Acute Myeloid Leukemia Diagnostics Research Articles

Erythroblastosis Transformation-Specific Regulated Gene 1 (ERG) Immunohistochemistry in the Diagnosis of Acute Myeloid Leukemia.

The erythroblastosis transformation-specific regulated gene 1 (ERG) is a transcription factor that can be used as an immunohistochemical (IHC) marker in the diagnosis and prognostication of malignancy.ERG was initially used in prostate cancer; however, it is a useful marker in extramedullary myeloid disease. Patients with acute myeloid leukemia (AML), dry bone marrow aspirate, and CD34, CD117-negative blast cells can be in a diagnostic dilemma. This audit aimed to (a) validate ERG IHC in bone marrow trephine samples, (b) quantify ERG IHC positivity in an AML cohort, and correlate concordance with CD34 and CD117 IHC, when available, and (c) to see whether ERG is a useful adjunct in the diagnosis of cases of AML. A retrospective audit was completed of all new and relapsed cases of AML over one year at a single center. For inclusion, patients needed a trephine specimen at presentation, and all had ahematoxylin and eosin(H&E) specimen, ERG IHC, and at least one or both of CD34and CD117 IHC. Four pathologists independently assessed the stains quantitatively and qualitatively in comparison to the morphology seen on the H&E sample. The kappa value was used to assess agreement. Seventeen patients with AML met the inclusion criteria. All specimens had H&E, CD34, and ERG stains; 9/17 (53%) had CD117 IHC. ERG demonstrated high concordance with blast cells on H&E morphology, with a high agreement among pathologists. Qualitatively, pathologists recognized that ERG spared lymphoid nodules; however, it also stained granulocytes at various maturation stages. ERG is a sensitive marker for the diagnosis of AML. ERG can help visualize blast cells that have been confirmed by ancillary tests. More research into the utility of ERG in AML diagnostics is recommended.

Label-Free Identification of Biochemical Footprints of Key Mutations in Acute Myeloid Leukemia Using Raman Spectroscopy

Introduction: With increasing understanding of the complexity and heterogeneity of acute myeloid leukemia (AML), the diagnostic process becomes more complicated and time-consuming. Therefore, there is a need to supplement AML diagnostics with a quick method to identify key, druggable genetic lesions that serve as a target for small molecule drugs. To address this need, we used Raman spectroscopy (RS)-based imaging methods. RS uses non-elastic scattering of laser light on cell biomolecules. When coupled to computational image segmentation and analysis, composition of the analyzed fragment of the cytoplasm can be characterized. In this way, by mapping the focal surface of the cell, we obtain a multidimensional image containing information about the distribution of its biochemical components. In our study, we utilized RS microscopy to investigate how single mutations affect the Raman spectral images of leukemic cells. The primary objective was to determine whether this technique could be utilized to identify mutations in key genes related to leukemia development. Methods: Genetic models of AML were generated by introducing wild-type and mutated forms of three frequently mutated and/or druggable genes (FLT3, IDH1/2, and MLL) into myeloid cell lines (THP1, HEL, HL60). The presence of the desired phenotype was confirmed using flow cytometry, immunoblotting, high-throughput kinase activity assay (Pamgene), and confocal microscopy. For RS experiments, the cells were fixed, and subjected to Raman imaging measurements using the WITec Alpha 300 microscope. Reference or control samples consisted of cells with wild-type genes (WT). The recorded hyperspectral data was subjected to multidimensional chemometric analysis, including k-means cluster analysis (KMCA), principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). To validate the findings from the cell models, primary AML cells from 30 patients diagnosed with FLT-3 ITD, MLL or IDH1/2 mutations were examined with RS. Peripheral blood mononuclear cells (PBMC) isolated from healthy donors blood served as reference. Results: The spectral differences between cells with wild-type FLT3 and FLT3/ITD were subtle, yet significant. The results revealed distinct variances in lipid (1440, 1240, 1660, and 2850 cm -1) and hemoprotein content (740-760 cm -1). Additionally, we successfully distinguished cells harboring IDH1/2 and MLL mutations from those with the wild-type genes. In these cases Raman bands corresponding to protein and nucleic acids composition were changed in comparison to control cells. Raman features in PCA loadings were also related to proteins and nucleic acids. Using the PLS-DA method and simple AI model, we built successful algorithm for distinguishing transgenic models carrying mutation from wild-type cells. PCA analysis also enabled us to distinguish AML primary cells from PBMC. Analysis weather primary cells carrying the selected mutations can be distinguished from non-mutated AML cells is concordant with our findings on models, however, it requires further analysis in larger group of patients to increase statistical power of these observations. Conclusions: Collectively, these findings suggest that Raman spectroscopy coupled with appropriate chemometric analysis may serve as rapid, label-free tool for identification of key druggable mutations in AML. Acknowledgements: The studies were performed as a part of the “ Label-free and rapid optical imaging, detection and sorting of leukemia cells” project carried out within the Team-Net programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund.

