Molecular measurement of BCR-ABL transcript variations in chronic myeloid leukemia patients in cytogenetic remission

Abstract Background The monitoring of BCR-ABL transcript levels by real-time quantitative polymerase chain reaction (RT-qPCR) has become important to assess minimal residual disease (MRD) and standard of care in the treatment of chronic myeloid leukemia (CML). In this study, we performed a prospective, sequential analysis using RT-qPCR monitoring of BCR-ABL gene rearrangements in blood samples from 91 CML patients in chronic phase (CP) who achieved complete cytogenetic remission (CCyR) and major molecular remission (MMR) throughout imatinib treatment. Methods The absolute level of BCR-ABL transcript from peripheral blood was serially measured every 4 to 12 weeks by RT-qPCR. Only level variations > 0.5%, according to the international scale, was considered positive. Sequential cytogenetic analysis was also performed in bone marrow samples from all patients using standard protocols. Results Based on sequential analysis of BCR-ABL transcripts, the 91 patients were divided into three categories: (A) 57 (62.6%) had no variation on sequential analysis; (B) 30 (32.9%) had a single positive variation result obtained in a single sample; and (C) 4 (4.39%) had variations of BCR-ABL transcripts in at least two consecutive samples. Of the 34 patients who had elevated levels of transcripts (group B and C), 19 (55.8%) had a < 1% of BCR-ABL/BCR ratio, 13 (38.2%) patients had a 1% to 10% increase and 2 patients had a >10% increase of RT-qPCR. The last two patients had lost a CCyR, and none of them showed mutations in the ABL gene. Transient cytogenetic alterations in Ph-negative cells were observed in five (5.5%) patients, and none of whom lost CCyR. Conclusions Despite an increase levels of BCR-ABL/BCR ratio variations by RT-qPCR, the majority of CML patients with MMR remained in CCyR. Thus, such single variations should neither be considered predictive of subsequent failure and nor an indication for altering imatinib dose or switching to second generation therapy. Changing of imatinib on the basis of BCR-ABL/BCR% sustained increase and mutational studies is a prudent approach for preserving other therapeutic options in imatinib-resistant patients.

Mechanism of resistance to tyrosine kinase inhibitors in philadelphia-positive acute lymphblastic leukaemia (all): from genetic alterations to impaired RNA editing

