Results of Conventional Cytogenetics and Interphase FISH (I-FISH) Analyses in Patients with a Clinical and Morphologic Diagnosis of CML: Analysis of 52 Cases.

Abstract The presence of the Philadelphia chromosome (Ph), derived from a balanced translocation between chromosomes 9q and 22q, serves as a hallmark for the diagnosis of CML or Ph-positive ALL. In recent years, I-FISH has become the method of choice to detect Ph-positive clones at diagnosis and during treatment. In addition, I-FISH analysis is also able to identify variant translocations and loss of DNA sequences, some of which are known to be predictors of poor clinical outcome. To determine the contribution of I-FISH in detecting genetic alterations at diagnosis and during therapy, we summarized our experience in a series of patients with CML and Ph+ ALL studied in a single institution between 2000–2004. A total of 52 patients had both cytogenetic and I-FISH analyses available for review. The 52 patients included 30 patients in chronic phase, 10 patients in accelerated phase, 9 patients in blastic phase, and 3 patients with acute lymphoblastic leukemia (ALL). Sixteen of the 52 patients had newly diagnosed CML, and the remaining 36 patients had studies performed while on imatinib. Conventional cytogenetics detected the Ph-chromosome in 44 patients (85%), whereas I-FISH detected Ph chromosome positivity in all 52 patients (100%). In three of the 16 patients with newly diagnosed disease, I-FISH identified variant translocations in the setting of a normal karyotype. Two of these 3 patients were found to be RT-PCR negative for bcr/abl transcripts. Nineteen of 52 patients (37%) had additional abnormalities detected by karyotype. Nine of these 19 patients (47%) had more than one additional cytogenetic abnormality. The most common abnormalities in the Ph+ clone included: 6 patients with 2 copies of the Ph chromosome, 4 patients with trisomy 21, 2 patients with deletion (20q), 2 patients with isochromosome 17, and 2 patients with trisomy 8. Independent clones with trisomy 8 were noted in an additional 2 patients on imatinib therapy. A total of 12 of the 52 patients (23%) had variant signal patterns by I-FISH; loss of DNA sequences on chromosomes 9 and 22 occurred in 4 and 3 cases respectively and a variant signal pattern involving additional chromosomes was seen in 5 patients. While in general we found a good correlation between the proportion of Ph-positive cells detected by conventional cytogenetics and I-FISH, differences between the two types of analyses were observed in 8 patients. Six patients had a normal karyotype (20 cells analyzed) with positive I-FISH analysis (range 3.2–99%). Two of the 8 patients had a small percentage of Ph-positive metaphases with negative I-FISH. These results underscore the significance of utilizing both conventional cytogenetics and I-FISH in CML patients at diagnosis as well as during therapy. The biologic and clinical implications of the disparity between conventional cytogenetics, I-FISH, and in some cases RT-PCR results are not yet fully realized.

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Myelodysplastic Syndromes: A Multidisciplinary Integrated Diagnostic Work-up for Patients' Risk Stratification

Blood ◽

10.1182/blood.v124.21.5579.5579 ◽

2014 ◽

Vol 124 (21) ◽

pp. 5579-5579

Author(s):

Elena Ciabatti ◽

Maria Immacolata Ferreri ◽

Angelo Valetto ◽

Alice Guazzelli ◽

Veronica Bertini ◽

...

Keyword(s):

Myelodysplastic Syndromes ◽

Mutational Analysis ◽

Conflicts Of Interest ◽

Normal Karyotype ◽

Diagnostic Workup ◽

Fish Analysis ◽

Rt Pcr ◽

Risk Scoring ◽

Conventional Cytogenetics ◽

Work Up

Abstract Conventional cytogenetics continues to have a fundamental role in the classification and risk scoring of myelodysplastic syndromes (MDS). Nevertheless, non-informative karyotypes represent up to 20% of cases. Some different molecular methods, not included in the routinary diagnostic workup, such as aCGH or mutational analysis, could be able to detect new abnormalities and improve the subtyping of MDS. The aim of this study was to propose a new diagnostic workup to determine the eventual adjunctive value offered by FISH, aCGH, and somatic mutation assays in respect of the the conventional cytogenetics only. In this study, we analyzed 50 patients: 29% female and 71% male, median age 71 (range 30-88 years), 66% at low/int1 IPSS risk, 54% at very-low/low R-IPSS risk, 33% with RCMD, 15% with RA, 14% with RARS, 14% with RAEB, 8% 5q-, and 16% with MMCL. We assessed these new MDS cases by different techniques: i) conventional cytogenetics; ii) FISH for chromosome 5, 7, PDGFRa, and PDGFRb; iii) aCGH, and iiii) specific RT-PCR for ASXL1, EZH2, TP53, and TET2 mutations. Conventional cytogenetics showed 42% of patients with at least one chromosomal aberration, including +8, del(11), del(7), del(5), -Y, +6, del(13), +14, del(20), and complex karyotypes (6% of cases). After FISH analysis, we were able to correctly classify as affected by the 5q- syndrome 2 cases who then received lenalidomide. The aGCH allowed to detect quantitative chromosomal aberrations in 44% of cases (del(13), -7, del(12), del(16), del(17), del(11), del(8), dupl(14), 5q-), including 10 cases (20%) showing a normal karyotype. After the RT-PCR, 32% of patients resulted mutated, with highest frequency for TP53 (22%). Four of these TP53-mutated patients showed normal karyotype, and resulted unmutated also by FISH and aCGH; in a case TP53 mutated we added treatment with steroid. Other 3 patients TP53-mutated did not respond to azacitidine Four low-risk patients (8%) showed ASXL1 gene mutation, three of them not earlier detected by cytogenetics or aCGH. One of these patients died after progression into acute leukemia. The identification of TP53 or ASXL1 mutations after RT-PCR and of dupl(14) by the aCGH prompted us to strictly follow patients at high risk of transformation. Only one case showed TET2 mutation; although TET2 mutations have been related to a better survival in patients receiving 5-azacitidine, this patient resulted not-responsive after 9 cycles. In conclusion, these results sustain the necessity of an integrated work-up for the diagnosis and the correct risk scoring of MDS patients. Disclosures No relevant conflicts of interest to declare.

