Prognostic Impact of Copy Number Alterations' Profile and AID/RAG Signatures in Acute Lymphoblastic Leukemia (ALL) with BCR::ABL and without Recurrent Genetic Aberrations (NEG ALL) Treated with Intensive Chemotherapy.

Adult acute lymphoblastic leukemia (ALL) is associated with poor outcomes. ALL is initiated by primary aberrations, but secondary genetic lesions are necessary for overt ALL. In this study, we reassessed the value of primary and secondary aberrations in intensively treated ALL patients in relation to mutator enzyme expression. RT-PCR, genomic PCR, and sequencing were applied to evaluate primary aberrations, while qPCR was used to measure the expression of RAG and AID mutator enzymes in 166 adult ALL patients. Secondary copy number alterations (CNA) were studied in 94 cases by MLPA assay. Primary aberrations alone stratified 30% of the patients (27% high-risk, 3% low-risk cases). The remaining 70% intermediate-risk patients included BCR::ABL1pos subgroup and ALL lacking identified genetic markers (NEG ALL). We identified three CNA profiles: high-risk bad-CNA (CNAhigh/IKZF1pos), low-risk good-CNA (all other CNAs), and intermediate-risk CNAneg. Furthermore, based on RAG/AID expression, we report possible mechanisms underlying the CNA profiles associated with poor outcome: AID stratified outcome in CNAneg, which accompanied most likely a particular profile of single nucleotide variations, while RAG in CNApos increased the odds for CNAhigh/IKZF1pos development. Finally, we integrated primary genetic aberrations with CNA to propose a revised risk stratification code, which allowed us to stratify 75% of BCR::ABL1pos and NEG patients.

IDH2 mutations in patients with normal karyotype AML predict favorable responses to daunorubicin, cytarabine and cladribine regimen.

Mutations in isocitrate dehydrogenase 1 and 2 (IDH1/2) genes occur in about 20% patients with acute myeloid leukemia (AML), leading to DNA hypermethylation and epigenetic deregulation. We assessed the prognostic significance of IDH1/2 mutations (IDH1/2+) in 398 AML patients with normal karyotype (NK-AML), treated with daunorubicine + cytarabine (DA), DA + cladribine (DAC), or DA + fludarabine. IDH2 mutation was an independent favorable prognostic factor for 4-year overall survival (OS) in total NK-AML population (p = 0.03, censoring at allotransplant). We next evaluated the effect of addition of cladribine to induction regimen on the patients' outcome according to IDH1/2 mutation status. In DAC group, 4-year OS was increased in IDH2+ patients, compared to IDH-wild type group (54% vs 33%; p = 0.0087, censoring at allotransplant), while no difference was observed for DA-treated subjects. In multivariate analysis, DAC independently improved the survival of IDH2+ patients (HR = 0.6 [0.37-0.93]; p = 0.024; censored at transplant), indicating that this group specifically benefits from cladribine-containing therapy. In AML cells with R140Q or R172K IDH2 mutations, cladribine restrained mutations-related DNA hypermethylation. Altogether, DAC regimen produces better outcomes in IDH2+ NK-AML patients than DA, and this likely results from the hypomethylating activity of cladribine. Our observations warrant further investigations of induction protocols combining cladribine with IDH1/2 inhibitors in IDH2-mutant.

Successful Use of Nilotinib in the Therapy of a Patient with a Chemoresistant Relapse of BCR-ABL1-Like Phenotype Acute Lymphoblastic Leukemia.

INTRODUCTION: Relapse of acute lymphoblastic leukemia (ALL) after allogeneic hematopoietic cell transplantation (HCT) is a therapeutic challenge. We present the case of a 20-year-old patient with a relapse of Philadelphia chromosome-negative ALL B-common over 2 years after HCT with no response to salvage chemotherapy or blinatumomab, who finally responded to a molecularly tailored therapy adjusted to the BCR-ABL1-like phenotype. METHODS: The BCR-ABL1-like phenotype was diagnosed on the basis of an increased expression of ABL1 and CRLF2 genes. RESULTS: We combined a nilotinib-based therapy targeting the overexpressed ABL1 gene with a proteasome inhibitor and Peg-asparaginase, achieving a spectacular response: the percentage of lymphoblasts in the bone marrow was reduced from 70% to 5%, which enabled a second HCT to be performed. Moreover, the relatively low toxicity of the treatment led to a good quality of life and no need for prolonged hospitalization. CONCLUSION: To our knowledge, this is the first successful use of nilotinib in BCR-ABL1-like phenotype ALL. This case should encourage routine clinical use of molecular data to individualize therapies targeting the overexpressed pathways responsible for leukemic cell proliferation, as a means to overcome chemoresistance.

CEBPA copy number variations in normal karyotype acute myeloid leukemia: Possible role of breakpoint-associated microhomology and chromatin status in CEBPA mutagenesis.