The Ph chromosome is the most frequent cytogenetic aberration associated with adult ALL and it represents the single most significant adverse prognostic marker. Despite imatinib has led to significant improvements in the treatment of patients with Ph+ ALL, in the majority of cases resistance developed quickly and disease progressed. Some mechanisms of resistance have been widely described but the full knowledge of contributing factors, driving both the disease and resistance, remains to be defined. The observation of rapid development of lymphoblastic leukemia in mice expressing altered Ikaros (Ik) isoforms represented the background of this study. Ikaros is a zinc finger transcription factor required for normal hemopoietic differentiation and proliferation, particularly in the lymphoid lineages. By means of alternative splicing, Ikaros encodes several proteins that differ in their abilities to bind to a consensus DNA-binding site. Shorter, DNA nonbinding isoforms exert a dominant negative effect, inhibiting the ability of longer heterodimer partners to bind DNA. The differential expression pattern of Ik isoforms in Ph+ ALL patients was analyzed in order to determine if molecular abnormalities involving the Ik gene could associate with resistance to imatinib and dasatinib. Bone marrow and peripheral blood samples from 46 adult patients (median age 55 yrs, 18-76) with Ph+ ALL at diagnosis and during treatment with imatinib (16 pts) or dasatinib (30 pts) were collected. We set up a fast, high-throughput method based on capillary electrophoresis technology to detect and quantify splice variants. 41% Ph+ ALL patients expressed high levels of the non DNA-binding dominant negative Ik6 isoform lacking critical N-terminal zinc-fingers which display abnormal subcellular compartmentalization pattern. Nuclear extracts from patients expressed Ik6 failed to bind DNA in mobility shift assay using a DNA probe containing an Ikaros-specific DNA binding sequence. In 59% Ph+ ALL patients there was the coexistence in the same PCR sample and at the same time of many splice variants corresponded to Ik1, Ik2, Ik4, Ik4A, Ik5A, Ik6, Ik6 and Ik8 isoforms. In these patients aberrant full-length Ikaros isoforms in Ph+ ALL characterized by a 60-bp insertion immediately downstream of exon 3 and a recurring 30-bp in-frame deletion at the end of exon 7 involving most frequently the Ik2, Ik4 isoforms were also identified. Both the insertion and deletion were due to the selection of alternative splice donor and acceptor sites. The molecular monitoring of minimal residual disease showed for the first time in vivo that the Ik6 expression strongly correlated with the BCR-ABL transcript levels suggesting that this alteration could depend on the Bcr-Abl activity. Patient-derived leukaemia cells expressed dominant-negative Ik6 at diagnosis and at the time of relapse, but never during remission. In order to mechanistically demonstrated whether in vitro the overexpression of Ik6 impairs the response to tyrosine kinase inhibitors (TKIs) and contributes to resistance, an imatinib-sensitive Ik6-negative Ph+ ALL cell line (SUP-B15) was transfected with the complete Ik6 DNA coding sequence. The expression of Ik6 strongly increased proliferation and inhibited apoptosis in TKI sensitive cells establishing a previously unknown link between specific molecular defects that involve the Ikaros gene and the resistance to TKIs in Ph+ ALL patients. Amplification and genomic sequence analysis of the exon splice junction regions showed the presence of 2 single nucleotide polymorphisms (SNPs): rs10251980 [A/G] in the exon2/3 splice junction and of rs10262731 [A/G] in the exon 7/8 splice junction in 50% and 36% of patients, respectively. A variant of the rs11329346 [-/C], in 16% of patients was also found. Other two different single nucleotide substitutions not recognized as SNP were observed. Some mutations were predicted by computational analyses (RESCUE approach) to alter cis-splicing elements. In conclusion, these findings demonstrated that the post-transcriptional regulation of alternative splicing of Ikaros gene is defective in the majority of Ph+ ALL patients treated with TKIs. The overexpression of Ik6 blocking B-cell differentiation could contribute to resistance opening a time frame, during which leukaemia cells acquire secondary transforming events that confer definitive resistance to imatinib and dasatinib.

Il cane come modello animale spontaneo di patologie neoplastiche dell'uomo: ene Ataxia-Telangiectasia Mutated (ATM) Nnella predisposizione al cancro ed importanza dei riarrangimanti genici dei geni Ig/TCR per la diagnosi e prognosi delle malattie linfoproliferative

“Naturally occurring cancers in pet dogs and humans share many features, including histological appearance, tumour genetics, molecular targets, biological behaviour and response to conventional therapies. Studying dogs with cancer is likely to provide a valuable perspective that is distinct from that generated by the study of human or rodent cancers alone. The value of this opportunity has been increasingly recognized in the field of cancer research for the identification of cancer-associated genes, the study of environmental risk factors, understanding tumour biology and progression, and, perhaps most importantly, the evaluation and development of novel cancer therapeutics”.(Paoloni and Khanna, 2008) In last years, the author has investigated some molecular features of cancer in dogs. The Thesis is articulated in two main sections. In section 1, the preliminary results of a research project aimed at investigating the role of somatic mutations of Ataxia-Telangiectasia mutated (ATM) gene in predisposing to cancer in boxer dogs, are presented. The canine boxer breed may be considered an unique opportunity to disclose the role of ATM somatic mutation since boxer dogs are known to be dramatically susceptible to cancer and since they may be considered a closed gene pool. Furthermore, dogs share with human the some environment. Overall, the abovementioned features could be considered extremely useful for our purposes. In the section 2, the results of our studies aimed at setting up accurate and sensitive molecular assays for diagnosing and assessing minimal residual disease in lymphoproliferative disorders of dogs, are presented. The results of those molecular assay may be directly translated in the field of Veterinary practice as well as the may be used to improve our objective evaluation of new investigational drugs effectiveness in canine cancer trials.