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Next Generation Cytogenetics in Myeloid Hematological Neoplasms: Detection of CNVs and Translocations

Cancers ◽

10.3390/cancers13123001 ◽

2021 ◽

Vol 13 (12) ◽

pp. 3001

Author(s):

María Chicano ◽

Diego Carbonell ◽

Julia Suárez-González ◽

Sergio Lois ◽

Mercedes Ballesteros-Culebras ◽

...

Keyword(s):

Mutational Analysis ◽

Lymphoblastic Leukemia ◽

Copy Number Variations ◽

Next Generation ◽

Trisomy 8 ◽

Chromosomal Alterations ◽

Hematological Neoplasms ◽

Myeloid Neoplasm ◽

Myeloid Neoplasms ◽

Conventional Cytogenetics

Conventional cytogenetics are the gold standard for the identification of chromosomal alterations recurrent in myeloid neoplasms. Some next-generation sequencing (NGS) panels are designed for the detection of copy number variations (CNV) or translocations; however, their use is far from being widespread. Here we report on the results of a commercial panel including frequent mutations, CNVs and translocations in myeloid neoplasms. Frequent chromosomal alterations were analyzed by NGS in 135 patients with myeloid neoplasms and three with acute lymphoblastic leukemia. NGS analysis was performed using the enrichment-capture Myeloid Neoplasm-GeneSGKit (Sistemas Genómicos, Spain) gene panel including 35 genes for mutational analysis and frequent CNVs and translocations. NGS results were validated with cytogenetics and/or MLPA when possible. A total of 66 frequent alterations included in NGS panel were detected, 48 of them detected by NGS and cytogenetics. Ten of them were observed only by cytogenetics (mainly trisomy 8), and another eight only by NGS (mainly deletion of 12p). Aside from this, 38 secondary CNVs were detected in any of the genes included mainly for mutational analysis. NGS represents a reliable complementary source of information for the analysis of CNVs and translocations. Moreover, NGS could be a useful tool for the detection of alterations not observed by conventional cytogenetics.

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CKS1B Over-Expression Significantly Predicts for a Lower Rate of Response to Primary Therapy with Thalidomide-Dexamethasone (Thali-Dex) for Newly Diagnosed Multiple Myeloma (MM) Patients.

Blood ◽

10.1182/blood.v108.11.371.371 ◽

2006 ◽

Vol 108 (11) ◽

pp. 371-371

Author(s):

Matteo Renzulli ◽

C. Terragna ◽

N. Testoni ◽

E. Montanari ◽

P. Tosi ◽

...

Keyword(s):