Acute Myeloid Leukemia: New Multiomics Molecular Signatures and Implications for Systems Medicine Diagnostics and Therapeutics Innovation.

Acute myeloid leukemia (AML) is a common, complex, and multifactorial malignancy of the hematopoietic system. AML diagnosis and treatment outcomes display marked heterogeneity and patient-to-patient variations. To date, AML-related biomarker discovery research has employed single omics inquiries. Multiomics analyses that reconcile and integrate the data streams from multiple levels of the cellular hierarchy, from genes to proteins to metabolites, offer much promise for innovation in AML diagnostics and therapeutics. We report, in this study, a systems medicine and multiomics approach to integrate the AML transcriptome data and reporter biomolecules at the RNA, protein, and metabolite levels using genome-scale biological networks. We utilized two independent transcriptome datasets (GSE5122, GSE8970) in the Gene Expression Omnibus database. We identified new multiomics molecular signatures of relevance to AML: miRNAs (e.g., mir-484 and miR-519d-3p), receptors (ACVR1 and PTPRG), transcription factors (PRDM14 and GATA3), and metabolites (in particular, amino acid derivatives). The differential expression profiles of all reporter biomolecules were crossvalidated in independent RNA-Seq and miRNA-Seq datasets. Notably, we found that PTPRG holds important prognostication potential as evaluated by Kaplan-Meier survival analyses. The multiomics relationships unraveled in this analysis point toward the genomic pathogenesis of AML. These multiomics molecular leads warrant further research and development as potential diagnostic and therapeutic targets.

Molecular Profiling of Kenyan Acute Myeloid Leukemia Patients.

Acute myeloid leukemia (AML) is an infrequent disease, and it is associated with high morbidity and mortality. It harbors a unique configuration of cytogenetic abnormalities and molecular mutations that can be detected using microscopic and molecular methods respectively. These genetic tests are core elements of diagnosis and prognostication in high-income countries. They are routinely incorporated in clinical decision making, allowing for the individualization of therapy. However, these tests are largely inaccessible to most patients in Kenya and therefore no data has been reported on this group of patients. The main purpose of this study is to describe the cytogenetic and molecular abnormalities of acute myeloid leukemia patients seen at the hemato-oncology unit of Kenyatta National Hospital. A cross-sectional descriptive study was carried out over a 3-month period on ten patients with a diagnosis of AML. Social demographics and clinical data were collected through a study proforma. A peripheral blood sample was collected for conventional metaphase G-banding technique and next generation sequencing. Particularly, targeted DNA sequencing (Illumina myeloid panel) and whole exome sequencing (WES) were performed. Cytogenetic analysis failed in 10/10 cases. Targeted sequencing was successfully obtained in 8 cases, whereas WES in 7. Cytogenetic studies yielded no results. There were 20 mutations detected across 10 commonly mutated genes. All patients had at least one clinically relevant mutation. Based on ELN criteria, NGS identified three patients with high-risk mutations, affecting TP53 (n = 2) and RUNX1 (n = 1). One patient was classified as favorable (PML-RARA) while 4 were standard risk. However, WT1 mutations associated with unfavorable prognosis were recorded in additional 2 cases. WES showed concordant results with targeted sequencing while unveiling more mutations that warrant further attention. In conclusion, we provide the first molecular profiling study of AML patients in Kenya including application of advanced next generation sequencing technologies, highlighting current limitations of AML diagnostics and treatment while confirming the relevance of NGS in AML characterization.

Fusion gene detection by RNA-sequencing complements diagnostics of acute myeloid leukemia and identifies recurring NRIP1-MIR99AHG rearrangements.

