26
|
Coccaro N, Tota G, Anelli L, Zagaria A, Specchia G, Albano F. Digital PCR: A Reliable Tool for Analyzing and Monitoring Hematologic Malignancies. Int J Mol Sci 2020; 21:ijms21093141. [PMID: 32365599 PMCID: PMC7247671 DOI: 10.3390/ijms21093141] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
The digital polymerase chain reaction (dPCR) is considered to be the third-generation polymerase chain reaction (PCR), as it yields direct, absolute and precise measures of target sequences. dPCR has proven particularly useful for the accurate detection and quantification of low-abundance nucleic acids, highlighting its advantages in cancer diagnosis and in predicting recurrence and monitoring minimal residual disease, mostly coupled with next generation sequencing. In the last few years, a series of studies have employed dPCR for the analysis of hematologic malignancies. In this review, we will summarize these findings, attempting to focus on the potential future perspectives of the application of this promising technology.
Collapse
|
27
|
Minervini CF, Cumbo C, Orsini P, Anelli L, Zagaria A, Specchia G, Albano F. Nanopore Sequencing in Blood Diseases: A Wide Range of Opportunities. Front Genet 2020; 11:76. [PMID: 32140171 PMCID: PMC7043087 DOI: 10.3389/fgene.2020.00076] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/23/2020] [Indexed: 12/20/2022] Open
Abstract
The molecular pathogenesis of hematological diseases is often driven by genetic and epigenetic alterations. Next-generation sequencing has considerably increased our genomic knowledge of these disorders becoming ever more widespread in clinical practice. In 2012 Oxford Nanopore Technologies (ONT) released the MinION, the first long-read nanopore-based sequencer, overcoming the main limits of short-reads sequences generation. In the last years, several nanopore sequencing approaches have been performed in various "-omic" sciences; this review focuses on the challenge to introduce ONT devices in the hematological field, showing advantages, disadvantages and future perspectives of this technology in the precision medicine era.
Collapse
|
28
|
Conserva MR, Redavid I, Anelli L, Zagaria A, Specchia G, Albano F. RARG Gene Dysregulation in Acute Myeloid Leukemia. Front Mol Biosci 2019; 6:114. [PMID: 31709264 PMCID: PMC6822255 DOI: 10.3389/fmolb.2019.00114] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/10/2019] [Indexed: 12/19/2022] Open
Abstract
Retinoic acid receptor γ (RARγ) belongs to the nuclear receptor superfamily and shares 90% homology with retinoic acid receptor α (RARα) and retinoic acid receptor β (RARβ). RARA rearrangements are well-known to be involved in acute promyelocytic leukemia (APL), but RARG rearrangements can also resemble this kind of leukemia. In this review we trace the role of RARγ, considering both its physiological and oncogenic contribution; from 2011 to date, nine cases of patients harboring RARG fusions have been reported. These patients showed typical APL features, including the clinical presentation, coagulation abnormalities and morphological features of bone marrow (BM), but are not responsive to APL standard therapy. We stress the urgent need for a better comprehension of the critical role of RARG dysregulation in the leukemogenesis process, since optimum therapy strategies have not yet been established.
Collapse
|
29
|
Tarantini F, Anelli L, Ingravallo G, Attolico I, Zagaria A, Russo Rossi A, Lospalluti L, Bufano T, Zanframundo G, Maiorano E, Specchia G, Albano F. Skin lesions in chronic myeloid leukemia patients during dasatinib treatment. Cancer Manag Res 2019; 11:7991-7996. [PMID: 31692557 PMCID: PMC6717053 DOI: 10.2147/cmar.s217872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 07/26/2019] [Indexed: 12/30/2022] Open
Abstract
Purpose In our work we sought to define the prevalence rates of cutaneous events during dasatinib therapy in chronic myeloid leukemia (CML) patients and to investigate the clinical and pathological characteristics of these reactions. Patients and methods In our institution, 67 CML patients were treated with dasatinib. it was given as first line treatment in 26 (39%) and subsequent treatment in 41 (61%) CML patients. Flow cytometry analysis of peripheral blood and cutaneous biopsy was done on all CML patients with dermatological lesions appearing during dasatinib treatment. Results Among 67 CML patients, 4 (5.9%) showed skin lesions during dasatinib treatment. The cutaneous manifestations were not generalized but mainly located on the back, abdomen, thorax or leg regions. The patients did not show peripheral lymphocytosis at the time when skin lesions appeared. Overall, histological analysis showed that the skin lesions were characterized by a mild perivascular small CD8+ T lymphocytes infiltrate with minimal epidermotropism. Conclusion The unusual T cytotoxic cutaneous infiltrate demonstrated in our CML cases could be the expression of a dasatinib-promoted lymphocyte expansion. However, the heterogeneity of the dermatologic manifestations reported in our CML patients could also be related to unknown factors specific to each CML patient. Our work highlights the finding that skin lesions may be associated with dasatinib treatment and that they should not be confused with viral or bacterial infections but rather interpreted as the clinical expression of lymphocytosis promoted by this TKI.