Response To Therapy ◽

Remission Induction ◽

Lower Probability ◽

High Dose ◽

Fish Analysis ◽

Primary Therapy ◽

Newly Diagnosed ◽

Rt Pcr ◽

Over Expression ◽

The Relationship

Abstract In MM tandem duplication and jumping translocations of the q21 band of chromosome (chr.) 1 are acquired during progression of the disease and can lead to chr.1q amplification. In several studies, chr. 1 amplification has been linked to poor prognosis after both conventional and high-dose chemotherapy. Recently, a subset of genes mapping on 1q21 band has been identified, whose increased expression may be due to increased DNA copy number. Among these genes, CKS1B has been one of the most significantly upregulated. CKS1B regulates SCF skp2 mediated ubiquitination and proteolysis of the cyclin dependent kinase inhibitor p27Kip1, whose low expression has been reported to be an independent adverse prognostic factor in MM patients. Aim of the present study was to investigate the relationship between CKS1B expression and response to primary therapy with thali-dex in a large series of patients with newly diagnosed MM. Secondary endpoint was to explore the relationship between CKS1B expression and del(13), as assessed by FISH analysis, and t(4;14), as evaluated by an RT-PCR assay designed to detect the presence of IgH/MMSET fusion gene. A total of 132 patients were analyzed. The presence of t(4;14) and CKS1B expression were investigated in all patients, while del(13) was studied in 129/132 patients. CKS1B expression was evaluated by Real-time RT-PCR. CKS1B values were separated in four different quartiles, with expression levels increasing progressively from quartile 1 to 4. Response to therapy was evaluated according to the criteria proposed by Bladè et al. The Fisher test and the Mann-Whitney test were applied for statistical analysis. On an intent-to-treat basis, the overall probability to respond (≥ partial response, PR) to up-front thali-dex therapy was 71%, while 38 patients (29%) either did not respond (NR) or progressed. Median CKS1B expression value was significantly higher in NR in comparison with patients who attained at least a PR: 1.42 (range 0.15–52.35) vs. 0.89 (range 0–11.88), respectively (p=0.01). In particular, the proportion of NR patients in the CKS1B expression quartile 4 was significantly higher as opposed to the frequency of NR in the CKS1B expression quartiles 1 to 3 (45.5% vs. 23.2%, respectively; p= 0.02). CKS1B over expression did not correlate with the presence of t(4;14) or del(13). Only 6 patients harbouring t(4;14) fell into the CKS1B expression quartile 4, as opposed to 32 patients included into the CKS1B expression quartiles 1–3 (18.2% vs. 32.3%; p, not significant). Similarly, the frequency of del(13) was comparable in the CKS1B expression quartile 4 and in the CKS1B expression quartiles 1–3 (34.4% vs. 44.3%; p, not significant). Likewise, only 2 patients carrying both t(4;14) and del(13) fell into the CKS1B expression quartile 4, as opposed to 15 patients who fell into the CKS1B expression quartiles 1–3 (6.5% vs. 15.3%; p, not significant). In conclusion, in patients with newly diagnosed MM, CKS1B over expression at baseline predicts for a significantly lower probability of response to primary remission induction therapy with thali-dex. Poor response to thali-dex conferred by CKS1B over expression is independent from the presence of t(4;14) and/or del(13). Supported by Università di Bologna, Progetti di Ricerca ex-60% (M.C.); Ministero dell’Università e Ricerca Scientifica (MIUR), progetto FIRB, RBAU012E9A_001 (M.C.); and Fondazione Carisbo.

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Two Distinct Subsets of dic(9;12)(p12;p11.2) among Children with B-Cell Precursor Acute Lymphoblastic Leukemia (ALL): PAX5-ETV6 and ETV6-RUNX1 Rearrangements: A Report from the Children’s Oncology Group.

Blood ◽

10.1182/blood.v110.11.1439.1439 ◽

2007 ◽

Vol 110 (11) ◽

pp. 1439-1439 ◽

Cited By ~ 1

Author(s):

Julie M. Gastier-Foster ◽

Andrew J. Carroll ◽

Denise Ell ◽

Richard Harvey ◽

I-Ming Chen ◽

...

Keyword(s):

B Cell ◽

Gene Rearrangement ◽

Fusion Gene ◽

Lymphoblastic Leukemia ◽

Cytogenetic Abnormality ◽

Fish Analysis ◽

Oncology Group ◽

Rt Pcr ◽

Cell Precursor ◽

Pediatric All

Abstract The dic(9;12)(p12;p11.2) has been described as a rare cytogenetic abnormality in pediatric precursor B-cell ALL. Initial studies suggested that the rearrangement is associated with a favorable outcome, and recent studies demonstrated the presence of a PAX5-ETV6 fusion gene was associated with this cytogenetic abnormality. Twenty cases with a cytogenetic dic(9;12) were identified in the Children’s Oncology Group (COG) cytogenetics databases. FISH analysis with the ETV6-RUNX1 (TEL-AML1) probes was done on 12 of these samples. Five cases were positive for fusion, indicating a cryptic t(12;21)(p13;q22), and also had loss of the ETV6 probe from the chromosome 12 not involved in the t(12;21). Seven cases were negative for fusion and had loss of an ETV6 signal, although one of the latter had a diminished ETV6 signal identified. To determine whether both PAX5-ETV6 and ETV6-RUNX1 rearrangements occurred in some patients, a diagnostic sample from each patient was analyzed by RT-PCR for the PAX5-ETV6 and ETV6-RUNX1 fusion genes. Primers from exon 3 of PAX5 and exon 3 of ETV6 were used for the PAX5-ETV6 analysis and from exon 5 of ETV6 and exon 4 of RUNX1 for the ETV6-RUNX1 analysis. Of the 20 cases, only 8 were RT-PCR positive for the PAX5-ETV6 fusion with the above primers; however, an additional 2 were RT-PCR positive with alternate primers, and all 10 of these were negative for the ETV6-RUNX1 fusion by RT-PCR. Of the remaining 10 patients, 9 were RT-PCR positive for the ETV6-RUNX1 fusion, including all of the ETV6-RUNX1 cases positive by FISH. The gene rearrangement associated with the dic(9;12) in these cases is not known. One patient was negative for both fusions by RT-PCR, negative by FISH for ETV6-RUNX1 rearrangement, yet had loss of an ETV6 signal. No cytogenetic differences could be seen between the 2 groups, either in the appearance of the dic(9;12) or in the other abnormalities identified. These results demonstrate the presence of two mutually exclusive dic(9;12) rearrangements in pediatric ALL; one associated with ETV6-RUNX1 rearrangement and one resulting in PAX5-ETV6 fusion. Both PAX5-ETV6 and ETV6-RUNX1 rearrangements are associated with a favorable prognosis. However, molecular analysis of the dic(9;12) patients must be performed to determine whether the dicentric chromosome results in PAX5-ETV6 fusion or whether the case has ETV6-RUNX1 fusion.