Astroblastoma with rhabdoid features and favorable long-term outcome: report of a case with a 12-year follow-up

Astroblastoma is a historically traded microscopic diagnosis to denote a rare neuroepithelial tumor of uncertain nosology, involving a distinctive pattern of pseudorosette arrangement of neoplastic cells. While displaying some glial properties, the latter shall not - by definition - be either reducible to or part of any conventional glioma type. We report on clinicopathologic correlations in a case of astroblastoma involving an extensive rhabdoid phenotype of tumor cells. The male patient was operated on at the age of 53 and 59 years for a left parietal tumor measuring 5.8 cm in diameter at the first presentation. On magnetic resonance imaging and angiography, both the primary and its recurrence were discrete, highly vascularized, and contrast-enhancing. The second surgery was complemented with radiotherapy of 66 Gy, followed by chemotherapy with Temozolomide. Twelve years into clinical history, the patient has stable minimal residual disease at the age of 65. A review of pathology samples from both surgeries showed well-differentiated astroblastoma according to current standards, with an MIB-1 labeling index of 1% and 4%, respectively. Neither of the specimens involved cellular anaplasia, overt mitotic activity, microvascular proliferation, or palisading necrosis. Most tumor cells harbored paranuclear filamentous rhabdoid inclusions that were immunostained for vimentin and, in part, also for GFAP. No polyantigenic reactivity was observed. This example contributes another facet to the spectrum of the so-called composite rhabdoid tumors. Involving a low-grade parent neoplasm, it also further substantiates the incipient perception that the rhabdoid phenotype neither is a peculiar but nonspecific convergence point of anaplastic evolution, nor are such lesions indiscriminately bound for a relentless course.

Dendritic Cell-Based Immunotherapy for Myeloid Leukemias

Acute and chronic myeloid leukemia (AML, CML) are hematologic malignancies arising from oncogene-transformed hematopoietic stem/progenitor cells known as leukemia stem cells (LSCs). LSCs are selectively resistant to various forms of therapy including irradiation or cytotoxic drugs. The introduction of tyrosine kinase inhibitors has dramatically improved disease outcome in patients with CML. For AML, however, prognosis is still quite dismal. Standard treatments have been established more than 20 years ago with only limited advances ever since. Durable remission is achieved in less than 30% of patients. Minimal residual disease (MRD), reflected by the persistence of LSCs below the detection limit by conventional methods, causes a high rate of disease relapses. Therefore, the ultimate goal in the treatment of myeloid leukemia must be the eradication of LSCs. Active immunotherapy, aiming at the generation of leukemia-specific cytotoxic T cells (CTLs), may represent a powerful approach to target LSCs in the MRD situation. To fully activate CTLs, leukemia antigens have to be successfully captured, processed, and presented by mature dendritic cells (DCs). Myeloid progenitors are a prominent source of DCs under homeostatic conditions, and it is now well established that LSCs and leukemic blasts can give rise to "malignant" DCs. These leukemia-derived DCs can express leukemia antigens and may either induce anti-leukemic T cell responses or favor tolerance to the leukemia, depending on co-stimulatory or -inhibitory molecules and cytokines. This review will concentrate on the role of DCs in myeloid leukemia immunotherapy with a special focus on their generation, application, and function and how they could be improved in order to generate highly effective and specific anti-leukemic CTL responses. In addition, we discuss how DC-based immunotherapy may be successfully integrated into current treatment strategies to promote remission and potentially cure myeloid leukemias.

Update as Evidence: Belief Expansion

We introduce a justification logic with a novel constructor for evidence terms, according to which the new information itself serves as evidence for believing it. We provide a sound and complete axiomatization for belief expansion and minimal change and explain how the minimality can be graded according to the strength of reasoning. We also provide an evidential analog of the Ramsey axiom.

Leukemic stem cell frequency: a strong biomarker for clinical outcome in acute myeloid leukemia.

