scholarly journals DNA Amplifications and Aneuploidy, High Proliferative Activity and Impaired Cell Cycle Control Characterize Breast Carcinomas with Poor Prognosis

2003 ◽  
Vol 25 (3) ◽  
pp. 103-114 ◽  
Author(s):  
Harald Blegen ◽  
John S. Will ◽  
B. Michael Ghadimi ◽  
Hesed‐Padilla Nash ◽  
Anders Zetterberg ◽  
...  

In order to explore whether specific cytogenetic abnormalities can be used to stratify tumors with a distinctly different clinical course, we performed comparative genomic hybridization (CGH) of tumors from patients who were diagnosed with metastatic disease after an interval of less than 2 years or who remained free from distant metastases for more than 10 years. All patients presented with distant metastases after mastectomy indicating that none of the patients in this study was cured and free of remaining tumor cells. Tumors in the group of short‐term survivors showed a higher average number of chromosomal copy alterations compared to the long‐term survivors. Of note, the number of sub‐chromosomal high‐level copy number increases (amplifications) was significantly increased in the group of short‐term survivors. In both short‐ and long‐term survivors recurrent chromosomal gains were mapped to chromosomes 1q, 4q, 8q, and 5p. Copy number changes that were more frequent in the group of short‐term survivors included gains of chromosome 3q, 9p, 11p and 11q and loss of 17p. Our results indicate that low‐ and high grade malignant breast adenocarcinomas are characterized by a specific pattern of chromosomal copy number changes. Furthermore, immunohistochemical evaluation of the expression levels of Ki‐67, p27KIP1, p21WAF1, p53, cyclin A and cyclin E revealed a correlation between increased proliferative activity and poor outcome.

2001 ◽  
Vol 22 (3) ◽  
pp. 123-131 ◽  
Author(s):  
Harald Blegen ◽  
B. Michael Ghadimi ◽  
Annukka Jauho ◽  
Anders Zetterberg ◽  
Elina Eriksson ◽  
...  

In order to evaluate biological and genetic properties of early breast carcinomas we analyzed microdissected tissue from 33 primary breast carcinomas stage T1b and T1c with respect to the nuclear DNA content, the expression pattern of Ki‐67, cyclin A, p27KIP1, p53 and p21WAF1, and chromosomal gains and losses. The results show that T1b carcinomas (6–10 mm,n=17) were frequently near‐diploid (53%) with low proliferative activity and staining patterns of p53 and p21WAF1that suggest the presence of wild type protein. The majority (12/16) of the T1c tumors (11–20 mm), however, was aneuploid, and proliferative activity and p53 expression were increased. Larger tumor size correlated with an increasing number of chromosomal copy number changes and in particular with regional amplifications. High level copy number increases (amplifications), however, were found exclusively in the aneuploid tumors. Amplification events correlated with elevated cyclin A and reduced p27 expression, respectively. Our results suggest that the sequential acquisition of genomic imbalances during tumor progression is accelerated in aneuploid tumors, and may contribute to the increased malignancy potential.


2001 ◽  
Vol 22 (3) ◽  
pp. 159-163 ◽  
Author(s):  
Kowan J. Jee ◽  
Young Tak Kim ◽  
Kyu Rae Kim ◽  
Yan Aalto ◽  
Sakari Knuutila

DNA copy number changes were studied by comparative genomic hybridization on 10 tumor specimens of squamous cell carcinoma of cervix obtained from Korean patients. DNA was extracted from paraffin‐embedded sections after removal of non‐malignant cells by microdissection technique. Copy number changes were found in 8/10 tumors. The most frequent changes were chromosome 19 gains (n=6) and losses on chromosomes 4 (n=4), 5 (n=3), and 3p (n=3). A novel finding was amplification in chromosome arm 9p21‐pter in 2 cases. Gains in 1, 3q, 5p, 6p, 8q, 16p, 17, and 20q and losses at 2q, 6q, 8p, 9q, 10p, 11, 13, 16q, and 18q were observed in at least one of the cases.