Collapse
|
30
|
Coccaro N, Anelli L, Zagaria A, Specchia G, Albano F. Next-Generation Sequencing in Acute Lymphoblastic Leukemia. Int J Mol Sci 2019; 20:ijms20122929. [PMID: 31208040 PMCID: PMC6627957 DOI: 10.3390/ijms20122929] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/04/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and accounts for about a quarter of adult acute leukemias, and features different outcomes depending on the age of onset. Improvements in ALL genomic analysis achieved thanks to the implementation of next-generation sequencing (NGS) have led to the recent discovery of several novel molecular entities and to a deeper understanding of the existing ones. The purpose of our review is to report the most recent discoveries obtained by NGS studies for ALL diagnosis, risk stratification, and treatment planning. We also report the first efforts at NGS use for minimal residual disease (MRD) assessment, and early studies on the application of third generation sequencing in cancer research. Lastly, we consider the need for the integration of NGS analyses in clinical practice for genomic patients profiling from the personalized medicine perspective.
Collapse
|
31
|
Conserva MR, Anelli L, Zagaria A, Specchia G, Albano F. The Pleiotropic Role of Retinoic Acid/Retinoic Acid Receptors Signaling: From Vitamin A Metabolism to Gene Rearrangements in Acute Promyelocytic Leukemia. Int J Mol Sci 2019; 20:ijms20122921. [PMID: 31207999 PMCID: PMC6627493 DOI: 10.3390/ijms20122921] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/07/2019] [Accepted: 06/13/2019] [Indexed: 12/18/2022] Open
Abstract
The family of retinoic acid receptors (RARs: RARα, -β, and -γ) has remarkable pleiotropy characteristics, since the retinoic acid/RARs pathway is involved in numerous biological processes not only during embryonic development, but also in the postnatal phase and during adulthood. In this review, we trace the roles of RA/RARs signaling in the immune system (where this pathway has both an immunosuppressive role or is involved in the inflammatory response), in hematopoiesis (enhancing hematopoietic stem cell self-renewal, progenitor cells differentiation or maintaining the bone marrow microenvironment homeostasis), and in bone remodeling (where this pathway seems to have controversial effects on bone formation or osteoclast activation). Moreover, in this review is shown the involvement of RAR genes in multiple chromosomal rearrangements generating different fusion genes in hematological neoplasms, with a particular focus on acute promyelocytic leukemia and its variant subtypes. The effect of different RARs fusion proteins on leukemic transformation, on patients’ outcome, and on therapy response is also discussed.
