ABSTRACT
The discovery of copy number variations (CNV) in the human genome opened new perspectives in the study of the genetic causes of inherited disorders and the etiology of common diseases. Differently patterned instances of somatic mosaicism in CNV regions have been shown to be present in monozygotic twins and throughout different tissues within an individual. A single-cell-level investigation of CNV in different human cell types led us to uncover mitotically derived genomic mosaicism, which is stable in different cell types of one individual. A unique study of immortalized B-lymphoblastoid cell lines obtained with 20 year interval from the same two subjects shows that mitotic changes in CNV regions may happen early during embryonic development and seem to occur only once, as levels of mosaicism remained stable. This finding has the potential to change our concept of dynamic human genome variation. We propose that further genomic studies should focus on the single-cell level, to understand better the etiology and physiology of aging and diseases mediated by somatic variations.
ABSTRACT
Eight cell lines newly established from glioblastoma multiforme were examined by comparative genomic hybridization for their patterns of genomic imbalance. The total number of DNA copy number alterations (CNAs) found in the eight cell lines varied between 15 and 24. This characterized the examined cell lines (or the tumors they were derived from) as distinctly progressed in karyotypic evolution. The most frequent CNAs were gains of the entire chromosome 6 or, at least, parts of it, and of 7p22, which were found in all eight cell lines. Other changes present in seven of the eight cell lines were gains of 3q26qter and the entire chromosome 7 and losses of segments on chromosome 4q (e.g., 4q34q35) and of the short arm of chromosome 10. Enh(3q21q25), dim(4q22q33) and dim(4qter), dim(13q22), enh(15q14), and enh(18q22q23) were found in six of the eight cell lines. Several other CNAs [e.g., dim(9p21)] were found in common in five or less of the eight lines. Using a hierarchical cluster analysis, the specific patterns of genomic imbalance allowed various groupings of the examined cell lines. Although a close relation could be confirmed among all examined lines on the basis of shared CNAs, two main groups could be roughly differentiated. Among those there were also more or less closely related subgroups. However, also alterations which were restricted to one single cell line each were found, e.g., dim(1q41qter), dim(2q22qter), enh(4p), dim(5p), dim(4p13pter), dim(8q21qter), enh(9p), dim(9q), dim(11p14pter), enh(12q15q23), enh(13q21), dim(14q21qter), dim(15q21qter), dim(19q), and enh(22q). The comparison of the obtained data on gains and losses of DNA copy numbers in specific chromosomal segments with the data on localization of genes possibly associated with the biology of glioblastoma multiforme additionally shows high conformity but also disparity of the examined cell lines among each other, as well as compared to primary glioblastoma multiforme. Eventually, each of the cell lines could be characterized by its specific pattern of genomic imbalance.
Subject(s)
Chromosome Aberrations , Chromosomes, Human/genetics , DNA, Neoplasm/genetics , Gene Dosage , Glioblastoma/genetics , Neoplasm Proteins/genetics , Aged , Chromosome Mapping , Female , Humans , Karyotyping , Male , Middle Aged , Nucleic Acid Hybridization , Tumor Cells, CulturedABSTRACT
Genomic imbalances were investigated in 15 T-cell acute lymphoblastic leukemia cell lines using the comparative genomic hybridization (CGH) technique. In addition, in vitro response to the cytostatic drug doxorubicin was evaluated by means of a growth inhibition assay. The number of significant DNA copy number alterations (CNAs) varied from 0 to 16 per cell line and the number of additional alterations with borderline significance was in a range of 0-7. Three of the cell lines had a total number of genomic changes of >/=20, five had 11-19, and eight had =10 CNAs. One cell line did not show any imbalance at all. Among the significant CNAs, losses of genomic material were slightly more frequent than gains (60:49). Gains dominated among the borderline alterations compared to losses (45:9). CNAs common to all cell lines examined were not found. The most frequent genomic imbalance (gain of 6q23) was shared by 9 of the 15 cell lines. A significant loss of 18q23 was observed in eight lines, however, often close to borderline significance. Seven of the cell lines were characterized by a loss of the entire short arm of chromosome 9 or parts of it with 9p21 as minimal band of overlap. Interestingly, cell lines with a 9p21 deletion exhibited twice the number of gains and 1.6 times the number of losses per line as compared with the cell lines without this deletion. A consistent pattern of the CNAs accompanying the 9p deletion could not be detected, although some associations were more obvious than others, e.g., gains of 6q22 in five cell lines with del(9p21), of 6p21 in four lines combined with a gain of 6q22, and of 20q in four cell lines, of 1p32 in three of these seven lines, a loss of 14q32 in three of them. Three of the lines with 9p deletion had gains of 6p21, 6q22 and 20q in common. Enh(6q22) or dim(14q32), respectively, were found in only one of the nine cell lines without the 9p deletion. Based on the dose response curves of the cell lines for doxorubicin, eight doxorubicin-sensitive cell lines had an inhibition concentration 50% (IC50) <10 nM (CCRF-CEM2, JURKAT, KE-37, MOLT-3, MOLT-4, P12-Ichikawa, PEER, and RPMI-8402) and seven doxorubicin-resistant cell lines had an IC50 >10 nM (BE-13, CCRF-CEM1, HUT-78, J-Jhan, Karpas-45, MOLT-17, and PF-382). The average number of CNAs per cell line was higher in the sensitive than in the resistant group (total 13.1:8.5; significant CNAs 9.1:5.8).