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Correlation between Immunoglobulin Gene Rearrangements and Chromosomal Abnormalities in Multiple Myeloma.

Blood ◽

10.1182/blood.v110.11.4771.4771 ◽

2007 ◽

Vol 110 (11) ◽

pp. 4771-4771

Author(s):

Giovanna Piras ◽

Maria Monne ◽

Antonella Uras ◽

Laura Pilo ◽

Luciana Arca ◽

...

Keyword(s):

Multiple Myeloma ◽

Chromosomal Abnormalities ◽

Normal Karyotype ◽

Fish Analysis ◽

Immunoglobulin Gene ◽

Cytogenetic Aberrations ◽

Oncogenic Pathways ◽

Clonality Analysis ◽

Conventional Cytogenetics ◽

Clonogenic Cell

Abstract Background: Multiple Myeloma (MM) is characterized by frequent and complex genetic abnormalities that contribute to the pathogenesis and its prognostic eterogeneity. There is evidence for two oncogenic pathways in the early development of clonal plasma cell disorder: i) non-hyperdiploid carring translocation of the immunoglobulin heavy-chain locus and various oncogenes ii) hyperdiploid tumors with infrequent IgH translocation. The MM clonogenic cell is positively selected during the development and reaction of the germinal center. The immunoglobulin gene (IG) repertoire in MM follows a pattern similar to that of the normal repertoire. However, available data from analysis of IGH and IGK/L genes according to cytogenetic aberrations are limited. In the present study we investigated the frequency and characteristics of IGK and incomplete DJH as well as complete VDJH rearrangements in parallel with chromosomal abnormalities in a series of untreated MM patients. Materials and Methods. Bone marrow aspirates were collected from 53 MM patients with a mean age of 69.6 (range 48–84) between 2003–2007. The serum monoclonal component was IgG and IgA in the 77% and 22% patients respectively; 1 patient presented with IgD k MM. Cytogenetics and FISH analysis were performed simultaneously in 37 MM. In 18 (50.5%) samples kariotype analysis was successful. Interphase FISH analysis was perfomed using a set of probes specific for RB-1 (13q14), D13S319 (13q14.3), IgH (14q32), and p53 (17p13.1) loci, t(4;14), t(14;16), t(11;14) and a multicolor probe set for detection of aneuploidy (Vysis, Downers Grove, IL, USA). Genomic DNA was isolated for clonality analysis. IGHV-J, IGHD-J, IGKV-J, IGKV-KDE, IGKJ-C-INTRON-KDE rearrangements were amplified by PCR and analyzed following the BIOMED-2 protocol. Results: Conventional cytogenetics allowed to detect 16 patients with a normal kariotype, 1 hyperdiploid kariotype with monosomy 13, 1 hyperdiploid kariotype with 3q21 deletion. FISH panel analysis resulted in 4 patients with hyperdiploid kariotype and 7 with abnormalities for RB-1 and/or D13S319. IGH rearrangements were detected in 3 patients and the t (4;14) was found in 1 case. The p53 deletion, t(11;14) and t(14;16) were not detected. The overall detection rate of clonality by amplifying VDJH and DJH rearrangements using family-specific primers was 90%. We found a high frequency (71.7%) of DJH rearrangements with DH3 segment under represented (4%). The DH7 segment was rearranged in the 15% of MM. Incomplete DJH and complete VDJH rearrangements were present at frequencies of 20% and 29.5%, respectively. IGK locus rearrangements were detected in 38 out of 53 MM and the 60% presented the non-productive IGKV-KDE and IGKJ-C-INTRON-KDE rearrangements. Parallel analysis of clonality pattern and chromosomal abnormalities showed that complete VDJH rearrangements were present in all hyperdiploid MM and in a small proportion (4/16) of the MM with normal karyotype. Conclusions: Our results confirm previous estimations about IgH repertoire usage. Despite the small numbers, our findings indicate that complete Ig rearrangements might be correlated with hyperdiploid MM. Combining cytogenetics and IgH clonality studies might help to identify distinct subgroups of MM and provide a framework for dissection of disease prognosis and clinical management. Research funded by Regione Autonoma Sardegna.

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Detection of 13q14 Deletion by FISH Is Not Sufficient to Define a Group of Good Prognosis Patients with Chronic Lymphocytic Leukemia.