INTRODUCTION Treatment failure in acute myeloid leukemia is probably caused by the presence of leukemia initiating cells, also referred to as leukemic stem cells, at diagnosis and their persistence after therapy. Specific identification of leukemia stem cells and their discrimination from normal hematopoietic stem cells would greatly contribute to risk stratification and could predict possible relapses. RESULTS For identification of leukemic stem cells, we developed flow cytometric methods using leukemic stem cell associated markers and newly-defined (light scatter) aberrancies. The nature of the putative leukemic stem cells and normal hematopoietic stem cells, present in the same patient's bone marrow, was demonstrated in eight patients by the presence or absence of molecular aberrancies and/or leukemic engraftment in NOD-SCID IL-2Rγ-/- mice. At diagnosis (n=88), the frequency of the thus defined neoplastic part of CD34+CD38- putative stem cell compartment had a strong prognostic impact, while the neoplastic parts of the CD34+CD38+ and CD34- putative stem cell compartments had no prognostic impact at all. After different courses of therapy, higher percentages of neoplastic CD34+CD38- cells in complete remission strongly correlated with shorter patient survival (n=91). Moreover, combining neoplastic CD34+CD38- frequencies with frequencies of minimal residual disease cells (n=91), which reflect the total neoplastic burden, revealed four patient groups with different survival. CONCLUSION AND PERSPECTIVE Discrimination between putative leukemia stem cells and normal hematopoietic stem cells in this large-scale study allowed to demonstrate the clinical importance of putative CD34+CD38- leukemia stem cells in AML. Moreover, it offers new opportunities for the development of therapies directed against leukemia stem cells, that would spare normal hematopoietic stem cells, and, moreover, enables in vivo and ex vivo screening for potential efficacy and toxicity of new therapies.

Immune restoration of patients with chronic myelogenous leukemia in complete cytogenetic remission

Imatinib mesylate (IM) and Interferon-alfa (IFN-α) are currently the two most efficacious therapies for patients with chronic myelogenous leukemia (CML). IFN-α induces durable complete cytogentic remission (CCR) in about 25% of CML patients whereas IM, a tyrosine kinase inhibitor, induces CCR in 50% of patients who are resistant to IFN-α and in 75% of patients in early chronic phase of CML. However, the detection of minimal residual disease without clinical relapse suggests that host immune surveillance plays a very important role in controlling the progression of disease. ^ T lymphocytes and dendritic cells (DC) are the two most crucial players in the immune system. In my study, we focused on the effects of treatment with either IM or IFN-α on the functions of both DC and T cells, as exemplified by the ability of DC to present antigen to T cells and activated T cells to synthesize cytokines. Our studies show that cytokine production by T cells activated through the T-cell receptor (TCR) was significantly lower in CML patients treated with IM, but not with IFN-α, when compared with activated T cells of control subjects. Suppression of T cell function by IM albeit transient and reversible, was through the downregulation of the phosphorylation of Zap-70, Lck, and LAT. ^ Our data also show that the myeloid DC (DC1) and the plasmacytoid DC (DC2) are lower in chronic phase CML. Whereas neither therapy restored the level of DC2 to normal levels, the number of DC1 was normalized by either therapy. However, only IFN-α, and not IM, restored DC2 function to normal, as exemplified by the production of IFN-α in response to exposure to live influenza virus. Moreover, in vitro differentiation and maturation of DC1 from monocyte precursors in patients receiving either therapy was not normal and was reflected in their ability to present antigen to autologous T cells. ^ In summary, we report that there are differences in immune responses of CML patients treated with IM or IFN-α that may be the result of long-term effects on the host immune system by the individual therapy. ^

Planktonic foraminiferal Cd/Ca ratios

Records of Cd/Ca in planktonic foraminiferal calcite of Globigerinoides bulloides in cores from the Subantarctic region of the Southern Ocean show large glacial-interglacial variations with lower Cd/Ca (by 0.06-0.10 µmol/mol) at glacial times. Interpretation of these records in terms of lower dissolved phosphate and inferred higher glacial nutrient utilization has significant implications for glacial atmospheric carbon dioxide (pCO2) draw-down. However, box core-top data for G. bulloides in the North Atlantic suggest that the incorporation of Cd into planktonic foraminifera relative to seawater (DCd) is temperature sensitive (DCd=0.637 exp 0.15T). When the Subantarctic planktonic Cd/Ca records are corrected for this temperature dependence, they show little or no glacial-interglacial diferences. If, as seems likely, this observation can be interpreted to indicate a minimal change (< 0.5 µmol/kg) in surface water phosphate concentrations, then the explanation for lowered glacial pCO2 must be looked for elsewhere.