Collapse
|
32
|
Anelli L, Orsini P, Minervini A, Zagaria A, Coccaro N, Parciante E, Minervini C, Cumbo C, Tota G, Impera L, Ricco A, Attolico I, Mallano S, Conserva M, Specchia G, Albano F. PF653 TARGETED NEXT-GENERATION SEQUENCING IDENTIFIES NOVEL GENE VARIANTS IN JAK2V617F NEGATIVE PATIENTS WITH ERYTHROCYTOSIS AND JAK2 GGCC_46/1 HAPLOTYPE. Hemasphere 2019. [DOI: 10.1097/01.hs9.0000560896.90309.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
33
|
Orsini P, Impera L, Parciante E, Cumbo C, Minervini CF, Minervini A, Zagaria A, Anelli L, Coccaro N, Casieri P, Tota G, Brunetti C, Ricco A, Carluccio P, Specchia G, Albano F. Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies. Diagn Pathol 2018; 13:98. [PMID: 30579366 PMCID: PMC6303857 DOI: 10.1186/s13000-018-0777-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/10/2018] [Indexed: 12/14/2022] Open
Abstract
Background Alu repeats, belonging to the Short Interspersed Repetitive Elements (SINEs) class, contain about 25% of CpG sites in the human genome. Alu sequences lie in gene-rich regions, so their methylation is an important transcriptional regulation mechanism. Aberrant Alu methylation has been associated with tumor aggressiveness, and also previously discussed in hematological malignancies, by applying different approaches. Moreover, today different techniques designed to measure global DNA methylation are focused on the methylation level of specific repeat elements. In this work we propose a new method of investigating Alu differential methylation, based on droplet digital PCR (ddPCR) technology. Methods Forty-six patients with hematological neoplasms were included in the study: 30 patients affected by chronic lymphocytic leukemia, 7 patients with myelodysplastic syndromes at intermediate/high risk, according with the International Prognostic Scoring System, and 9 patients with myelomonocytic leukemia. Ten healthy donors were included as controls. Acute promyelocytic leukemia-derived NB4 cell line, either untreated or treated with decitabine (DEC) hypomethylating agent, was also analyzed. DNA samples were investigated for Alu methylation level by digestion of genomic DNA with isoschizomers with differential sensitivity to DNA methylation, followed by ddPCR. Results Using ddPCR, a significant decrease of the global Alu methylation level in DNA extracted from NB4 cells treated with DEC, as compared to untreated cells, was observed. Moreover, comparing the global Alu methylation levels at diagnosis and after azacytidine (AZA) treatment in MDS patients, a statistically significant decrease of Alu sequences methylation after therapy as compared to diagnosis was evident. We also observed a significant decrease of the Alu methylation level in CLL patients compared to HD, and, finally, for CMML patients, a decrease of Alu sequences methylation was observed in patients harboring the SRSF2 hotspot gene mutation c.284C>D. Conclusions In our work, we propose a method to investigate Alu differential methylation based on ddPCR technology. This assay introduces ddPCR as a more sensitive and immediate technique for Alu methylation analysis. To date, this is the first application of ddPCR to study DNA repetitive elements. This approach may be useful to profile patients affected by hematologic malignancies for diagnostic/prognostic purpose. Electronic supplementary material The online version of this article (10.1186/s13000-018-0777-x) contains supplementary material, which is available to authorized users.
Collapse
|
34
|
Coccaro N, Zagaria A, Orsini P, Anelli L, Tota G, Casieri P, Impera L, Minervini A, Minervini CF, Cumbo C, Parciante E, Mestice A, Delia M, Brunetti C, Specchia G, Albano F. RARA and RARG gene downregulation associated with EZH2 mutation in acute promyelocytic-like morphology leukemia. Hum Pathol 2018; 80:82-86. [PMID: 29530751 DOI: 10.1016/j.humpath.2018.02.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/15/2018] [Accepted: 02/21/2018] [Indexed: 12/17/2022]
Abstract
Most acute promyelocytic leukemia (APL) patients express PML-RARA fusion; in rare cases, RARA is rearranged with partner genes other than PML. To date, only 2 patients presenting features similar to APL showing the RARG gene rearrangement have been described. We report an acute myeloid leukemia patient with morphology resembling APL without involvement of the RARA gene. Molecular and fluorescent in situ hybridization analyses excluded PML-RARA fusion and variant rearrangements involving RARA and RARG loci. Targeted next-generation sequencing showed EZH2- D185H mutation. As this mutation involved the region of interaction with DNA methyltransferases, we speculate an epigenetic alteration of genes involved in the APL-like phenotype. Expression analysis by droplet digital polymerase chain reaction revealed downregulation of the RARA and RARG genes. We hypothesize a novel mechanism of EZH2 function alteration, which may be responsible for an acute myeloid leukemia with APL-like phenotype featuring dysregulation of the RARA and RARG genes.