Copy number variations (CNV) in CEBPA locus represent heterogeneous group of mutations accompanying acute myeloid leukemia (AML). The aim of this study was to characterize different CEBPA mutation categories in regard to biological data like age, cytology, CD7, and molecular markers, and identify possible factors affecting their etiology. We report here the incidence of 12.6% of CEBPA mutants in the population of 262 normal karyotype AML (NK-AML) patients. We confirmed that double mutant AMLs presented uniform biological features when compared to single CEBPA mutations and accompanied mostly younger patients. We hypothesized that pathogenesis of distinct CEBPA mutation categories might be influenced by different factors. The detailed sequence analysis revealed frequent breakpoint-associated microhomologies of 2 to 12bp. The analysis of distribution of microhomology motifs along CEBPA gene showed that longer stretches of microhomology at the mutational junctions were relatively rare by chance which suggests their functional role in the CEBPA mutagenesis. Additionally, accurate quantification of CEBPA transcript levels showed that double CEBPA mutations correlated with high-level CEBPA expression, whereas single N-terminal CEBPA mutations were associated with low-level CEBPA expression. This might suggest that high-level CEBPA expression and/or accessibility of CEBPA locus contribute to B-ZIP in-frame duplications.

[Development of a novel real-time PCR method for detection of HSV types 1 and 2 DNA using HybProbe chemistry]. / Wykrywanie oraz roznicowanie wirusów opryszczki typu 1 i 2 metoda real-time PCR z wykorzystaniem sond HybProbe.

Herpes simplex viruses types 1 and 2 are members of the Alphaherpesviridae subfamily, as they can infect both skin and nerves and develop latent infection within the dorsal root and trigeminal ganglia. Infections with these viruses are common worldwide and cause wide range of clinical syndromes. Although HSV-1/2 infect healthy children and adults, disease is more severe and extensive in the immunocompromised individuals and/or during neuroinfections. The aim of the study was development of real-time PCR assay for detection and differentiation of herpes simplex viruses type 1 and 2. DNA in clinical samples, using specific dual-channel HybProbe chemistry. The nalytical sensitivity of assay was tested using serial dilutions of HSV-1 and HSV-2 DNA in range between 10 degrees and 10(-5). (4.35 x 10(5)-4.00 x 10(2) copies/ml and 4.18 x 10(5)-3.82 x 10(2) copies/ml, respectively). Thirty four cell line isolates and sixteen clinical samples taken from a group of adult patients with neurological signs were tested for the presence of HSV-1/2 DNA in the LightCycler instrument. Described in-house real-time PCR assay detected herpesviral DNA in all cell line isolates (31 of them were HSV-1 positive; 3 were HSV-2 positive) and in 10 clinical samples (positive only for HSV-1). The conclusion is that developed HybProbe-based real-time PCR test is very reliable and valuable tool for detection and differentiation of HSV-1/2 viremia in different kind of samples. The high level of sensitivity and accuracy provided by this assay is favorable for the quantification of herpes simplex virus 1 and 2 DNA in clinical specimens, especially during low-copy infections.

[Application of real-time PCR assay for investigating the presence of herpes simplex virus type 1 DNA]. / Zastosowanie techniki real-time PCR do wykrywania DNA ludzkiego wirusa opryszczki typu 1.

Herpes simplex virus type 1 is a member of the Alphaherpesviridae subfamily, as it can infect both skin and nerves and develop latent infection within the dorsal root and trigeminal ganglia. Infection with this virus is common and causes a wide range of clinical syndromes. Although HSV-1 infect healthy children and adults, disease is more severe and extensive in the immunocompromised individuals. The goal of the study was development of real-time PCR assay for detection of herpes simplex virus type 1 DNA in clinical samples, using primers targeting a conserved region of the viral DNA glycoprotein G gene and a specific TaqMan hydrolyzing probe. The analytical sensitivity of assay was tested using serial dilutions of HSV-1 DNA in range between 10(0) and 10(-6) (4,35 x 10(5) - 4,00 x 10(1) copies/ml). Fifteen cell line isolates and twenty plasma samples taken from a group of adult recipients of allogeneic HSCT were tested for the presence of HSV-1 DNA in the LightCycler system. For comparison commercial quantitative HSV-1/2 LC PCR Kit (Artus/Qiagen) was used, according to the manufacturer's instructions. Both LightCycler assays, including in-house real-time PCR, detected HSV-1 DNA in 23 specimens. The conclusion is that developed TaqMan-based probe real-time PCR test is very reliable and valuable for detection of HSV-1 viremia in different kind of samples. The high level of sensitivity and accuracy provided by the LightCycler instrument is favorable for the use of this method in the detection of herpes simplex virus 1 DNA also in clinical specimens.