Geochemistry of sediment cores of the Southern Ocean

We examine the possibility that glacial increase in the areal extent of reducing sediments might have changed the oceanic Cd inventory, thereby decoupling Cd from PO4. We suggest that the precipitation of Cd-sulfide in suboxic sediments is the single largest sink in the oceanic Cd budget and that the accumulation of authigenic Cd and U is tightly coupled to the organic carbon flux into the seafloor. Sediments from the Subantarctic Ocean and the Cape Basin (South Atlantic), where oxic conditions currently prevail, show high accumulation rates of authigenic Cd and U during glacial intervals associated with increased accumulation of organic carbon. These elemental enrichments attest to more reducing conditions in glacial sediments in response to an increased flux of organic carbon. A third core, overlain by Circumpolar Deep Water (CPDW) as are the other two cores but located south of the Antarctic Polar Front, shows an approximately inverse pattern to the Subantarctic record. The contrasting patterns to the north and south of the Antarctic Polar Front suggest that higher accumulation rates of Cd and U in Subantarctic sediments were driven primarily by increased productivity. This proposal is consistent with the hypothesis of glacial stage northward migration of the Antarctic Polar Front and its associated belt of high siliceous productivity. However, the increase in authigenic Cd and U glacial accumulation rates is higher than expected simply from a northward shift of the polar fronts, suggesting greater partitioning of organic carbon into the sediments during glacial intervals. Lower oxygen content of CPDW and higher organic carbon to biogenic silica rain rate ratio during glacial stages are possible causes. Higher glacial productivity in the Cape Basin record very likely reflects enhanced coastal up-welling in response to increased wind speeds. We suggest that higher productivity might have doubled the areal extent of suboxic sediments during the last glacial maximum. However, our calculations suggest low sensitivity of seawater Cd concentrations to glacial doubling of the extent of reducing sediments. The model suggests that during the last 250 kyr seawater Cd concentrations fluctuated only slightly, between high levels (about 0.66 nmol/kg) on glacial initiations and reaching lowest values (about 0.57 nmol/kg) during glacial maxima. The estimated 5% lower Cd content at the last glacial maximum relative to modern levels (0.60 nmol/kg) cannot explain the discordance between Cd and delta13C, such as observed in the Southern Ocean. This low sensitivity is consistent with foraminiferal data, suggesting minimal change in the glacial Cd mean oceanic content.

Mean sortable silt values from Holocene and glacial Scotia Sea sediments

The Antarctic Circumpolar Current is key to the mixing and ventilation of the world's oceans. This current flows from west to east between about 45° and 70° S connecting the Atlantic, Pacific and Indian oceans, and is driven by westerly winds and buoyancy forcing. High levels of productivity in the current regulate atmospheric CO2 concentrations. Reconstructions of the current during the last glacial period suggest that flow speeds were faster or similar to present, and it is uncertain whether the strength and position of the westerly winds changed. Here we reconstruct Antarctic Circumpolar Current bottom speeds through the constricting Drake Passage and Scotia Sea during the Last Glacial Maximum and Holocene based on the mean grain size of sortable silt from a suite of sediment cores. We find essentially no change in bottom flow speeds through the region, and, given that the momentum imparted by winds, and modulated by sea-ice cover, is balanced by the interaction of these flows with the seabed, this argues against substantial changes in wind stress. However, glacial flow speeds in the sea-ice zone south of 56° S were significantly slower than present, whereas flow in the north was faster, but not significantly so. We suggest that slower flow over the rough topography south of 56° S may have reduced diapycnal mixing in this region during the last glacial period, possibly reducing the diapycnal contribution to the Southern Ocean overturning circulation.