCR::ABL1 rearrangement. A high correlation between the BCR::ABL1 transcript levels (PCR-MRD) and a standardized FCM-based method for MRD detection (FCM-MRD) was observed (r = 0.7801, p < 0.001), with a concordance rate of 88% (κ = 0.761). The FCM detected MRD in 82.9% of the samples with transcript levels of > 0.01%. The CD34+CD38-/dim blast pattern was significantly more frequent in Ph+ ALL (77.7%), compared to other B-ALL cases (20.2%, p < 0.0001). Additionally, Ph+ ALL exhibited a higher expression of CD66c+/CD73+ (94.0% vs. 56.9%), CD66c+/CD304+ (58.8% vs. 6.9%), and CD73+/CD304+ (75.5% vs. 15.5%) than the other B-ALL subtypes (p < 0.001). In conclusion, this high-sensitivity FCM-MRD demonstrated comparable performance to the PCR-MRD, serving as a complementary tool for MRD assessment in Ph+ ALL. Moreover, a distinct leukemia-associated immunophenotype was identified, highlighting potential biomarkers for MRD monitoring.

Minimal residual disease monitoring in childhood Philadelphia chromosome-positive acute lymphoblastic leukemia: prognostic significance and correlation between multiparameter flow cytometry and real-time quantitative polymerase chain reaction

Not available.

Automation of 3D digital rolling circle amplification using a 3D-printed liquid handler

Automation of liquid handling is indispensable to improve throughput and reproducibility in biochemical assays. However, the incorporation of automated systems into laboratory workflows is often hindered by the high cost and complexity associated with building robotic liquid handlers. Here, we report a 3D-printed liquid handler based on a fluidic manifold, thereby obviating the need for complex robotic mechanisms. The fluidic manifold, termed a dispensing and aspirating (DA) device, comprises parallelized multi-pipette structures connected by distribution and aspiration channels, enabling the precise supply and removal of reagents, respectively. Leveraging the versatility of 3D printing, the DA device can be custom-designed and printed to fit specific applications. As a proof-of-principle, we engineered a 3D-printed liquid handler dedicated for 3D digital rolling circle amplification (4DRCA), an advanced biochemical assay involving multiple sample preparation steps such as antibody incubation, cell fixation, nucleic acid amplification, probe hybridization, and extensive washing. We demonstrate the efficacy of the 3D-printed liquid handler to automate the preparation of clinical samples for the simultaneous, in situ analysis of oncogenic protein and transcript markers in B-cell acute lymphoblastic leukemia cells using 4DRCA. This approach provides an effective and accessible solution for liquid handling automation, offering high throughput and reproducibility in biochemical assays.

A critical review of management of allogeneic transplant-eligible adults with Ph+ acute lymphoblastic leukaemia

Acute lymphoblastic leukaemia (ALL) in 20%-30% of adult patients contains the Philadelphia (Ph+) chromosome. Historically, Ph+ ALL denoted a markedly inferior outcome and long-term survival in the absence of an allograft was uncommon. However, the advent of targeted therapy directed against the BCR::ABL1 fusion protein with various tyrosine kinase inhibitors (TKIs) has markedly improved the prognosis, resulting in a number of treatment controversies in allograft-eligible patients. Which is the best TKI to use in induction? What is the clinical relevance of the subdivision of Ph+ ALL into multilineage vs lymphoid types? Do all patients in first morphological complete remission (CR1) after induction and consolidation with chemotherapy/TKI require an allograft? If not, what risk factors predict a poor outcome without an allograft? Can chemotherapy-free approaches, such as blinatumomab in conjunction with more potent TKIs, obviate the need for an allograft in high-risk patients? What is the best strategy to deal with persistent or emerging minimal residual disease both pre- and post-transplant? Is maintenance TKI indicated in all patients post allograft? Can salvage therapy and a subsequent allograft cure patients who relapse after not being transplanted in CR1? This manuscript reviews the latest data influencing contemporary management and discusses these controversies.

