Use of dual-color interphase FISH for the detection of inv(16) in acute myeloid leukemia at diagnosis, relapse and during follow-up: a study of 23 patients

Measuring response to therapy in AML: Difference from normal flow cytometry vs RQ-PCR

Multiple technologies have been used to monitor response to therapy in acute myeloid leukemia (AML) to improve detection of leukemia over the standard of practice, morphologic counting of blasts. The two techniques most frequently used in a routine clinical setting, flow cytometry and RQ-PCR, differ in their targets, sensitivity, and ability to detect residual disease. Both flow cytometry and RQ-PCR detect the expression of abnormal gene products, at the protein level or RNA level, respectively. Flow cytometry can be applied to a broad range of AML cases while RQ-PCR is limited to specific genetic abnormalities identified in subsets of AML. This article compares the results when both techniques were used in a reference laboratory to monitor AML over the course of treatment, comparing quantitative and qualitative results.

Relapse assessment following allogeneic SCT in patients with MDS and AML

Options to pre-emptively treat impending relapse of myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML) after allogeneic haematopoietic stem cell transplantation (allo-SCT) continuously increase. In recent years, the spectrum of diagnostic methods and parameters to perform post-transplant monitoring in patients with AML and MDS has grown. Cytomorphology, histomorphology, and chimaerism analysis are the mainstay in any panel of post-transplant monitoring. This may be individually combined with multiparameter flow cytometry (MFC) for the detection of residual cells with a leukaemia phenotype and quantitative real-time polymerase chain reaction (RQ-PCR) to assess gene expression, e.g., of WT1 or the residual mutation load (e.g., in case of an NPM1 mutation). Data evaluating the aforementioned methods alone or in combination are discussed in this review with particular emphasis on data pointing towards their suitability to steer pre-emptive post-transplant interventions such as immunotherapy, chemotherapy or therapy with demethylating agents.

Molecular-based classification of acute myeloid leukemia and its role in directing rational therapy: personalized medicine for profoundly promiscuous proliferations

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.

Directional genomic hybridization for chromosomal inversion discovery and detection

Chromosomal rearrangements are a source of structural variation within the genome that figure prominently in human disease, where the importance of translocations and deletions is well recognized. In principle, inversions—reversals in the orientation of DNA sequences within a chromosome—should have similar detrimental potential. However, the study of inversions has been hampered by traditional approaches used for their detection, which are not particularly robust. Even with significant advances in whole genome approaches, changes in the absolute orientation of DNA remain difficult to detect routinely. Consequently, our understanding of inversions is still surprisingly limited, as is our appreciation for their frequency and involvement in human disease. Here, we introduce the directional genomic hybridization methodology of chromatid painting—a whole new way of looking at structural features of the genome—that can be employed with high resolution on a cell-by-cell basis, and demonstrate its basic capabilities for genome-wide discovery and targeted detection of inversions. Bioinformatics enabled development of sequence- and strand-specific directional probe sets, which when coupled with single-stranded hybridization, greatly improved the resolution and ease of inversion detection. We highlight examples of the far-ranging applicability of this cytogenomics-based approach, which include confirmation of the alignment of the human genome database and evidence that individuals themselves share similar sequence directionality, as well as use in comparative and evolutionary studies for any species whose genome has been sequenced. In addition to applications related to basic mechanistic studies, the information obtainable with strand-specific hybridization strategies may ultimately enable novel gene discovery, thereby benefitting the diagnosis and treatment of a variety of human disease states and disorders including cancer, autism, and idiopathic infertility.