Identification of fusion genes in clinical routine is mostly based on cytogenetics and targeted molecular genetics, such as metaphase karyotyping, fluorescence in situ hybridization and reverse-transcriptase polymerase chain reaction. However, sequencing technologies are becoming more important in clinical routine as processing time and costs per sample decrease. To evaluate the performance of fusion gene detection by RNAsequencing compared to standard diagnostic techniques, we analyzed 806 RNA-sequencing samples from patients with acute myeloid leukemia using two state-of-the-art software tools, namely Arriba and FusionCatcher. RNA-sequencing detected 90% of fusion events that were reported by routine with high evidence, while samples in which RNA-sequencing failed to detect fusion genes had overall lower and inhomogeneous sequence coverage. Based on properties of known and unknown fusion events, we developed a workflow with integrated filtering strategies for the identification of robust fusion gene candidates by RNA-sequencing. Thereby, we detected known recurrent fusion events in 26 cases that were not reported by routine and found discrepancies in evidence for known fusion events between routine and RNA-sequencing in three cases. Moreover, we identified 157 fusion genes as novel robust candidates and comparison to entries from ChimerDB or Mitelman Database showed novel recurrence of fusion genes in 14 cases. Finally, we detected the novel recurrent fusion gene NRIP1- MIR99AHG resulting from inv(21)(q11.2;q21.1) in nine patients (1.1%) and LTN1-MX1 resulting from inv(21)(q21.3;q22.3) in two patients (0.25%). We demonstrated that NRIP1-MIR99AHG results in overexpression of the 3' region of MIR99AHG and the disruption of the tricistronic miRNA cluster miR-99a/let-7c/miR-125b-2. Interestingly, upregulation of MIR99AHG and deregulation of the miRNA cluster, residing in the MIR99AHG locus, are known mechanisms of leukemogenesis in acute megakaryoblastic leukemia. Our findings demonstrate that RNA-sequencing has a strong potential to improve the systematic detection of fusion genes in clinical applications and provides a valuable tool for fusion discovery.

Fusion genes in acute myeloid leukemia: do acute myeloid leukemia diagnostics need to fuse with RNA-sequencing?

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MRD Tailored Therapy in AML: What We Have Learned So Far.

Acute myeloid leukemia (AML) is a heterogeneous clonal disease associated with a dismal survival, partly due to the frequent occurrence of relapse. Many patient- and leukemia-specific characteristics, such as age, cytogenetics, mutations, and measurable residual disease (MRD) after intensive chemotherapy, have shown to be valuable prognostic factors. MRD has become a rich field of research where many advances have been made regarding technical, biological, and clinical aspects, which will be the topic of this review. Since many laboratories involved in AML diagnostics have experience in immunophenotyping, multiparameter flow cytometry (MFC) based MRD is currently the most commonly used method. Although molecular, quantitative PCR based techniques may be more sensitive, their disadvantage is that they can only be applied in a subset of patients harboring the genetic aberration. Next-generation sequencing can assess and quantify mutations in many genes but currently does not offer highly sensitive MRD measurements on a routine basis. In order to provide reliable MRD results, MRD assay optimization and standardization is essential. Different techniques for MRD assessment are being evaluated, and combinations of the methods have shown promising results for improving its prognostic value. In this regard, the load of leukemic stem cells (LSC) has also been shown to add to the prognostic value of MFC-MRD. At this moment, MRD after intensive chemotherapy is most often used as a prognostic factor to help stratify patients, but also to select the most appropriate consolidation therapy. For example, to guide post-remission treatment for intermediate-risk patients where MRD positive patients receive allogeneic stem cell transplantation and MRD negative receive autologous stem cell transplantation. Other upcoming uses of MRD that are being investigated include: selecting the type of allogeneic stem cell transplantation therapy (donor, conditioning), monitoring after stem cell transplantation (to allow intervention), and determining drug efficacy for the use of a surrogate endpoint in clinical trials.

Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing

Acute myeloid leukemia (AML) is caused by genetic aberrations that also govern the prognosis of patients and guide risk-adapted and targeted therapy. Genetic aberrations in AML are structurally diverse and currently detected by different diagnostic assays. This study sought to establish whole transcriptome RNA sequencing as single, comprehensive, and flexible platform for AML diagnostics. We developed HAMLET (Human AML Expedited Transcriptomics) as bioinformatics pipeline for simultaneous detection of fusion genes, small variants, tandem duplications, and gene expression with all information assembled in an annotated, user-friendly output file. Whole transcriptome RNA sequencing was performed on 100 AML cases and HAMLET results were validated by reference assays and targeted resequencing. The data showed that HAMLET accurately detected all fusion genes and overexpression of EVI1 irrespective of 3q26 aberrations. In addition, small variants in 13 genes that are often mutated in AML were called with 99.2% sensitivity and 100% specificity, and tandem duplications in FLT3 and KMT2A were detected by a novel algorithm based on soft-clipped reads with 100% sensitivity and 97.1% specificity. In conclusion, HAMLET has the potential to provide accurate comprehensive diagnostic information relevant for AML classification, risk assessment and targeted therapy on a single technology platform.

PF262 COMPREHENSIVE DIAGNOSTICS OF ACUTE MYELOID LEUKEMIA BY WHOLE TRANSCRIPTOME RNA SEQUENCING

Background:Acute myeloid leukemia (AML) is characterized by uncontrolled proliferation of malignant myeloid precursor cells in the bone marrow. Genetic aberrations play an important role in pathogenesis as well as in classification of AML, which is relevant for accurate diagnosis, risk assessment and personalized treatment of AML. Genetic aberrations in AML are structurally diverse and currently measured by different diagnostic tests.Aims:The aim of the study is to establish whole transcriptome messenger RNA sequencing (RNAseq) as single and flexible diagnostic platform for AML classification, prognostication, and choice of targeted agents.Methods:Whole transcriptome RNA sequencing was performed on 100 AML cases and the bioinformatics pipeline HAMLET (Human AML Expedited Transcriptomics) was developed for simultaneous detection of fusion genes, small variants, long tandem duplications and gene expression. HAMLET results were validated by reference assays and targeted resequencing.Results:HAMLET accurately detected all fusion genes and overexpression of EVI1 irrespective of 3q26 aberrations. In addition, small variants in 13 genes that are often mutated in AML were called with 99.2% sensitivity and 100% specificity, and internal tandem duplications in FLT3 (FLT3‐ITD) and partial tandem duplications in KMT2A (KMT2A‐PTD) were detected by a novel algorithm based on soft clipped reads with 100% sensitivity and 97.1% specificity.Summary/Conclusion:HAMLET accurately provides comprehensive diagnostic information relevant for AML classification, risk assessment and personalized therapy on a single technology platform. Instead of current AML diagnostics based on various assays that target selected aberrations, RNAseq‐HAMLET represents a new diagnostic paradigm according to a “measure all – analyse relevant” approach, which can be adapted to advances in sequencing technology and novel insights in AML pathogenesis, and allows individual retrospective reassessment.

Genetic polymorphisms of histone methyltransferase SETD2 predicts prognosis and chemotherapy response in Chinese acute myeloid leukemia patients

BackgroundSETD2, the single mediator of trimethylation of histone 3 at position lysine 36, has been reported associated with initiation progression and chemotherapy resistance in acute myeloid leukemia (AML). Whether polymorphisms of SETD2 affect prognosis and chemotherapy response of AML remains elusive.MethodsThree tag single-nucleotide polymorphisms (tagSNPs) of SETD2 were genotyped in 579 AML patients by using Sequenom Massarray system. Association of the SNPs with complete remission (CR) rate after Ara-C based induction therapy, overall survival (OS) and relapse-free survival (RFS) were analyzed.ResultSurvival analysis indicated that SETD2 rs76208147 TT genotype was significantly associated with poor prognosis of AML (TT vs. CC + CT hazard ratio: HR = 1.838, 95% confidence interval (CI) 1.005–3.360, p = 0.048). After adjusting for the known prognostic factors including risk stratification, age, allo-SCT, WBC count and LDH count, rs76208147 TT genotype was still associated with OS in the multivariate analysis (TT vs. CC + CT HR = 1.923, 95% CI 1.007–3.675, p = 0.048). In addition, after adjusting by other clinical features, patients with rs4082155 allele G carries showed higher rate of complete remission which indicated by CR rate (AG + GG vs. AA odd ratio (OR) = 0.544, 95% CI 0.338–0.876, p = 0.012).ConclusionsSETD2 genetic polymorphism is associated with AML prognosis and chemotherapy outcome, suggesting the possibility for development in AML diagnostics and therapeutics towards SETD2.