Blood ◽  
1996 ◽  
Vol 87 (12) ◽  
pp. 5269-5278 ◽  
Author(s):  
O Monni ◽  
H Joensuu ◽  
K Franssila ◽  
S Knuutila

We studied DNA copy number changes in diffuse large B-cell lymphoma using comparative genomic hybridization analysis on 20 primary tumors and on 12 recurrent tumors excised after chemotherapy or radiotherapy. Twenty-nine (91%) of the cases showed abnormal copy number karyotypes. Chromosomal regions at X (41%), 1q (38%), 7 (31%), 3 (24%), 6p (21%), 11 (21%), 12 (21%), and 18 (21%) were most frequently gained, and the most common losses involved 6q (38%), X (21%), 1p (14%), and 8p (10%). High-level amplifications were observed at 6p23-ter, 10p12–14, 17p1l.2, 18q21-ter, and Xq22-ter, all but 18q appearing only in the recurrent tumors. Gains (median, 2; range, 0 to 10) were more frequent than losses (median, 1; range, 0 to 7; P = .0004). The median number of aberrations found in the recurrent tumors (6.5) was greater than that in the primary tumors (2; P = .01). The copy number changes found in the recurrent tumors were more random than those found in the primary tumors, which were mainly located in the most frequently affected regions. Our findings are in line with those observed using conventional cytogenetic analysis, but especially novel high-level amplifications were detected. Southern blot analysis showed BCL2 amplification, but not translocation t(14;18)(q32;q21), in cases in which a gain at 18q was detected by comparative genomic hybridization, which strongly suggests that, in addition to translocation, gene amplification is another mechanism for the overexpression of the BCL2 protein.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 142-142 ◽  
Author(s):  
Matthew J. Walter ◽  
Rhonda E. Ries ◽  
Jon Armstrong ◽  
Brian O’Gara ◽  
James W. Vardiman ◽  
...  

Abstract Cytogenetics and comparative genomic hybridization (CGH) have been used to identify large genomic amplifications and deletions in all subtypes of acute myeloid leukemia (AML). Up to 15–20% of AML patients have a normal karyotype at diagnosis. While cytogenetic abnormalities confer important prognostic information for patients with AML, there remain differences in the therapeutic response and outcome among patients with the same cytogenetic profile, implying that other, more subtle, genetic abnormalities may exist. We hypothesized that a subset of AML patients with normal cytogenetics may contain genomic DNA copy number changes that are too small to be detected using standard cytogenetic techniques. To address this possibility, we used high-resolution bacterial artificial chromosome (BAC) array CGH technology to examine 31 AML patients with normal cytogenetics. The BAC arrays contain 2,464 BAC clones spotted in triplicate on glass slides, and provide a 1 Mb resolution of the entire human genome. Technical generation of the arrays, hybridization parameters, and analysis were similar to that reported for murine BAC array CGH (Nat Genet. 2001 Dec;29(4):459–64). The 31 AML samples included 4 M0, 8 M1, 10 M2, and 9 M4 patients. Array CGH experiments were performed using 500 nanograms of Cyanine 5 labeled genomic DNA from unmanipulated AML bone marrow, mixed with an equal amount of control DNA (a pool of DNA from 4 cancer-free individuals) labeled with Cyanine 3. Using the human 1 Mb BAC arrays, we identified amplifications and deletions from multiple samples that were confirmed with G-banding cytogenetics [del(7)(q31), del(7)(p11.2), +8, del(11)(q13q23), +21, add(21)(q22), −X, −Y, +Y]. In addition, BAC arrays robustly detected copy number alterations that were identified in as few as 4/21 metaphases. We identified 5/31 (16%) patients with normal cytogenetics that contained altered genomic DNA copy numbers using BAC array CGH. Copy number changes were confirmed for several of these genomic loci using a dye-swap experiment, where the AML DNA was labeled with Cyanine 3, and the control DNA with Cyanine 5. Two of the 5 patients with abnormalities detected using array CGH would be reclassified from “intermediate” to “unfavorable” cytogenetics [del(7)(q31.31q34), add(11)(q23.3qter), and 17(p12pter)]. These results suggest that a subset of AML patients with normal cytogenetics contain genomic copy number alterations that may effect treatment and outcome. Patient # FAB subtype Genomic location Gain or loss Size (Megabase) Dye-Swap confirmed 1 M0 7(q31.31q34) loss 2.0 Not done 1 11(q23.3qter) gain 16.5 Not done 2 M1 11(p14) loss 7.4 Yes 3 M1 11(q13.2q14.1) gain 15.8 Yes 3 19(p) gain 64.0 Yes 4 M2 17(p12pter) gain 8.6 Not Done 5 M2 19(p13.1pter) loss 14.8 Yes 5 12(q13) loss 5.0 Yes


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1510-1510
Author(s):  
Katerina Pokorna ◽  
Carole Le Pogam ◽  
Martine Chopin ◽  
Bruno Cassinat ◽  
Pierre Fenaux ◽  
...  