Blood ◽

10.1182/blood.v114.22.2332.2332 ◽

2009 ◽

Vol 114 (22) ◽

pp. 2332-2332

Author(s):

Virginie Eclache ◽

Vincent Levy ◽

Fanny Baran-Marszak ◽

Remi Letestu ◽

Florence Cymbalista

Keyword(s):

Prognostic Markers ◽

Prognostic Significance ◽

Genetic Alterations ◽

Large Cohort ◽

Fish Analysis ◽

Prognostic Impact ◽

Trisomy 12 ◽

Conventional Cytogenetics ◽

The Impact ◽

13Q Deletion

Abstract Abstract 2332 Poster Board II-309 Deletion of a 13q14.3 region is by far the most common genomic alteration in CLL. In a large cohort of CLL patients, the presence of deletion 13q as sole anomaly detected by FISH was predominantly found in Binet stage A CLL and associated with a favorable outcome (Dohner et al., N Engl J Med 2000). Further studies have evidenced some heterogeneity among CLL cases with 13q deletion, such as the size of the clone carrying the deletion, the existence of mono versus biallelic deletions, and the presence of other concomitant genetic aberrations. Therefore, we aimed at analysing the impact of this heterogeneity on the prognostic value of 13q14 deletion (del13q) in CLL. Patients and methods In a cohort of 329 previously untreated newly diagnosed stage A CLL, we detected del13q by FISH in 172 patients (52%) using the D13S319 probe. Conventional cytogenetics was performed in the 105 cases with del13q followed in our institution. The other important prognostic markers ( ZAP70, IgVH, CD38, proliferation markers) and clinical progression were also available for all patients. Results We first studied the large cohort of stage A patients and found that deletion 13q had no prognostic impact on PFS. When considering more specifically the presence of deletion 13q as sole anomaly (n=143), PFS was not significantly different from that of patients with no aberration detected by FISH analysis (del 13q, del11q, del17p and trisomy 12) (n=98). Moreover, the distribution of prognostic factors (ZAP70, sTK, mutational status, CD38 expression, lymphocytosis) was not statistically different among these two groups. We aimed at deciphering further these del13q cases through analysis of the percentage of deleted cells, the presence of mono versus biallelic deletions, and the presence of additional aberrations as detected by FISH and conventional cytogenetics in the 105 del13q cases followed in our institution. The size of the del13q clone, as reflected by the percentage of del13q cells by FISH, was highly variable, ranged from 7 to 90 %, and had no prognostic significance on PFS. Monoallelic deletions were present in 77 cases, fully biallelic deletions in 9 cases, and concomitant bi and monoallelic deletions in 19 cases. The 9 cases with biallelic deletions had a significantly shorter PFS and were associated with other unfavorable prognostic markers. As biallelic deletions are most likely to represent progression from monoallelic cases, it is understandable that no clear prognostic impact was evidenced between cases with monoallelic deletions and with concomitant variable amount of bi and monoallelic deleted cells. Twenty cases (20 monoallelic and 6 biallelic) were further studied by array-CGH. Minimal deleted region (MDR) was included in all deletions but the size of the deletion was variable and in most cases much larger than MDR. Among the 6 bi allelic cases, one of the deletions was restricted to the MDR in all cases, pointing out to the importance of the level of miRNA expression. Additional aberrations were found in 44/105 del13q cases. In 17 patients, one or more alterations were detected by FISH techniques : del11q (n=8), trisomy 12 (n=8) or del17p (n=5). By conventional cytogenetic all these aberrations were also detected, as well as other rare ones in 16 additional cases, either isolated or associated in a complex karyotype in 5 cases. Presence of additional aberrations had a significant unfavourable impact on PFS, even when excluding del11q, del17p and tri12, and considering the non recurrent aberrations that were detected by conventional cytogenetics only. Conclusion Presence of 13q deletion should not be considered as a good prognostic marker by itself among stage A patients. Moreover, del13q cases are highly heterogeneous, and the presence of deletion 13q should not be interpreted without considering both alleles or the presence of concomitant genetic alterations. Disclosures: No relevant conflicts of interest to declare.

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Bone Marrow Failure with 13q Deletion: A Distinct Clinicopathological Entity with Immune Pathophysiology,

Blood ◽

10.1182/blood.v118.21.3420.3420 ◽

2011 ◽

Vol 118 (21) ◽

pp. 3420-3420

Author(s):

Kohei Hosokawa ◽

Takamasa Katagiri ◽

Naomi Sugimori ◽

Ken Ishiyama ◽

Yumi Sasaki ◽

...

Keyword(s):