Collapse
|
35
|
Coccaro N, Anelli L, Zagaria A, Casieri P, Tota G, Orsini P, Impera L, Minervini A, Minervini CF, Cumbo C, Parciante E, Carluccio P, Brunetti C, Specchia G, Albano F. Droplet Digital PCR Is a Robust Tool for Monitoring Minimal Residual Disease in Adult Philadelphia-Positive Acute Lymphoblastic Leukemia. J Mol Diagn 2018; 20:474-482. [DOI: 10.1016/j.jmoldx.2018.03.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/13/2018] [Accepted: 03/09/2018] [Indexed: 12/16/2022] Open
|
36
|
Coccaro N, Tota G, Zagaria A, Anelli L, Casieri P, Impera L, Minervini A, Minervini CF, Orsini P, Cumbo C, Parciante E, Delia M, Brunetti C, Specchia G, Albano F. Monitoring minimal residual disease by ddPCR in acute lymphoblastic leukemia associated with the FGFR1 gene rearrangement. Int J Lab Hematol 2018; 40:e117-e120. [DOI: 10.1111/ijlh.12879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
37
|
Anelli L, Zagaria A, Specchia G, Albano F. The JAK2 GGCC (46/1) Haplotype in Myeloproliferative Neoplasms: Causal or Random? Int J Mol Sci 2018; 19:ijms19041152. [PMID: 29641446 PMCID: PMC5979434 DOI: 10.3390/ijms19041152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 12/11/2022] Open
Abstract
The germline JAK2 haplotype known as “GGCC or 46/1 haplotype” (haplotypeGGCC_46/1) consists of a combination of single nucleotide polymorphisms (SNPs) mapping in a region of about 250 kb, extending from the JAK2 intron 10 to the Insulin-like 4 (INLS4) gene. Four main SNPs (rs3780367, rs10974944, rs12343867, and rs1159782) generating a “GGCC” combination are more frequently indicated to represent the JAK2 haplotype. These SNPs are inherited together and are frequently associated with the onset of myeloproliferative neoplasms (MPN) positive for both JAK2 V617 and exon 12 mutations. The association between the JAK2 haplotypeGGCC_46/1 and mutations in other genes, such as thrombopoietin receptor (MPL) and calreticulin (CALR), or the association with triple negative MPN, is still controversial. This review provides an overview of the frequency and the role of the JAK2 haplotypeGGCC_46/1 in the pathogenesis of different myeloid neoplasms and describes the hypothetical mechanisms at the basis of the association with JAK2 gene mutations. Moreover, possible clinical implications are discussed, as different papers reported contrasting data about the correlation between the JAK2 haplotypeGGCC_46/1 and blood cell count, survival, or disease progression.
Collapse
|
38
|
Minervini A, Francesco Minervini C, Anelli L, Zagaria A, Casieri P, Coccaro N, Cumbo C, Tota G, Impera L, Orsini P, Brunetti C, Giordano A, Specchia G, Albano F. Droplet digital PCR analysis of NOTCH1 gene mutations in chronic lymphocytic leukemia. Oncotarget 2018; 7:86469-86479. [PMID: 27835908 PMCID: PMC5349927 DOI: 10.18632/oncotarget.13246] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 10/28/2016] [Indexed: 11/25/2022] Open
Abstract
In chronic lymphocytic leukemia (CLL), NOTCH1 gene mutations (NOTCH1mut) have been associated with adverse prognostic features but the independence of these as a prognostic factor is still controversial. In our study we validated a c.7541-7542delCT NOTCH1 mutation assay based on droplet digital PCR (ddPCR); we also analyzed the NOTCH1mut allelic burden, expressed as fractional abundance (FA), in 88 CLL patients at diagnosis to assess its prognostic role and made a longitudinal ddPCR analysis in 10 cases harboring NOTCH1mut to verify the FA variation over time. Our data revealed that with the ddPCR approach the incidence of NOTCH1mut in CLL was much higher (53.4%) than expected. However, longitudinal ddPCR analysis of CLL cases showed a statistically significant reduction of the NOTCH1mut FA detected at diagnosis after treatment (median FA 11.67 % vs 0.09 %, respectively, p = 0.01); the same difference, in terms of NOTCH1mut FA, was observed in the relapsed cases compared to the NOTCH1mut allelic fraction observed in patients in complete or partial remission (median FA 4.75% vs 0.43%, respectively, p = 0.007). Our study demonstrated a much higher incidence of NOTCH1mut in CLL than has previously been reported, and showed that the NOTCH1mut allelic burden evaluation by ddPCR might identify patients in need of a closer clinical follow-up during the “watch and wait” interval and after standard chemotherapy.