Abstract Abstract 1510 Background: Relapses are now relatively rare in APL and occur mainly in the bone marrow (BM) within 3 years of complete response achievement, but later BM relapses can also occur (Kelaidi, Leukemia 2006), while a few cases of extramedullary (EM) relapse are observed, particularly in the central nervous system (CNS) (De Botton, Leukemia 2006). The transplantable transgenic mouse model of APL is a well characterized preclinical model which mimics human APL in its biological characteristics. We have previously reported the response of these mice to ATRA and a combination of ATRA with a DNA vaccine (Padua, Nat Med 2003, Fuguraki, Blood 2010). We analyzed in those treated mice the presence of PML-RARα transcripts in the peripheral blood (PB), BM and various organs and tissues. Methods: The reproducible APL development was obtained, as previously described (Padua Nat Med 2003) by intravenous injection of 104 spleen cells from APL transgenic mice expressing the human PML-RARα cDNA (bcr1) into syngeneic recipients. ATRA and the DNA vaccine (a plasmid containing PML-RARα cDNA (bcr1) sequence fused to the tetanus toxin fragment C) were administered as described (Padua Nat Med 2003). In this model, ATRA alone gives transient remissions, while about 30 % of APL mice treated with ATRA combined with a DNA vaccine achieve long-term remissions. A standardized RT-qPCR MRD monitoring protocol was applied to assess PML-RARα-positive cell clearance in PB and BM. In this assay, the number of PML-RARα transcripts was normalized (normalized copy number or NCN) to 106 copies of 18S rRNA transcripts, allowing us to detect up to 1 PML-RARα-positive cell among 104 negative cells. Taking advantage of the presence of PML-RARα cDNA transgene in the transplanted leukemia cells, we next used genomic DNA as template for a qPCR assay, allowing us to use 10 times more template and increased sensitivity (1 in 105) in order to examine the presence of PML-RARα-positive cells in various organs and tissues of long-term survivors (LTS, ie with survival > 120 days). Results: APL mice treated with ATRA alone (n=55), ATRA combined with PML-RARαFrC DNA (n=94) or untreated (n=65) were analyzed. Untreated APL mice always remained positive in the PB and BM for PML-RARα transcripts, and in organs and tissues positive for PML-RARα cDNA. On day 60, in the surviving ATRA-treated mice (n=21), 15 (71%) had PB PML-RARα normalized copy number (NCN)>100, 6 (29 %) an NCN between 10–100 and none an NCN<10, while in ATRA+DNA-treated mice (n=35), 11 (31%) had NCN>100, 9 (26%) NCN between 10–100 and 15 (43%) NCN<10 (p<0.01). ATRA+DNA-treated mice achieving NCN<10 (43%) constituted the group with the best survival (p<0.0001). To further assess tumour burden, LTS were sacrificed at different time intervals. No PML-RARα transcripts were detected in PB and BM of any LTS (n=15) suggesting complete molecular remission. On the other hand, while PML-RARα cDNA, analyzed by qPCR in skin, salivary glands, thymus, kidney, muscle, heart, spleen, liver, lung and CNS was negative in all tissues in 10 (67%) LTS, it was positive in 5 (33%) LTS, including 4 in the CNS (2 of them were also positive in the spleen) and 1 in the spleen only. Conclusion: In this preclinical model, analyzed with sensitive molecular assays, while two thirds treated long-term survivors were in molecular remission in PB, BM and other organs studied, about one third still had leukemic cells, mainly in the CNS and to a lesser extent in the spleen. This model could be of interest to better understand relapses in APL patients, especially late and CNS relapses and to evaluate drugs aimed at eliminating those reservoirs of residual cells. Disclosures: No relevant conflicts of interest to declare.


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