Philadelphia-chromosome positive acute lymphoblastic leukemia: ten frequently asked questions

Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ ALL) constitutes a distinctive cytogenetic entity associated with challenging outcomes, particularly in adult patients. Current upfront chemotherapy-tyrosine kinase inhibitor (TKI)-based therapies include first, second and third-generation TKIs that have revolutionized patient outcomes including molecular remission and overall survival. Chemotherapy-free regimens such as blinatumomab-dasatinib or blinatumomab-ponatinib offer exciting possibilities, yet challenges arise, particularly in preventing central nervous system relapse. Monitoring measurable residual disease is now a cornerstone particularly using next-generation sequencing (NGS)-Clonoseq for accurate assessment. Controversy regarding the ability to omit consolidation with allogeneic stem cell transplantation, specifically for patients achieving early molecular remission, is related to the excellent survival achieved with novel combinations in the upfront setting, however challenged by the lower disease control when transplant is utilized beyond first remission. Post-transplant maintenance introduces new dilemmas: the optimal TKI, dosing, and duration of therapy are open questions. Meanwhile, a myriad of new combinations and cellular therapies are used for relapsed Ph+ ALL, prompting us to unravel the optimal sequencing of these promising regimen. In this review, we delve into the breakthroughs and controversies in Ph+ ALL with ten commonly asked questions.

3D Amplified Single-Cell RNA and Protein Imaging Identifies Oncogenic Transcript Subtypes in B-Cell Acute Lymphoblastic Leukemia

Simultaneous in situ detection of transcript and protein markers at the single-cell level is essential for gaining a better understanding of tumor heterogeneity and for predicting and monitoring treatment responses. However, the limited accessibility to advanced 3D imaging techniques has hindered their rapid implementation. Here, we present a 3D single-cell imaging technique, termed 3D digital rolling circle amplification (4DRCA), capable of the multiplexed and amplified simultaneous digital quantification of single-cell RNAs and proteins using standard fluorescence microscopy and off-the-shelf reagents. We generated spectrally distinguishable DNA amplicons from molecular markers through an integrative protocol combining single-cell RNA and protein assays and directly enumerated the amplicons by leveraging an open-source algorithm for 3D deconvolution with a custom-built automatic gating algorithm. With 4DRCA, we were able to simultaneously quantify surface protein markers and cytokine transcripts in T-lymphocytes. We also show that 4DRCA can distinguish BCR-ABL1 fusion transcript positive B-cell acute lymphoblastic leukemia cells with or without CD19 protein expression. The accessibility and extensibility of 4DRCA render it broadly applicable to other cell-based diagnostic workflows, enabling sensitive and accurate single-cell RNA and protein profiling.

Ph+ ALL in 2022: is there an optimal approach?

Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukemia (ALL) carried a very poor prognosis prior to the advent of tyrosine kinase inhibitors (TKIs) that block the activity of the BCR-ABL1 oncoprotein. With improvements in TKI efficacy and allogeneic hematopoietic cell transplantation (HCT), survival has improved over the past 3 decades, and the role of chemotherapy and allogeneic HCT is now changing. Better risk stratification, the application of the third-generation TKI ponatinib, and the use of immunotherapy with the CD19-CD3 bifunctional T-cell engaging antibody blinatumomab in place of chemotherapy has made therapy for Ph+ ALL more tolerable and arguably more efficacious, especially for older patients who comprise most patients with Ph+ ALL.

Single-cell RNA sequencing to explore composition of peripheral blood NK cells in patients with chronic myeloid leukemia in treatment-free remission

This study was to explore the role of NK cell subsets and gene expression in maintaining TFR status. We identified six types of NK cells in the PBMCs over both groups (healthy controls and patients with TFR). Gene Oncology analysis showed that up regulated genes were enriched in the categories of "immune response," "reaction to tumor cells," and "cytolysis." In addition, we found that the three NK cell subsets, mature and terminal NK cells, CD56 bright NK cells, and transitional NK cells, contained many significantly up regulated genes in both groups, and that CD56 bright NK cells and transitional NK cells in patients with CML-TFR were in a proliferating and activated state. Through single-cell RNA sequencing analysis, we confirmed that the mature and terminal, CD56 bright, and transitional subsets of NK cells play an indispensable role in maintaining TFR in patients with CML.