Comprehensive Genetic Diagnostics of Acute Myeloid Leukemia By Next Generation Sequencing

BackgroundAcute Myeloid Leukemia (AML) is the most common acute leukemia in adults with a poor overall prognosis. Although the disease has been extensively characterized on the molecular level, this knowledge is translating only slowly into the clinic, particularly with regard to novel therapeutic concepts. Presumably, this striking imbalance substantially is due to the long time required to complete genetic analyses so that results are not available when treatment has to be initiated. Specifically, cytogenetic examinations to determine the karyotype of the malignant blasts, which has been the most important parameter for risk stratification for more than thirty years, take up to two weeks. Next generation sequencing (NGS) technology essentially catalyzed efforts to dissect the genomic landscape of AML, leading to the identification of a large variety of AML driver genes and distinct molecular risk groups. However, these emerging molecular classes of AML do not cover all patients, implying that karyotyping is not dispensable for AML diagnostics at this point. Here we present an integrated approach to AML diagnostics that incorporates these complementary genetic examinations - focused mutational screening of AML-related genes and karyotyping - in one NGS assay.MethodsWe combined targeted resequencing of DNA and RNA using commercially available panels (TruSigth Myeloid, Illumina and FusionPlex Heme, ArcherDx) to detect AML-associated short sequence variants and gene fusions with low coverage whole genome sequencing for copy number variation analysis. Sequencing was performed on an Illumina MiSeq instrument with a read length of 2x150 bp and a coverage of 3.75 M reads for the TruSight Myeloid panel, 2.25 M reads for the FusionPlex panel and 1.5 M reads for the whole genome library. Variants and fusions were called using the manufacturers' analysis software and a previously published algorithm to identify ITDs (ITD-seek, Au et al., 2016). CNV analysis was performed by comparing read distribution in an AML whole genome library to in silico randomly sampled reads from the reference genome using an in house-developed algorithm.ResultsInitial testing of our approach on leukemia cell lines and peripheral blood leukocytes from healthy donors revealed sensitivities of 2% and 1-25% for the detection of DNA variants and fusions, respectively. Applying stringent filter criteria, we recovered 75% of verified COSMIC variants and 100% of known fusions in undiluted AML samples without false positives. Chromosomal gains and losses were detected with high confidence with a sensitivity of 10%. We were able to reliably distinguish between normal and complex karyotypes, although NGS-karyotyping based on known fusions and CNV-analysis missed some details of highly aberrant karyotypes such as derivative chromosomes and chromosomal translocations that did not involve genes included in the FusionPlex panel. Our preliminary experience on our method in a diagnostic setting confirms high correlation with reference laboratory results and no relevant differences with regard to treatment decisions. Moreover, we find that NGS considerably accelerates genetic diagnostics of AML as the entire workflow from sample to report including three parallel library preparations, sequencing and data analysis can be completed within 5 days. Operational costs amount approximately 1,700 USD (1,500 EUR) per sample with the low throughput equipment used in this work, which is in the range of expenses for currently established AML diagnostics.ConclusionsNGS allows for comprehensive translocation and mutation screening, however, some technical and bioinformatics optimization is required to achieve consistently high sensitivity and specificity for all target genes. CNV analysis of low coverage whole genome sequencing data adds valuable information on numerical chromosomal aberrations, thus allowing construction of a virtual karyotype to substitute for difficult and time-consuming cytogenetics. In summary, we present a reliable, fast and cost-effective strategy to combine molecular and cytogenetics for AML diagnostics in a single NGS run in order to pave the way for a more differentiated clinical management of AML patients in the near future. DisclosuresKiehl:Roche: Consultancy, Other: Travel grants, Speakers Bureau.