Collapse
|
39
|
Cumbo C, Impera L, Minervini CF, Orsini P, Anelli L, Zagaria A, Coccaro N, Tota G, Minervini A, Casieri P, Brunetti C, Rossi AR, Parciante E, Specchia G, Albano F. Genomic BCR-ABL1 breakpoint characterization by a multi-strategy approach for "personalized monitoring" of residual disease in chronic myeloid leukemia patients. Oncotarget 2018. [PMID: 29541390 PMCID: PMC5834283 DOI: 10.18632/oncotarget.23971] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
For monitoring minimal residual disease (MRD) in chronic myeloid leukemia (CML) the most recommended method is quantitative RT-PCR (RT-qPCR) for measuring BCR-ABL1 transcripts. Several studies reported that a DNA-based assay enhances the sensitivity of detection of the BCR-ABL1 genomic rearrangement, even if its characterization results difficult. We developed a DNA-based method for detecting and quantifying residual BCR-ABL1 positive leukemic stem cells in CML patients. We propose two alternative approaches: the first one is a fluorescence in situ hybridization (FISH)-based step followed by Sanger sequencing; the second one employs MinION, a single molecule sequencer based on nanopore technology. Finally, after defining the BCR-ABL1 genomic junction, we performed the target CML patient–specific quantification, using droplet digital PCR (ddPCR). FISH and MinION steps, respectively, together with ddPCR analysis, greatly reduce the complexity that has impeded the use of “personalized monitoring” of CML in clinical practice. Our report suggests a feasible pipeline, in terms of costs and reproducibility, aimed at characterizing and quantifying the genomic BCR-ABL1 rearrangement during MRD monitoring in CML patients.
Collapse
|
40
|
Brunetti C, Anelli L, Zagaria A, Specchia G, Albano F. CPX-351 in acute myeloid leukemia: can a new formulation maximize the efficacy of old compounds? Expert Rev Hematol 2017; 10:853-862. [DOI: 10.1080/17474086.2017.1369400] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
41
|
Zagaria A, Anelli L, Coccaro N, Tota G, Brunetti C, Minervini A, Casieri P, Impera L, Minervini CF, Giordano A, Orsini P, Cumbo C, Specchia G, Albano F. Systemic Mastocytosis with Associated Chronic Lymphocytic Leukemia: A Matter of Diseases or Prognostic Factors? Turk J Haematol 2017; 34:276-277. [PMID: 28351827 PMCID: PMC5544054 DOI: 10.4274/tjh.2017.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|
42
|
Minervini CF, Cumbo C, Orsini P, Anelli L, Zagaria A, Impera L, Coccaro N, Brunetti C, Minervini A, Casieri P, Tota G, Russo Rossi A, Specchia G, Albano F. Mutational analysis in BCR - ABL1 positive leukemia by deep sequencing based on nanopore MinION technology. Exp Mol Pathol 2017; 103:33-37. [DOI: 10.1016/j.yexmp.2017.06.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/22/2017] [Accepted: 06/25/2017] [Indexed: 01/11/2023]
|
43
|
Coccaro N, Brunetti C, Tota G, Pierri CL, Anelli L, Zagaria A, Casieri P, Impera L, Minervini CF, Minervini A, Cumbo C, Ricco A, Carluccio P, Orsini P, Specchia G, Albano F. A novel t(3;9)(q21.2; p24.3) associated with SMARCA2 and ZNF148 genes rearrangement in myelodysplastic syndrome. Leuk Lymphoma 2017; 59:996-999. [DOI: 10.1080/10428194.2017.1352093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
44
|
Brunetti C, Anelli L, Zagaria A, Minervini A, Minervini CF, Casieri P, Coccaro N, Cumbo C, Tota G, Impera L, Orsini P, Specchia G, Albano F. Droplet Digital PCR Is a Reliable Tool for Monitoring Minimal Residual Disease in Acute Promyelocytic Leukemia. J Mol Diagn 2017; 19:437-444. [DOI: 10.1016/j.jmoldx.2017.01.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/21/2016] [Accepted: 01/09/2017] [Indexed: 12/29/2022] Open
|
45
|
