Fusion transcript analysis reveals slower response kinetics than multiparameter flow cytometry in childhood acute myeloid leukaemia

Funding Information: We thank the employees at the Department of Clinical Chemistry at Sahlgrenska University Hospital, Haemodiagnostic Laboratory at the Aarhus University Hospital, and Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet for sample collection, processing and analyses. Publisher Copyright: © 2022 The Authors. International Journal of Laboratory Hematology published by John Wiley & Sons Ltd.Introduction: Analysis of measurable residual disease (MRD) is increasingly being implemented in the clinical care of children and adults with acute myeloid leukaemia (AML). However, MRD methodologies differ and discordances in results lead to difficulties in interpretation and clinical decision-making. The aim of this study was to compare results from reverse transcription quantitative polymerase chain reaction (RT-qPCR) and multiparameter flow cytometry (MFC) in childhood AML and describe the kinetics of residual leukaemic burden during induction treatment. Methods: In 15 children who were treated in the NOPHO-AML 2004 trial and had fusion transcripts quantified by RT-qPCR, we compared MFC with RT-qPCR for analysis of MRD during (day 15) and after induction therapy. Eight children had RUNX1::RUNX1T1, one CBFB::MYH11 and six KMT2A::MLLT3. Results: When ≥0.1% was used as cut-off for positivity, 10 of 22 samples were discordant. The majority (9/10) were MRD positive with RT-qPCR but MRD negative with MFC, and several such cases showed the presence of mature myeloid cells. Fusion transcript expression was verified in mature cells as well as in CD34 expressing cells sorted from diagnostic samples. Conclusions: Measurement with RT-qPCR suggests slower response kinetics than indicated from MFC, presumably due to the presence of mature cells expressing fusion transcript. The prognostic impact of early measurements with RT-qPCR remains to be determined.Peer reviewe

Harnessing the Immune System to Fight Multiple Myeloma

Multiple myeloma (MM) is a heterogeneous plasma cell malignancy differing substantially in clinical behavior, prognosis, and response to treatment. With the advent of novel therapies, many patients achieve long-lasting remissions, but some experience aggressive and treatment refractory relapses. So far, MM is considered incurable. Myeloma pathogenesis can broadly be explained by two interacting mechanisms, intraclonal evolution of cancer cells and development of an immunosuppressive tumor microenvironment. Failures in isotype class switching and somatic hypermutations result in the neoplastic transformation typical of MM and other B cell malignancies. Interestingly, although genetic alterations occur and evolve over time, they are also present in premalignant stages, which never progress to MM, suggesting that genetic mutations are necessary but not sufficient for myeloma transformation. Changes in composition and function of the immune cells are associated with loss of effective immune surveillance, which might represent another mechanism driving malignant transformation. During the last decade, the traditional view on myeloma treatment has changed dramatically. It is increasingly evident that treatment strategies solely based on targeting intrinsic properties of myeloma cells are insufficient. Lately, approaches that redirect the cells of the otherwise suppressed immune system to take control over myeloma have emerged. Evidence of utility of this principle was initially established by the observation of the graft-versus-myeloma effect in allogeneic stem cell-transplanted patients. A variety of new strategies to harness both innate and antigen-specific immunity against MM have recently been developed and intensively tested in clinical trials. This review aims to give readers a basic understanding of how the immune system can be engaged to treat MM, to summarize the main immunotherapeutic modalities, their current role in clinical care, and future prospects

Novel scripts for improved annotation and selection of variants from whole exome sequencing in cancer research

Sequencing the exome is quickly becoming the preferred method for discovering disease-inducing mutations. While obtaining data sets is a straightforward procedure, the subsequent analysis and interpretation of the data is a limiting step for clinical applications. Thus, while the initial mutation and variant calling can be performed by a bioinformatician or trained researcher, the output from robust packages such as MuTect and GATK is not directly informative for the general life scientists. In attempt to obviate this problem we have created complementary Wolfram scripts, which enable easy downstream annotation and selection, presented here in the perspective of hematological relevance. It also provides the researcher with the opportunity to extend the analysis by having a full-fledged programming and analysis environment of Mathematica at hand. In brief, post-processing is performed by: • Mapping of germ line and somatic variants to coding regions, and defining variant sets within Mathematica. • Processing of variants in variant effect predictor. • Extended annotation, relevance scoring and defining focus areas through the provided functions

Distal chromosome 1q aberrations and initial response to ibrutinib in central nervous system relapsed mantle cell lymphoma

Relapse involving the central nervous system (CNS) is an infrequent event in the progression of mantle cell lymphoma (MCL) with an incidence of approximately four percent. We report four cases of MCL with CNS relapse. In three of the four patients a large chromosomal copy-number alteration (CNA) of 1q was demonstrated together with TP53 mutation/deletion. These patients experienced brief response to ibrutinib, whereas a fourth patient harboring mutated ATM demonstrated a long-term effect to ibrutinib and no CNA. Although it is unclear whether chromosome 1q CNA contribute to specific phenotypes these reports may be of value as such lesions are uncommon features of MCL