Results of the “Evaluation of NGS in AML-Diagnostics (ELAN)” Study – an Inter-Laboratory Comparison Performed in 10 European Laboratories

Background: The invention of Next Generation Sequencing (NGS) has spurred research into human diseases, especially in the field of malignancy. In acute myeloid leukemia (AML), a plethora of novel alterations have been identified, including mutations in epigenetic regulator genes (e.g. IDH1, IDH2, DNMT3A), genes coding for proteins of the cohesin complex (e.g. SMC1A, SMC3, STAG2) and spliceosome genes (e.g. SF3B1, U2AF1). Although the diagnostic and prognostic implications of many of these alterations are not yet clear, there is increasing evidence that several of them might have major implications for understanding the disease biology or for patient-treatment. Thus, there is increasing need to reliably detect these mutations in large patient groups in clinically relevant time-frames and at an affordable cost. Due to the large number of genes to be screened, amplicon-based NGS represents an attractive detection method. Although, several assays have been reported, integrating different numbers of genes, it is currently unclear whether they really allow reliable detection of alterations in a reproducible way. Here we report our results from a round robin comparison of the detection of known AML-variants using a highly multiplexed, single tube assay coamplifying a total of 568 amplicons covering 54 entire genes or hot spot gene regions involved in leukemia (TruSight Myeloid sequencing panel; Illumina), with respect to the sensitivity, reproducibility and quantitative accuracy.Material and Methods: Ten European laboratories routinely involved in molecular AML diagnostics participated in this study. All groups performed two sequencing runs, each containing 8 samples. These samples were centrally aliquoted and distributed, the analyses were done in a blinded fashion. Six out of the 8 samples on each run were derived from a set of 9 samples composed of DNA isolated from the blasts of 18 different newly diagnosed AML patients mixed at a 1:1 ratio, with 50 ng of DNA being used for the library preparation. Three of these 9 samples were analyzed in replicate in separate runs by each group. The remaining two samples were a commercial test DNA containing 10 known single nucleotide variants (SNV) or insertion/deletion (InDel) alterations with defined variant allele frequencies (VAF) between 4 and 25% and DNA derived from the OCI-AML3 AML cell line (mutant for DNMT3A and NPM1). Sequencing was performed on MiSeq NGS systems (Illumina) using 2x151 bp-runs. Sequencing data were analyzed by all laboratories using the VariantStudio software (Illumina), with the threshold for mutation calling set at 3%.Results: Analysis of data quality indicated that 85% of the samples met the predefined acceptance criteria (>=95% amplicons with at least 500 reads/amplicon), the median coverage was 7379 reads/amplicon (range 0-47403 reads). Of the 9 mutations present in the positive control, 7 were called at least once in the two replicates by all labs, two mutations with a VAF of 5% were missed by 1 and 4 participants, respectively. Overall, the VAF calls for this sample showed a high level of accuracy across the participants (median coefficient of variation 5%, range 0-22.5%) as well as excellent intra- and inter-laboratory reproducibility (Fig.1). In total, the 9 primary leukemic samples contained 43 known variants in 19 genes, including all commonly mutated genes in AML, i.e. CEBPA, DNMT3A,RUNX1, NPM1, FLT3, WT1. For these samples, the sensitivity was 95.7%. Based on the entire data set (positive control and leukemic samples), the calculated sensitivity of the assay for known variants with an expected VAF>=5% was 93.3%. The rate of non-calls was slightly higher for InDels (14/179; 7.8%) than for SNVs (25/407; 6.1%; P=.47). Two 57-bp long insertions in FLT3 exons 14/15 were not called, which is expected due to the specifications of the assay (max. detectable InDel length <=25 bps). The standard deviation of VAF estimates for the primary leukemic samples was 1.7% with a mean CV of 0.094.Conclusions: This inter-laboratory comparison shows a high sensitivity and impressive quantitative accuracy of NGS-based characterization for known variants down to a minor VAF of 5%. Although additional optimization in individual parameters might be necessary, these initial results clearly indicate that rapid comprehensive molecular characterization of patient samples appears feasible, even in the clinical setting. [Display omitted] DisclosuresThiede:AgenDix GmbH: Equity Ownership, Research Funding; Illumina: Research Support, Research Support Other. Bullinger:Illumina: Research Support Other. Hernández-Rivas:Illumina: Research Support Other. Heuser:Illumina: Research Support Other. Preudhomme:Illumina: Research Support Other. Lo Coco:Illumina: Research Support Other. Martinelli:Illumina: Research Support Other. Schuh:Illumina: Research Support Other. Enjuanes:Illumina: Research Support Other. Lea:Illumina: Research Support Other. Schlesinger:Illumina: Employment.

