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Tang Z, Kanagal-Shamanna R, Tang G, Patel K, Medeiros LJ, Toruner GA. Analytical and clinical performance of chromosomal microarrays compared with FISH panel and conventional karyotyping in patients with chronic lymphocytic leukemia. Leuk Res 2021; 108:106616. [PMID: 34022744 DOI: 10.1016/j.leukres.2021.106616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 11/19/2022]
Abstract
In this single center retrospective analysis on 102 CLL patients, we assessed analytical and clinical performance of CMA against a targeted FISH panel (ATM, TP53, CEP12, D13S319 and LAMP1 loci) and karyotyping. CMA yielded additional information compared to karyotype in 39 cases (38 %). On the other hand, while CMA detected aberrations were also detected by FISH in all 31 cases (30 %), aberrations with low clonal size (<30 %) detected by FISH were missed by CMA. When evaluated with National Cancer Center Network (NCCN) guidelines, the capture rate of prognostic relevant cytogenetic information for FISH only, FISH + Chromosomes and FISH + CMA analyses were 95, 96 and 100 % respectively. With Cancer Cytogenomics Consortium (CGC) Criteria, these figures for FISH only, FISH + Chromosomes and FISH + CMA were 88 %, 92 and 100 % respectively. In conclusion, CMA provides additional analytical information to FISH and karyotyping, but this information has a clinical utility only in a small number of patients. Limit of detection (LOD) issues preclude replacement of FISH by CMA, but CMA may be a viable alternative to karyotyping. Further research is warranted.
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Affiliation(s)
- Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Keyur Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Gokce A Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States.
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2
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Kong D, Fan S, Sun L, Chen X, Zhao Y, Zhao L, Guo Z, Li Y. Growth inhibition and suppression of the mTOR and Wnt/β-catenin pathways in T-acute lymphoblastic leukemia by rapamycin and MYCN depletion. Hematol Oncol 2020; 39:222-230. [PMID: 33300153 DOI: 10.1002/hon.2831] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/01/2020] [Accepted: 12/06/2020] [Indexed: 12/12/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy. Understanding of the molecular pathogenesis may lead to novel therapeutic targets. Rapamycin, the mammalian target of rapamycin (mTOR) inhibitor, showed inhibitory effects on T-ALL cells. In this study, we showed that rapamycin significantly reduced MYCN mRNA and protein in a concentration-dependent manner in T-ALL cells. Selective knockdown of MYCN by small interfering RNA had similar effects to rapamycin to inhibit T-ALL proliferation and colony formation and to induce G1-phase cell-cycle arrest and apoptosis. The inhibitory effects of rapamycin and MYCN depletion were also found in a Molt-4 xenograft model. Rapamycin and MYCN inhibition suppressed both Wnt/β-catenin and mTOR signaling pathways. The results suggest the effects of rapamycin on adult T-ALL is likely mediated by downregulation of MYCN. The findings suggest MYCN a potential target for the treatment of adult T-ALL. Additionally, dual targeting of mTOR and Wnt/β-catenin pathways may represent a novel strategy in the treatment of adult T-ALL.
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Affiliation(s)
- Desheng Kong
- Department of Hematology, The Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Shengjin Fan
- Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Lili Sun
- Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xi Chen
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yanqiu Zhao
- Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Linlin Zhao
- Department of Blood Transfusion, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Zhibo Guo
- Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yinghua Li
- Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
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3
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Assessing copy number aberrations and copy-neutral loss-of-heterozygosity across the genome as best practice: An evidence-based review from the Cancer Genomics Consortium (CGC) working group for chronic lymphocytic leukemia. Cancer Genet 2018; 228-229:236-250. [DOI: 10.1016/j.cancergen.2018.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/29/2018] [Accepted: 07/01/2018] [Indexed: 01/18/2023]
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4
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Mehrotra M, Luthra R, Ravandi F, Sargent RL, Barkoh BA, Abraham R, Mishra BM, Medeiros LJ, Patel KP. Identification of clinically important chromosomal aberrations in acute myeloid leukemia by array-based comparative genomic hybridization. Leuk Lymphoma 2015; 55:2538-48. [PMID: 24446873 DOI: 10.3109/10428194.2014.883073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Array-based comparative genomic hybridization (aCGH) chromosomal analysis facilitates rapid detection of cytogenetic abnormalities previously undetectable by conventional cytogenetics. In this study, we analyzed 48 uniformly treated patients with acute myeloid leukemia (AML) by 44K aCGH and correlated the findings with clinical outcome. aCGH identified previously undetected aberrations, as small as 5 kb, of currently unknown significance. The 36.7 Mb minimally deleted region on chromosome 5 lies between 5q14.3 and 5q33.3 and contains 634 genes and 15 microRNAs, whereas loss of chromosome 17 spans 3194 kb and involves 342 genes and 12 microRNAs. Loss of a 155 kb region on 5q33.3 (p < 0.05) was associated with achievement of complete remission (CR). In contrast, loss of 17p11.2-q11.1 was associated with a lower CR rate and poorer overall survival (Kaplan-Meier analysis, p < 0.0096). aCGH detected loss of 17p in 12/48 patients as compared to 9/48 by conventional karyotyping. In conclusion, aCGH analysis adds to the prognostic stratification of patients with AML.