Anelli L, Pasciolla C, Zagaria A, Specchia G, Albano F. Monosomal karyotype in myeloid neoplasias: a literature review. Onco Targets Ther 2017; 10:2163-2171. [PMID: 28461756 PMCID: PMC5404799 DOI: 10.2147/ott.s133937] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In 2008, the concept of the monosomal karyotype (MK) in adult acute myeloid leukemia (AML) patients was introduced, defined by the presence of a chromosomal aberration pattern characterized by the presence of at least two autosomal monosomies or of one monosomy plus one or more structural aberrations (not including loss of a chromosome). We present a systematic review of the literature about the influence of the MK on the outcome of patients affected by myeloid malignancies (AML, myelodysplastic syndromes, and primary myelofibrosis). For this review, a comprehensive literature search using the term “monosomal karyotype” was performed, considering articles listed in MEDLINE. This analysis of the literature confirms the negative prognostic impact on survival of the MK in myeloid neoplasias. The detrimental effect of MK on AML patients’ outcome is independent of other variables, including adverse cytogenetic features, supporting the identification of this entity as a challenging subgroup of patients with distinct biologic and clinical features.
Collapse
|
46
|
Coccaro N, Tota G, Zagaria A, Anelli L, Specchia G, Albano F. SETBP1 dysregulation in congenital disorders and myeloid neoplasms. Oncotarget 2017; 8:51920-51935. [PMID: 28881700 PMCID: PMC5584301 DOI: 10.18632/oncotarget.17231] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 03/30/2017] [Indexed: 01/19/2023] Open
Abstract
Myeloid malignancies are characterized by an extreme molecular heterogeneity, and many efforts have been made in the past decades to clarify the mechanisms underlying their pathogenesis. In this scenario SET binding protein 1 (SETBP1) has attracted a lot of interest as a new oncogene and potential marker, in addition to its involvement in the Schinzel-Giedon syndrome (SGS). Our review starts with the analysis of the structural characteristics of SETBP1, and extends to its corresponding physiological and pathological functions. Next, we describe the prevalence of SETBP1 mutations in congenital diseases and in hematologic malignancies, exploring how its alterations might contribute to tumor development and provoke clinical effects. Finally, we consider to understand how SETBP1 activation could be exploited in molecular medicine to enhance the cure rate.
Collapse
|
47
|
Minervini CF, Cumbo C, Orsini P, Brunetti C, Anelli L, Zagaria A, Minervini A, Casieri P, Coccaro N, Tota G, Impera L, Giordano A, Specchia G, Albano F. TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing. Diagn Pathol 2016; 11:96. [PMID: 27724982 PMCID: PMC5057401 DOI: 10.1186/s13000-016-0550-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/07/2016] [Indexed: 01/26/2023] Open
Abstract
Background The assessment of TP53 mutational status is becoming a routine clinical practice for chronic lymphocytic leukemia patients (CLL). A broad spectrum of molecular techniques has been employed so far, including both direct Sanger sequencing and next generation sequencing. Oxford Nanopore Technologies recently released the MinION an USB-interfaced sequencer. In this paper we report our experience, with the MinION technology for the detection of the TP53 gene mutation in CLL patients. Twelve CLL patients at diagnosis were included in this study. All except one patient showed the TP53 gene deletion in Fluorescence in situ hybridization experiments. Patients were investigated for TP53 mutation by Sanger and by MinION sequencing. Analysis by Sanger was performed according with the IARC protocol. Analysis by MinION was performed adopting a strategy based on long template PCR, read error correction, and post variant calling filtering. Results Due to the high error rate of nanopore technology, sequence data were both used directly and before correction with two different in silico methods: ALEC and nanocorrect. A mean error rate of 15 % was detected before correction that was reduced to 4-5 % after correction. Analysis by Sanger sequencing was able to detect four patients mutated for TP53. MinION analysis detected one more mutated patient previously not detected from Sanger. Conclusion In our hands, the Nanopore technology shows correlation with Sanger sequencing but more sensitive, manageable and less expensive, and therefore has proven to be a useful tool for TP53 gene mutation detection. Electronic supplementary material The online version of this article (doi:10.1186/s13000-016-0550-y) contains supplementary material, which is available to authorized users.