Monitoring of WT1 expression in PB and CD34(+) donor chimerism of BM predicts early relapse in AML and MDS patients after hematopoietic cell transplantation with reduced-intensity conditioning

Relapse of malignant disease remains the major complication in patients with acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS) after hematopoietic cell transplantation (HCT) with reduced-intensity conditioning (RIC). In this study, we investigated the predictive value of disease-specific markers (DSMs), donor chimerism (DC) analysis of unsorted (UDC) or CD34(+) sorted cells and Wilms' tumor gene 1 (WT1) expression. Eighty-eight patients with AML or MDS were monitored after allogenic HCT following 2 Gy total-body irradiation with (n=84) or without (n=4) fludarabine 3 × 30 mg/m(2), followed by cyclosporin A and mycophenolate mofetil. DSMs were determined by fluorescence in situ hybridization (FISH) and WT1 expression by real-time polymerase chain reaction. Chimerism analysis was performed on unsorted or CD34(+) sorted cells, by FISH or short tandem repeat polymerase chain reaction. Twenty-one (24%) patients relapsed within 4 months after HCT. UDC, CD34(+) DC and WT1 expression were each significant predictors of relapse with sensitivities ranging from 53 to 79% and specificities of 82-91%. Relapse within 28 days was excluded almost entirely on the basis of WT1 expression combined with CD34(+) DC kinetics. Monitoring of WT1 expression and CD34(+) DC predict relapse of AML and MDS after RIC-HCT.

From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumorsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process

Genome rearrangements have long been recognized as hallmarks of human tumors and have been used to diagnose cancer. Techniques used to detect genome rearrangements have evolved from microscopic examinations of chromosomes to the more recent microarray-based approaches. The availability of next-generation sequencing technologies may provide a means for scrutinizing entire cancer genomes and transcriptomes at unparalleled resolution. Here we review the methods that have been used to detect genome rearrangements and discuss the scope and limitations of each approach. We end with a discussion of the potential that next-generation sequencing technologies may offer to the field.

Evaluation of complete disease remission in acute myeloid leukemia

BACKGROUND

Different diagnostic methods add information to define complete remission (CR) in patients with acute myeloid leukemia (AML). The detection of minimal residual disease (MRD) for predicting prognosis and for therapeutic planning still are under discussion.

METHODS

The authors studied 216 patients with AML at the time of initial diagnosis and during follow-up and correlated cytomorphology, interphase fluorescence in situ hybridization (FISH), and flow cytometry results to evaluate response status. They further tested the prognostic impact of those results, especially in patients who achieved a morphologic CR.

RESULTS

Interphase FISH was found to be correlated significantly with the clinical course at the time of complete cytomorphologic remission and was more reliable than morphology for defining CR. Furthermore, interphase FISH was correlated with immunophenotyping results at all times during follow-up.

CONCLUSIONS

The current results indicated that interphase FISH may be used as a valid MRD parameter in patients with AML. Multiparameter immunophenotyping for MRD also was correlated strongly with the clinical course, and the authors suggest integrating such immunophenotyping into the routine diagnostic panel at the time of diagnosis and during the clinical course in patients with AML.

Detection of minimal residual disease in acute myelogenous leukemia

Acute myelogenous leukemia (AML) is considered to be in complete remission when fewer than 5% of the cells in bone marrow are blasts. Nevertheless, approximately two thirds of patients relapse due to persisting leukemic blasts. The persistence of these cells, below the threshold of morphological detection, is termed minimal residual disease (MRD) and various methods are used for its detection. These methods include classical cytogenetics, fluorescence in situ hybridization, qualitative and quantitative RT-PCR and multiparametric flow cytometry. Currently, less than half of the AML patients have a specific marker detectable by RT-PCR techniques. The major specific molecular markers are involvement of the MLL gene with up to 50 different partners and partial tandem duplications, the core binding factor leukemias with AML1/ETO and CBFbeta/MYH11 rearrangements, PML/RARalpha in acute promyelocytic leukemia, internal tandem duplications and mutations of FLT3 and some other rare translocations. In addition, several other genes show abnormal expression levels in AML, including the Wilms tumor gene, the PRAME gene and Ig/TCR rearrangements. Most of these genetic abnormalities can be detected by qualitative but more importantly by quantitative RT-PCR. The kinetics of disappearance of molecular markers in AML differs between the various types of leukemias, although at least a 2 log reduction of transcript after induction chemotherapy is necessary for long-term remission in all types. Conversely, the change of PCR from negativity to positivity is highly predictive of relapse. Whereas in acute lymphoblastic leukemia, multiparametric flow cytometry is an established method for MRD detection, this is less so in AML. The reason is the absence of well-characterized leukemia-specific antigens and the existence of phenotypic changes at relapse. On the other hand, this method is convenient due to its simplicity and universal applicability. In conclusion, several methods can be used for MRD detection in AML patients; each has its pros and cons. Several issues still remain to be settled including the choice of the best method and the timing for MRD monitoring and above all the practical clinical implications of MRD in the various types of AML.