Bone Marrow ◽

Conflicts Of Interest ◽

Bone Marrow Failure ◽

Survival Rates ◽

Snp Array ◽

Normal Karyotype ◽

Genetic Alterations ◽

Fish Analysis ◽

Hematopoietic Stem ◽

Who 2008

Abstract Abstract 3420 Background: Numerical karyotypic abnormalities such as −7/del(7q) and del(13q) are occasionally seen in patients with bone marrow (BM) failure who do not have typical signs of myelodysplasia. The WHO 2008 defined this subset of BM failure as MDS-U because of its likely association with a risk of evolving into leukemia, while the presence of isolated abnormalities including +8, del(20q), and -Y was not considered to be presumptive evidence of MDS. Previous studies showed that BM failure patients with del(13q) responded to immunosuppressive therapy (IST) and had a favorable prognosis (Ishiyama K et al, Br J Haematol; 117: 747. 2002; Sloand, JCO 2010). However, the clinical features of del(13q) BM failure remain unclear due to its low incidence as well as the frequently associated karyotypic abnormalities. Objectives/Methods: To characterize the clinicopathological features of patients with BM failure with del(13q), this study reviewed the clinical data of 1705 BM failure patients (733 with AA, 286 with MDS-RCUD, 149 with RCMD, 60 with MDS-U) whose blood was examined for the presence of glycosylphosphatidyl-inositol anchored protein (GPI-AP)-deficient granulocytes and erythrocytes from May 1999 through July 2010. Genomic DNA was isolated from the peripheral blood cells of 7 patients with 13q- and was subjected to SNP array-based genome-wide analysis for genetic alterations using GeneChip® 250K arrays to identify the gene locus that is commonly deleted as a result of 13q-. Results: The 13q- clone was found in 25 (1.5%) of the 1705 patients. All the 13q- patients were classified as MDS-U, due to the absence of significant dysplasia to fulfill the criteria for MDS defined by the WHO 2008 classification. BM was hypocellular in 17 patients and normocellular in 6. Seventeen patients had a clone with 13q- alone, while the remaining 8 patients had a clone with 13q- and other numerical abnormalities including –Y, +mar in 2, and −20, del(7q), +8, der(1;7) in 1. A significant increase in the percentage of GPI-AP- granulocytes was detected in 366 (50%) of 733 patients with AA and 115 (23%) of 495 patients with MDS. GPI-AP- cells were detected in all (100%) of the 17 patients with 13q- alone. On the other hand, the prevalence of increased GPI-AP− cells in patients with 13q- plus other abnormalities and in those with the normal karyotype was 38% (3/8) and 43% (405/937), respectively. Fifteen patients with 13q- alone were treated with IST (ATG + cyclosporine in 6 and cyclosporine ± anabolic steroid in 9) and all of them achieved either a PR or a CR, while in the patients with 13q- plus other abnormalities, the response rate to IST was 40%. A total of 106 patients with the normal karyotype were treated with ATG+CsA (48) or CsA±AS (58) and the response rates were 73% and 85%, respectively. None of the 17 13q- patients progressed to advanced MDS or AML during the follow-up period of 3 to 108 months (median: 52 months) while 2 of 8 patients with 13q- plus other abnormalities developed AML. The 5-year overall survival rates of the patients with 13q-, those with 13q- plus other abnormalities, and patients with a normal karyotype were 84%, 45%, and 91%, respectively. The percentage of 13q- clones increased in 5 patients, and decreased in 3 patients after successful IST. When GPI-AP- and GPI-AP+ granulocytes were subjected to a FISH analysis using a 13q probe (13q14.3), the 13q- clones were detected only in of GPI-AP+ granulocytes, suggesting that 13q- cells are derived from non-PIG-A mutant HSCs. SNP arrays identified 13q13.3 to 13q14.3 regions in all cases. Conclusions: MDS-U with 13q- is a benign BM failure syndrome characterized by a good response to IST and a markedly high prevalence of GPI-AP cells. Patients with this type of BM failure may be inappropriately treated with hypomethylating agents or hematopoietic stem cell transplantation from unrelated donors, which is associated with high therapy-related mortality. Therefore, del(13q) should be eliminated from the intermediate prognosis group defined by the IPSS, and BM failure with del(13q) should be managed as idiopathic AA. Disclosures: No relevant conflicts of interest to declare.

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Novel Chromosomal Rearrangements and Sequence Mutations in High-Risk Ph-Like Acute Lymphoblastic Leukemia

Blood ◽

10.1182/blood.v118.21.67.67 ◽

2011 ◽

Vol 118 (21) ◽

pp. 67-67

Author(s):