Collapse
|
48
|
Anelli L, Zagaria A, Coccaro N, Tota G, Minervini A, Casieri P, Impera L, Minervini CF, Brunetti C, Ricco A, Orsini P, Cumbo C, Specchia G, Albano F. Droplet digital PCR assay for quantifying of CALR mutant allelic burden in myeloproliferative neoplasms. Ann Hematol 2016; 95:1559-60. [PMID: 27365140 DOI: 10.1007/s00277-016-2739-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/16/2016] [Indexed: 10/21/2022]
|
49
|
Coccaro N, Tota G, Anelli L, Zagaria A, Casieri P, Cellamare A, Minervini CF, Minervini A, Cumbo C, Impera L, Brunetti C, Orsini P, Parciante E, Mestice A, Specchia G, Albano F. MYEOV gene overexpression in primary plasma cell leukemia with t(11;14)(q13;q32). Oncol Lett 2016; 12:1460-1464. [PMID: 27446453 DOI: 10.3892/ol.2016.4759] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/26/2016] [Indexed: 12/25/2022] Open
Abstract
Primary plasma cell leukemia (pPCL) is an uncommon form of plasma cell dyscrasia, and the most aggressive of the human monoclonal gammopathies. The t(11;14)(q13;q32) rearrangement is the most common alteration in pPCL, promoting cyclin D1 (CCND1) gene overexpression caused by its juxtaposition with the immunoglobulin heavy locus chromosome region. The myeloma overexpressed (MYEOV) gene maps very close to the CCND1 gene on chromosome 11, but its overexpression is rarely observed in multiple myeloma. The present study describes a case of pPCL with t(11;14) characterized by a breakpoint on der(11), unlike the one usually observed. Droplet digital polymerase chain reaction analysis revealed overexpression of CCND1 and MYEOV. To the best of our knowledge, MYEOV gene overexpression has never been previously described in pPCL.
Collapse
|
50
|
Albano F, Zagaria A, Anelli L, Coccaro N, Tota G, Brunetti C, Minervini CF, Impera L, Minervini A, Cellamare A, Orsini P, Cumbo C, Casieri P, Specchia G. Absolute quantification of the pretreatment PML-RARA transcript defines the relapse risk in acute promyelocytic leukemia. Oncotarget 2016; 6:13269-77. [PMID: 25944686 PMCID: PMC4537013 DOI: 10.18632/oncotarget.3773] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/06/2015] [Indexed: 12/05/2022] Open
Abstract
In this study we performed absolute quantification of the PML-RARA transcript by droplet digital polymerase chain reaction (ddPCR) in 76 newly diagnosed acute promyelocytic leukemia (APL) cases to verify the prognostic impact of the PML-RARA initial molecular burden. ddPCR analysis revealed that the amount of PML-RARA transcript at diagnosis in the group of patients who relapsed was higher than in that with continuous complete remission (CCR) (272 vs 89.2 PML-RARA copies/ng, p = 0.0004, respectively). Receiver operating characteristic analysis detected the optimal PML-RARA concentration threshold as 209.6 PML-RARA/ng (AUC 0.78; p < 0.0001) for discriminating between outcomes (CCR versus relapse). Among the 67 APL cases who achieved complete remission after the induction treatment, those with >209.6 PML-RARA/ng had a worse relapse-free survival (p = 0.0006). At 5-year follow-up, patients with >209.6 PML-RARA/ng had a cumulative incidence of relapse of 50.3% whereas 7.5% of the patients with suffered a relapse (p < 0.0001). Multivariate analysis identified the amount of PML-RARA before induction treatment as the sole independent prognostic factor for APL relapse. Our results show that the pretreatment PML-RARA molecular burden could therefore be used to improve risk stratification in order to develop more individualized treatment regimens for high-risk APL cases.
Collapse
|