Pre-transplant prognostic factors for patients with high-risk leukemia undergoing an unrelated cord blood transplantation

From July 1995 to December 2001, 42 patients with leukemia aged 1-42 years underwent cord blood transplant (CBT) from unrelated, < or = 2 antigen HLA mismatched donors. In all, 26 patients were in < or = 2nd complete remission and 16 in more advanced phase. Conditioning regimens, graft-versus-host disease (GVHD) prophylaxis and supportive policy were uniform for all patients. The cumulative incidence of engraftment was 90% (95% CI: 0.78-0.91). The cumulative incidence of III-IV grade acute- and chronic-GVHD was 9% (95% CI: 0.04-0.24) and 35% (95% CI: 0.21-0.60), respectively. The 4-year cumulative incidence of transplant-related mortality (TRM) and relapse was 28% (95% CI: 0.17-0.47) and 25% (95% CI: 0.14-0.45), respectively. The 4-year overall survival (OS), leukemia-free survival (LFS) and event-free survival (EFS) were 45% (95% CI: 0.27-0.63), 47% (95% CI: 0.30-0.64) and 46% (95% CI: 0.30-0.62), respectively. In multivariate analysis, the most important factor affecting outcomes was the CFU-GM dose, associated with CMV serology (P=0.003 and 0.04, respectively) in influencing OS and with patient sex (P=0.008 and 0.03, respectively) in influencing LFS. Finally, CFU-GM dose was the only factor that affected EFS significantly (P=0.02). In conclusion, the infused cell dose expressed as in vitro progenitor cell growth is highly predictive of outcomes after an unrelated CBT and should be considered the main parameter in selecting cord blood units for transplant.

Expression of the neural cell adhesion molecule CD56 is not associated with P-glycoprotein overexpression in core-binding factor acute myeloid leukemia

Acute myeloid leukemia (AML) with rearrangement of the core-binding factor (CBF) alpha or beta subunit gene has a favorable prognosis, but CD56 expression in CBFalpha-AML is associated with short disease-free survival. A proposed mechanism is overexpression of the multidrug resistance (MDR) protein P-glycoprotein (Pgp). CD56 expression, Pgp expression and function, and expression of the additional MDR proteins multidrug resistance protein-1 (MRP-1), lung resistance protein (LRP) and breast cancer resistance protein (BCRP) were studied in pretreatment blasts from 25 CBF-AML patients. CD56 expression was frequent in CBFalpha but rare in CBFbeta, and Pgp expression and function were frequent in both subtypes. CD56 expression did not correlate with Pgp expression or function, nor with expression of the other MDR proteins. Treatment failure associated with CD56 expression in CBFalpha-AML is not likely attributable to Pgp.

A novel method for single cell detection of in situ telomerase or histone H3 in combination with clonal analysis by FISH

A novel method for simultaneously detecting clonality by FISH, and presence of telomerase activity (telo+ cells) or histone H3 mRNA (H3+) in single cells from a mixed leukemic population is reported. The methods were validated using K562 cells mixed with peripheral blood granulocytes and bone marrow aspirate cells from newly diagnosed AML patients. Fifty patients with AML were analyzed for telo+ cells, while eight AML patients were analyzed for FISH-Telomerase and FISH-H3+ during remission induction therapy. Our results demonstrate that: (1). changes in the leukemic populations during therapy could be followed; (2). a favorable response to chemotherapy occurred when there was a reduction in both the cytogenetically abnormal cells along with reduction in telo+ cells within this abnormal population; (3). reduction of either telo+ cells or FISH+ cells alone did not correlate with good response. H3+ could be detected in only 4% of the leukemic population, most of which were cytogenetically abnormal. These newly established methods allow sub-populations of cells to be followed during disease progression and treatment and to elucidate factors that give a specific clone proliferative advantage.