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Affiliation(s)
- Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas M. D. Anderson Cancer Center , Houston, TX , USA
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Mehrotra M, Patel KP, Chen T, Miranda RN, Wang Y, Zuo Z, Muddasani R, Mishra BM, Abraham R, Luthra R, Lu G. Genomic and Clinicopathologic Features of Primary Myelofibrosis With Isolated 13q Deletion. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2015; 15:496-505.e1-2. [PMID: 26027540 DOI: 10.1016/j.clml.2015.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 03/05/2015] [Accepted: 03/18/2015] [Indexed: 12/21/2022]
Abstract
BACKGROUND Primary myelofibrosis (PMF) is a rare myeloproliferative stem cell disorder. The genomic features in PMF are poorly understood. Characterization of genomic alternations in PMF helps to determine their association with clinicopathologic features for further therapeutic implications. PATIENTS AND METHODS In this retrospective study, we investigated genomic changes using array-based comparative genomic hybridization (aCGH) in 17 PMF patients with isolated del(13q) and confirmed our aCGH findings with quantitative polymerase chain reaction (PCR) assay. We also compared the clinicopathologic features of patients with del(13q) (n = 17) with those of patients with a normal karyotype (NK) (n = 26). RESULTS Clinicopathologically, del(13q) PMF patients had significantly higher blast counts (P = .03) than did NK patients, who had significantly higher marrow cellularity (P = .02). The degree of bone marrow fibrosis of PMF-3 was higher in the del(13q) group than in the NK group. Splenomegaly was present significantly more often in the del(13q) PMF group than in the NK group (P = .03). Genomically, the Janus Kinase 2 V617F mutation was observed less often in del(13q) PMF patients (P = .07). The common deleted region in del(13q) was confined to 13q13-13q14.3 according to G-band karyotyping, demonstrating a minimal deleted region (MDR) of 15.323 Mb, identified using aCGH. The tumor suppressor genes, Retinoblastoma, Forkhead box protein O1, and Succinyl -CoA ligase [ADP-forming] subunit beta in the MDR were deleted, confirmed using real-time PCR to confirm our aCGH findings. CONCLUSION Accurate molecular characterization of del(13q) in PMF using aCGH and quantitative PCR provided further insight to define the MDR and analyze the genomic changes in del(13q) PMF patients.
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Affiliation(s)
- Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Tianjian Chen
- Hayward Genetics Center, Tulane University School of Medicine, New Orleans, LA
| | - Roberto N Miranda
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Yaping Wang
- Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Zhuang Zuo
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Ramya Muddasani
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Bal M Mishra
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Ronald Abraham
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Gary Lu
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX.