Kathryn G. Roberts ◽

Ryan D Morin ◽

Jinghui Zhang ◽

Martin Hirst ◽

Richard C. Harvey ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

High Risk ◽

Lymphoblastic Leukemia ◽

Genetic Alterations ◽

Cytokine Receptor ◽

Negative Regulator ◽

Rna Seq ◽

Kinase Signaling ◽

Rt Pcr ◽

B Lineage

Abstract Abstract 67 Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy, and relapsed B-lineage ALL remains a leading cause of cancer death in young people. Recent genomic analyses by our group and others identified a unique subtype of BCR-ABL-negative, high-risk B-ALL, with deletion or mutation of IKZF1 and a gene expression profile similar to BCR-ABL1-positive ALL (Ph-like ALL). Up to 50% of Ph-like patients harbor rearrangements of the cytokine receptor gene, CRLF2, with concomitant JAK mutations detected in ∼30%. However, the nature of genetic alterations activating kinase signaling in the remaining cases is unknown. To identify novel genetic alterations in Ph-like ALL, we performed transcriptome sequencing (RNA-seq) on 11 cases of Ph-like B-ALL (10 from the P9906 Children's Oncology Group trial and 1 from the St Jude Total XV study), and whole genome sequencing (WGS) on two of these. Using multiple complementary analysis pipelines including deFuse, Mosaik, CREST and CONSERTING, we identified novel rearrangements, structural variations and sequence mutations dysregulating cytokine receptor and kinase signaling in 10 cases. Putative rearrangements and sequence mutations were validated using RT-PCR, genomic PCR and Sanger sequencing. The spectrum of alterations included 3 cases with known IGH@CRLF2 rearrangement, 2 cases with the NUP214-ABL1 rearrangement, 1 case each with the in-frame fusions EBF1-PDGFRB, BCR-JAK2 or STRN3-JAK2, and 1 case with a cryptic IGH@-EPOR rearrangement. Detailed analysis of RNA-seq data revealed a 7.5 kb insertion of EPOR downstream of the enhancer domain in the IGH@ locus, which was not detected by fluorescence in situ hybridization. WGS identified an in-frame activating insertion in the transmembrane domain of IL7R (L242>FPGVC) in 1 index case, and recurrence screening identified similar IL7R sequence mutations in 8 cases from the P9906 cohort (N=188). This patient also harbored a focal homozygous deletion removing the first two exons of SH2B3 that was not evident by SNP array analysis. SH2B3 encodes LNK, a negative regulator of JAK2 signaling. Notably, all patients harbor genetic lesions affecting B-lymphoid development (e.g IKZF1), suggesting these events cooperate to drive B-lineage ALL. To determine the frequency of each fusion, candidate RT-PCR was performed on 231 cases from the COG AALL0232 trial of high-risk B-ALL, 40 (17%) of which were identified as Ph-like using Predictor Analysis of Microarrays (PAM). The EBF1-PDGFRB fusion was detected in 3 additional patients, each containing an intact PDGFRB kinase domain. No additional cases of NUP214-ABL1, BCR-JAK2, or STRN3-JAK2 were identified. Phosphoflow analysis on 3 primary ALL samples demonstrated increased CKRL phosphorylation in the NUP214-ABL1 case and tyrosine phosphorylation in the cases with BCR-JAK2 and STRN3-JAK2 fusions. Importantly, this activation was reduced with the tyrosine kinase inhibitors (TKI) imatinib, dasatinib and the T315I inhibitor XL228 in cells harboring the ABL1 fusion, and the JAK2 inhibitor, XL019, in the JAK2-rearranged samples. Furthermore, the novel EBF1-PDGFRB fusion transformed Ba/F3 cells to growth factor independence, induced constitutive activation of pSTAT5, pAkt, pERK1/2, and responded with low IC50 values to imatinib, dasatinib and the specific PDGFRB/FGFR inhibitor, dovitinib. Using complementary genomic approaches we show that rearrangements, sequence mutations and DNA copy number alterations dysregulating cytokine receptor and kinase signaling are a hallmark of Ph-like ALL. These data support the screening of patients at diagnosis to identify those with Ph-like ALL, characterize the genomic lesions driving this phenotype, and to determine those that may benefit from TKI treatment. Disclosures: Hunger: Bristol-Myers Squibb: Author's children own stock in BMS, Membership on an entity's Board of Directors or advisory committees.

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The Efficacy of Tyrosine Kinase Inhibitors with Steroid As First Line Induction Therapy in Ph+ Acute Lymphoblastic Leukemia

Blood ◽

10.1182/blood.v124.21.5281.5281 ◽

2014 ◽

Vol 124 (21) ◽

pp. 5281-5281

Author(s):

Gunhan Gurman ◽

Mustafa Merter ◽

Pinar Ataca ◽

Mehmet Ozen ◽

Berna Atesagaoglu ◽

...

Keyword(s):