Impact of treatment on the outcome of acute myeloid leukemia with inversion 16: a single institution's experience

To identify treatment factors that may affect the survival of children with inv(16)(p13.1q22), we compared the outcomes of 19 patients with this genetic feature treated at our institution during two treatment eras. Nine patients were treated during era 1 (1980 to 1987), and 10 were treated during era 2 (1988 to 1996). All entered complete remission (CR) with induction therapy. Eight of the nine children treated in era 1 died, seven of relapsed leukemia. In contrast, three of 10 patients treated during era 2 have died, all of non-disease-related causes. Event-free survival (EFS) estimates were significantly higher for patients treated during era 2 than for those treated during era 1 (P = 0.03); the 6-year estimates were 70 +/- 15% (s.e.) and 11 +/- 7%, respectively. Era 2 treatment protocols differed from those of era 1 in their use of higher doses of cytarabine and etoposide during induction and consolidation chemotherapy and in their use of 2-chlorodeoxyadenosine (2-CDA). These results suggest that dose intensification of cytarabine benefits children with AML and inv(16), as is the case in adults. They also suggest that dose intensification of etoposide and addition of 2-CDA may also offer an advantage. This study underscores the dependence of the prognostic impact of cytogenetic features on the efficacy of treatment.

An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles

We have developed a statistical regression modeling approach to discover genes that are differentially expressed between two predefined sample groups in DNA microarray experiments. Our model is based on well-defined assumptions, uses rigorous and well-characterized statistical measures, and accounts for the heterogeneity and genomic complexity of the data. In contrast to cluster analysis, which attempts to define groups of genes and/or samples that share common overall expression profiles, our modeling approach uses known sample group membership to focus on expression profiles of individual genes in a sensitive and robust manner. Further, this approach can be used to test statistical hypotheses about gene expression. To demonstrate this methodology, we compared the expression profiles of 11 acute myeloid leukemia (AML) and 27 acute lymphoblastic leukemia (ALL) samples from a previous study (Golub et al. 1999) and found 141 genes differentially expressed between AML and ALL with a 1% significance at the genomic level. Using this modeling approach to compare different sample groups within the AML samples, we identified a group of genes whose expression profiles correlated with that of thrombopoietin and found that genes whose expression associated with AML treatment outcome lie in recurrent chromosomal locations. Our results are compared with those obtained using t-tests or Wilcoxon rank sum statistics.

Loss of heterozygosity and heterogeneity of its appearance and persisting in the course of acute myeloid leukemia and myelodysplastic syndromes

Screening for loss of heterozygosity (LOH) of the panel of 18 highly polymorphic microsatellite markers, especially from the region 11p15, was carried out on 154 samples from 26 patients with acute myeloid leukemia and eight with myelodysplastic syndromes (MDS). LOH was detected at the majority (72%) of the loci tested: 47% of informative patients displayed LOH for at least one of the microsatellite locus from the region 11p15 and 23.5% of patients displayed LOH among the other markers tested within the study. A longitudinal follow-up of patients showed a remarkable heterogeneity of LOH appearance and its persistance during the course of the disease suggesting an intratumor clonal heterogeneity, or alternatively, presence of LOH in more than one cell clone. The data revealed two regions of high loss of one allele in 11p15.5, defined by markers D11S1363 and D11S1338, indicating that LOH at the subtelomeric region of the short arm of chromosome 11 is a much common event in hematological malignancies than it was previously reported.