Strategies to Reduce Relapse after Allogeneic Hematopoietic Cell Transplantation in Acute Myeloid Leukemia

The incidence of acute myeloid leukemia (AML) is expected to increase in conjunction with our ageing population. Although it is proving to be a heterogeneous disease process, the only treatment with proven survival benefit for poor risk AML remains allogeneic hematopoietic cell transplant. Although this is presumed to be a curative strategy, many patients relapse after transplant, prompting us to examine various ways that we can improve outcomes. These efforts involve every step of AML diagnostics and therapy, including the intricate processes of conditioning, graft manipulation and immunomodulation. The hope is that improvement in these steps will ultimately improve survival and decrease relapse rates for AML patients after transplant.

Molecular-Based Classification of Acute Myeloid Leukemia and Its Role in Directing Rational Therapy

Acute myeloid leukemia (AML) is not a single pathologic entity but represents a heterogeneous group of malignancies. This heterogeneity is exemplified by the variable clinical outcomes that are observed in patients with AML, and it is largely the result of diverse mutations within the leukemic cells. These mutations range from relatively large genetic alterations, such as gains, losses, and translocations of chromosomes, to single nucleotide changes. Detection of many of these mutations is required for accurate diagnosis, prognosis, and treatment of patients with AML. As such, many testing modalities have been developed and are currently employed in clinical laboratories to ascertain mutational status at prognostically and therapeutically critical loci. The assays include those that specifically identify large chromosomal alterations, such as conventional metaphase analysis and fluorescence in situ hybridization, and methods that are geared more toward analysis of small mutations, such as PCR with allele-specific oligonucleotide primers. Furthermore, newer tests, including array analysis and next-generation sequencing, which can simultaneously probe numerous molecular aberrancies within tumor cells, are likely to become commonplace in AML diagnostics. Each testing method clearly has advantages and disadvantages, an understanding of which should influence the choice of test in various clinical circumstances. To aid such understanding, this review discusses both genetic mutations in AML and the clinical tests-including their pros and cons-that may be used to probe these abnormalities. Additionally, we highlight the significance of genetic testing by describing cases in which results of genetic testing significantly influence clinical management of patients with AML.

Molecular Diagnostics of Acute Myeloid Leukemia: It's a (Next) Generational Thing

This commentary highlights the article by Spencer et al that outlines a novel next-generation sequencing-based method for the detection of FLT3 mutations.

Comparative proteomics in acute myeloid leukemia

The term proteomics was used for the first time in 1995 to describe large-scale protein analyses. At the same time proteomics was distinguished as a new domain of the life sciences. The major object of proteomic studies is the proteome, i.e. the set of all proteins accumulating in a given cell, tissue or organ. During the last years several new methods and techniques have been developed to increase the fidelity and efficacy of proteomic analyses. The most widely used are two-dimensional electrophoresis (2DE) and mass spectrometry (MS).In the past decade proteomic analyses have also been successfully applied in biomedical research. They allow one to determine how various diseases affect the pattern of protein accumulation. In this paper, we attempt to summarize the results of the proteomic analyses of acute myeloid leukemia (AML) cells. They have increased our knowledge on the mechanisms underlying AML development and contributed to progress in AML diagnostics and treatment.

A Rapid and Sensitive Method for Large-Scale Screening of CEBPA Mutations in AML Patients with Normal Karyotype.