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Fabris S, Mosca L, Cutrona G, Lionetti M, Agnelli L, Ciceri G, Barbieri M, Maura F, Matis S, Colombo M, Gentile M, Recchia AG, Anna Pesce E, Di Raimondo F, Musolino C, Gobbi M, Di Renzo N, Mauro FR, Brugiatelli M, Ilariucci F, Lipari MG, Angrilli F, Consoli U, Fragasso A, Molica S, Festini G, Vincelli I, Cortelezzi A, Federico M, Morabito F, Ferrarini M, Neri A. Chromosome 2p gain in monoclonal B-cell lymphocytosis and in early stage chronic lymphocytic leukemia. Am J Hematol 2013; 88:24-31. [PMID: 23044996 DOI: 10.1002/ajh.23340] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/03/2012] [Accepted: 09/05/2012] [Indexed: 12/17/2022]
Abstract
Recent studies have described chromosome 2p gain as a recurrent lesion in chronic lymphocytic leukemia (CLL). We investigated the 2p gain and its relationship with common prognostic biomarkers in a prospective series of 69 clinical monoclonal B-cell lymphocytosis (cMBL) and 218 early stage (Binet A) CLL patients. The 2p gain was detected by FISH in 17 patients (6%, 16 CLL, and 1 cMBL) and further characterized by single nucleotide polymorphism-array. Overall, unfavorable cytogenetic deletions, i.e., del(11)(q23) and del(17)(p13) (P = 0.002), were significantly more frequent in 2p gain cases, as well as unmutated status of IGHV (P < 1 × 10(-4) ) and CD38 (P < 1 × 10(-4) ) and ZAP-70 positive expression (P = 0.003). Furthermore, 2p gain patients had significantly higher utilization of stereotyped B-cell receptors compared with 2p negative patients (P = 0.009), and the incidence of stereotyped subset #1 in 2p gain patients was significantly higher than that found in the remaining CLLs (P = 0.031). Transcriptional profiling analysis identified several genes significantly upregulated in 2p gain CLLs, most of which mapped to 2p. Among these, NCOA1 and ROCK2 are known for their involvement in tumor progression in several human cancers, whereas among those located in different chromosomes, CAV1 at 7q31.1 has been recently identified to play a critical role in CLL progression. Thus, 2p gain can be present since the early stages of the disease, particularly in those cases characterized by other poor prognosis markers. The finding of genes upregulated in the cells with 2p gain provides new insights to define the pathogenic role of this lesion.
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MESH Headings
- Adult
- Aged
- Biomarkers, Tumor/biosynthesis
- Biomarkers, Tumor/genetics
- Chromosomes, Human, Pair 2/genetics
- Chromosomes, Human, Pair 2/metabolism
- Chromosomes, Human, Pair 7/genetics
- Chromosomes, Human, Pair 7/metabolism
- Female
- Gene Expression Regulation, Leukemic
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Lymphocytosis/diagnosis
- Lymphocytosis/genetics
- Lymphocytosis/metabolism
- Male
- Middle Aged
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Neoplasm Staging
- Prognosis
- Prospective Studies
- Up-Regulation/genetics
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Affiliation(s)
- Sonia Fabris
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano e Ematologia 1 CTMO, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Italy
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7
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Schweighofer CD, Coombes KR, Majewski T, Barron LL, Lerner S, Sargent RL, O'Brien S, Ferrajoli A, Wierda WG, Czerniak BA, Medeiros LJ, Keating MJ, Abruzzo LV. Genomic variation by whole-genome SNP mapping arrays predicts time-to-event outcome in patients with chronic lymphocytic leukemia: a comparison of CLL and HapMap genotypes. J Mol Diagn 2012; 15:196-209. [PMID: 23273604 DOI: 10.1016/j.jmoldx.2012.09.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 09/20/2012] [Accepted: 09/27/2012] [Indexed: 02/06/2023] Open
Abstract
Genomic abnormalities, such as deletions in 11q22 or 17p13, are associated with poorer prognosis in patients with chronic lymphocytic leukemia (CLL). We hypothesized that unknown regions of copy number variation (CNV) affect clinical outcome and can be detected by array-based single-nucleotide polymorphism (SNP) genotyping. We compared SNP genotypes from 168 untreated patients with CLL with genotypes from 73 white HapMap controls. We identified 322 regions of recurrent CNV, 82 of which occurred significantly more often in CLL than in HapMap (CLL-specific CNV), including regions typically aberrant in CLL: deletions in 6q21, 11q22, 13q14, and 17p13 and trisomy 12. In univariate analyses, 35 of total and 11 of CLL-specific CNVs were associated with unfavorable time-to-event outcomes, including gains or losses in chromosomes 2p, 4p, 4q, 6p, 6q, 7q, 11p, 11q, and 17p. In multivariate analyses, six CNVs (ie, CLL-specific variations in 11p15.1-15.4 or 6q27) predicted time-to-treatment or overall survival independently of established markers of prognosis. Moreover, genotypic complexity (ie, the number of independent CNVs per patient) significantly predicted prognosis, with a median time-to-treatment of 64 months versus 23 months in patients with zero to one versus two or more CNVs, respectively (P = 3.3 × 10(-8)). In summary, a comparison of SNP genotypes from patients with CLL with HapMap controls allowed us to identify known and unknown recurrent CNVs and to determine regions and rates of CNV that predict poorer prognosis in patients with CLL.
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Affiliation(s)
- Carmen D Schweighofer
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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