Induction Therapy ◽

Myeloid Leukemia ◽

Kinase Inhibitors ◽

Lymphoblastic Leukemia ◽

Patient Characteristics ◽

Induction Treatment ◽

Rt Pcr ◽

First Line ◽

Ph Chromosome ◽

Tki Treatment

Abstract Introduction: Philadelphia chromosome positive acute lymphoblastic leukemia (Ph+ ALL) is a biologically and clinically distinct variant of ALL and accounts for approximately 20 to 30 percent of ALL in adults. Ph chromosome and BCR-ABL fusion gene have been associated with a poor prognosis in ALL patients especially when patients were treated with chemotherapy alone. Better response rates have been reported with the introduction of tyrosine kinase inhibitors (TKIs) and incorporation of TKI into the treatment regimens. This development has allowed more patients to proceed to allogeneic hematopoietic stem cell transplantation (Allo-HSCT). In recent years some studies evaluated the efficacy of TKIs combined with steroids as first-line induction treatment in Ph+ ALL patients. Patients and methods: Here we present 5 patients who were newly diagnosed as Ph+ de novo (n=2) or secondary ALL transformed from chronic myeloid leukemia (n=3) and received TKI plus methylprednisolone (MP) as an induction regimen. All of our patients were male. Additional cytogenetic abnormality was detected in two patients (monosomy 7). This therapy was preferred in 3 patients due to comorbid disease and advanced age. Other patients received the therapy for bridging to allogeneic stem cell transplantation. Three patients received imatinib 800 mg daily and 40 mg/m2 MP for 45 days, one patient received dasatinib 140 mg daily and 60 mg/m2 MP for 32 days. TKI treatment after the induction has been continuing in maintenance therapy in all patients, except one patient whose TKI treatment was interrupted due to Allo-HSCT. One patient had a history of resistance to imatinib, nilotinib and dasatinib while he was in chronic phase of chronic myeloid leukemia. Therefore he was treated with bosutinib 500 mg daily plus MP 60 mg/m2 for 32 days. After completing of induction therapy 3 patients received 6-mercaptopurine 70mg/m2 daily, methotrexate 20mg/m2 weekly, vincristine 2 mg/day in every two months, MP 40mg/m2 for 5 days in every month and TKI daily as the maintenance therapy. Central nervous system (CNS) involvement was detected in two patients during the induction treatment on days 30 and 65, respectively. One of them received high dose methotrexate and then underwent Allo-HSCT from an HLA identical sibling donor at fourth month of diagnosis. The other patient was ordered cranial and spinal irradiation together with intrathecal chemotherapy. Results: Four patients achieved complete hematologic remission (CHR) at day 22 and one patient achieved CHR at day 45. Complete molecular remission was not obtained in our patients after the induction therapy. After a median follow-up of 7 months (range 3-22), four patients are alive currently. One patient died due to pulmonary infection after 22 months of diagnosis and he was still in CHR at the time of dead. Patient characteristics are given in table. Conclusions: Our observations suggest that TKI plus steroid therapy as the first line treatment for remission-induction in Ph+ ALL has been more tolerable and associated with less toxicity. Despite the poor prognostic effect of Ph chromosome in ALL patients, TKI plus steroid regimens may improve outcome and may allow to patients to proceed to Allo-HSCT. As shown among the elderly Ph+ ALL patients, this regimen might also be appropriate for younger Ph+ ALL patients. Table: Patient characteristics Patient 1 Patient 2 Patient 3 Patient 4 Patient 5 Age 69 65 38 70 29 WBC count at presentation (x10 9 /L) 3500 46000 6000 26500 232000 BCR-ABL fusion protein (kD) 190 190 210 210 210 TKI (dose) Imatinib(800mg) Imatinib(800mg) Imatinib(800mg) Bosutinib(500mg) Dasatinib(200mg) BCR-ABL (FİSH)% at presentation 96 90 85 90 - BCR-ABL ratio (RT-PCR) at presentation 3,8 - 30,76 40,9 2,7 BCR-ABL ratio (RT-PCR) at day 22 0,0006 0,1411 0,2964 25 0,2794 Disease status at days 22&45 Hematologic Remission Hematologic Remission Hematologic Remission Hematologic Remission Hematologic Remission Disclosures No relevant conflicts of interest to declare.

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Evaluation of MRD after Administration of Imatinib by Measurement of Real-Time Quantitative PCR-Based Major bcr/abl mRNA.

Blood ◽

10.1182/blood.v104.11.4407.4407 ◽

2004 ◽

Vol 104 (11) ◽

pp. 4407-4407

Author(s):

Mutsumi Takahata ◽

Satoshi Hashino ◽

Fumie Fujisawa ◽

Takeshi Kondo ◽

Syuichi Ota ◽

...

Keyword(s):

Real Time ◽

Residual Disease ◽

Lymphoblastic Leukemia ◽

Quantitative Polymerase Chain Reaction ◽

Donor Lymphocyte Infusion ◽

Pcr Analysis ◽

Fish Analysis ◽

Rt Pcr ◽

Prognostic Information ◽

Real Time Quantitative Pcr

Abstract Evaluation of minimal residual disease (MRD) provides prognostic information on various hematological malignancies. We describe here the efficacy of real-time quantitative polymerase chain reaction (RQ-PCR)-based analysis of major bcr/abl mRNA in cases of chronic myeloid leukemia (CML) and Ph-positive acute lymphoblastic leukemia (Ph+ALL), especially in cases administered imatinib mesilate (imatinib) followed by stem cell transplantation (SCT). Twenty-one patients with CML or Ph+ALL were enrolled as subjects to determine the usefulness of RQ-PCR-based measurement of bcr-abl/abl ratios. Seven of the 21 patients were administered imatinib before allogeneic SCT. Hematological relapse or failure of treatment by SCT was observed in 2 out of those patients who showed bcr-abl/abl ratios of more than 0.002%, and 5 of the 7 patients showed both RQ-PCR and RT-PCR negativity immediately after SCT. All of the 5 patients who were not administered imatinib before allogeneic SCT showed RQ-PCR negativity immediately after SCT, but the results of RT-PCR were positive in 3 patients at the same time points, and the results became negative by donor lymphocyte infusion (DLI) or appearance of graft-versus-host disease (GVHD). Administration of imatinib before SCT was thought to result in an earlier remission. On the other hand, 8 patients who were administered imatinib without SCT showed a remarkable decrease in bcr-abl/abl ratios. However, the ratio gradually rose in one patient with Ph+ALL, enabling prediction of hematological relapse preceding detection by fluorescence in situ hybridization (FISH) analysis. Standardization of RQ-PCR analysis of bcr-abl mRNA will help prediction of early hematological relapse in patients with MRD. In conclusion, RQ-PCR positivity immediately after SCT in patients pre-treated with imatinib suggests risk of recurrence.

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