In 45% of patients with de novo acute myeloid leukemia (AML) no cytogenetic abnormalities can be detected (normal karyotype AML, NK-AML). Recently, several molecular markers with prognostic significance have been described which define distinct subgroups of NK-AML patients. Mutations in the CEBPA gene have shown to occur at about 8% of NK-AML in Western countries and confer a favorable prognosis. The C/EBPα protein, a member of the family of basic region leucine zipper (bZIP) transcriptional regulators, is important for normal granulocytic differentiation and is frequently disrupted in AML. We retrospectively analyzed bone-marrow samples of 442 patients with de novo NK-AML for the presence of CEBPA mutations and established a fast and sensitive screening method. A multiplex-PCR-gene scanning assay for combined detection of CEBPA and NPM mutation has recently been described in which, however, the primers did not cover the whole CEBPA gene. CEBPA mutations have been found to be distributed over the entire CEBPA gene and their functional and clinical consequences are not yet clear. Therefore, we designed a rapid CEBPA specific multiplex PCR-gene scanning assay covering the entire coding region of the CEBPA gene. Four primer pairs were designed, fluorescently labeled and included in 2 multiplex PCR reactions. The PCR products were electrophoresed on a genetic analyzer and the amplicon sizes were compared to wildtype CEBPA of U937 cell line by fragment length analysis. In order to evaluate our method, we analyzed 120 patient samples in parallel by both multiplex PCR and sequencing analysis. Using sequencing analysis as a gold standard, all of the CEBPA mutations could be detected by multiplex PCR and fragment length analysis. Thus, our multiplex PCR assay reached a sensitivity of 100%. The specificity was 89% due to the false positive detection of a 6 basepair duplication polymorphism in 2.5% of patients (Wouters BJ et al, Blood, 2007). 322 patient samples were subsequently screened for CEBPA mutations by the multiplex PCR assay. In case of alterations in the fragment length analysis, the relevant CEBPA region was sequenced to identify the exact type of mutation. Among 442 patients with NK-AML, 32 patients (7%) showed CEBPA mutations. Taken together, we identified 47 mutations in 32 patients, of which 17 patients had a single CEBPA mutation and 15 patients had more than one CEBPA mutation. We identified 30 out of frame insertion/deletion nonsense mutations resulting in an N-terminal stopcodon and 14 in frame insertion/deletion mutations as well as 3 out of frame insertion/deletion mutations in the C-terminal bZIP region. The only limitation of this method might be that single basepair substitutions, which do not affect the length of the amplicon, cannot be detected. Substitutions in the CEBPA gene are, however, rare events and often silent. In 120 sequenced AML patients we did not find any non-silent substitution. We established a fast and sensitive screening method suitable for large-scale detection of CEBPA mutation and applicable for inclusion in routine AML diagnostics. This is so far the largest reported analysis of CEBPA mutations in patients with NK-AML and might provide further insights into the functional and clinical relevance of the different types of CEBPA mutations and their correlation to other molecular markers in NK-AML.

Proteomics of p53 in Diagnostics and Therapy of Acute Myeloid Leukemia

The anti-oncogene TP53 is frequently mutated in human cancer, but in hematological malignancies this is a rare feature. In acute myeloid leukemia (AML) more than 90% of the patients comprise wild type TP53 in their cancer cells, but if TP53 is mutated or deleted the disease is often found to be chemoresistant. In this review we define proteomics of the oncogene product p53 as the study of proteins in the p53 regulating signaling networks, as well as the protein study of members of the p53 family itself. Various messenger RNA splice forms as well as a multitude of post-translational modifications give a high number of protein isoforms in the p53 family. Some of the proteomic techniques allow detection of various isoforms, such as two-dimensional gel electrophoresis in combination with tandem mass spectrometry (MS/MS) and this methodology may therefore increasingly be used as a diagnostic tool in human disease. We introduce the p53 protein as an illustration of the complexity of post-translational modifications that may affect one highly connected protein and discuss the possible impact in AML diagnostics if the p53 profile is reflecting cell stress and status of signal transduction systems of the malignancy.

Proteomic Strategies for Individualizing Therapy of Acute MyeloidLeukemia (AML)

Acute myeloid leukemia (AML) is an aggressive hematological malignancy characterized by accumulating myeloid precursor cells in the bone marrow, with approximately 2-3 months 50% survival if left untreated. With current treatment modalities the five years overall survival hardly exceeds 50%. Cytogenetics and molecular diagnostics guide the clinician to select individualized therapy in certain subsets of AML, achieving long-term survival above 70% of these cases. However, approximately half of the AML patients have no risk stratifying features, and early reports indicate that proteomic approaches may be utilized for disease classification as well as development of novel biomarkers related to prognosis, diagnosis, and choice of therapeutic regimen. Proteomics, here defined as the analysis of all proteins in a cell, in a cell compartment or in a signaling pathway, has probably its greatest potential in investigating pathways that are easily targeted by small molecules or therapeutic antibodies. The major methodological challenges include detection sensitivity in a limited clinical material, a problem that in some cases can be solved through designated multiplexed protein assays based on single cells or cell extracts. In this review we will discuss pharmacoproteomic studies of drugs regulating leukemia specific targets like all-trans retinoic acid, histone deacetylase inhibitors, proteasome inhibitors and tyrosine kinase inhibitors, as well as studies on drug resistance and graft-versus-host studies during stem cell transplantations. These studies indicate new avenues in AML diagnostics, individualized therapy design and therapy response surveillance for the clinician.