Genomic gains and losses influence expression levels of genes located within the affected regions: a study on acute myeloid leukemias with trisomy 8, 11, or 13, monosomy 7, or deletion 5q

Prediction of chromosomal aneuploidy from gene expression data

Chromosomal aneuploidy is commonly observed in neoplastic diseases and is an important prognostic marker. Here we examine how gene expression profiles reflect aneuploidy and whether these profiles can be used to detect changes in chromosome copy number. We developed two methods for detecting such changes in the gene expression profile of a single sample. The first method, fold-change analysis, relies on the availability of gene expression data from a large cohort of patients with the same disease. The expression profile of the sample is compared with that of the dataset. The second method, chromosomal relative expression analysis, is more general and requires the expression data from the tested sample only. We found that the relative expression values are stable among different chromosomes and exhibit little variation between different normal tissues. We exploited this novel finding to establish the set of reference values needed to detect changes in the copy number of chromosomes in a single sample on the basis of gene expression levels. We measured the accuracy of the performance of each method by applying them to two independent leukemia datasets. The second method was also applied to two solid tumor datasets. We conclude that chromosomal aneuploidy can be detected and predicted by analysis of gene expression profiles. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.

Impact of trisomy 8 on expression of genes located on chromosome 8 in different AML subgroups

Trisomy 8 is the most frequently observed trisomy in acute myeloid leukemia (AML) occurring as a sole karyotype abnormality or in addition to other chromosome aberrations. It was the aim of this study to analyze the impact of trisomy 8 on the expression of genes located on chromosome 8 in distinct AML subgroups characterized by different chromosome abnormalities in addition to trisomy 8. Gene expression analyses were performed on a total of 567 AML cases comprising the following subgroups: +8 sole, +8 within a complex aberrant karyotype, +8 in addition to t(15;17), inv(16), t(8;21), 11q23/MLL, or other abnormalities, AML with normal karyotype and the before mentioned subgroups without trisomy 8. A significant higher mean expression of genes located on chromosome 8 was observed in subgroups with +8 in comparison to their respective control groups. A varying number of significantly higher expressed genes was identified in all comparisons. No gene was significantly overexpressed in all comparisons, and no distinct gene expression pattern was identified allowing the identification of cases with trisomy 8. In conclusion, the gain of chromosome 8 leads to a higher expression of genes located on chromosome 8. However, no consistent pattern of genes was identified, which shows a higher expression in all AML subtypes with trisomy 8. These data suggest that trisomy 8 rather provides a platform for a higher expression of chromosome 8 genes which are individually up-regulated by the respective primary genetic abnormalities. Therefore, trisomy 8 in AML determines no specific disease characteristic but is a disease modulating secondary event.

Multiplex-FISH (M-FISH): technique, developments and applications

Multiplex FISH (M-FISH) represents one of the most significant developments in molecular cytogenetics of the past decade. Originally designed to generate 24 colour karyotyping, the technique has spawned many variations and an equally diverse range of applications. In tumour and leukaemia cytogenetics, the two groups that have been targeted represent both ends of the cytogenetic spectrum: those with an apparently normal karyotype (suspected of harbouring small rearrangements not detectable by conventional cytogenetics) and those with a complex aberrant karyotype (which are difficult to karyotype accurately due to the sheer number of aberrations). In research, mouse M-FISH provides a powerful tool to characterize mouse models of a disease. In addition, the ability to accurately karyotype single metaphases without selection makes M-FISH the perfect tool in chromosome breakage studies and for characterizing clonal evolution of tumours. Finally, M-FISH has emerged as the perfect partner for the developing genomic microarray (array CGH) technologies, providing a powerful approach to gene discovery.

Granulocyte colony-stimulating factor preferentially stimulates proliferation of monosomy 7 cells bearing the isoform IV receptor

Granulocyte colony-stimulating factor (GCSF) administration has been linked to the development of monosomy 7 in severe congenital neutropenia and aplastic anemia. We assessed the effect of pharmacologic doses of GCSF on monosomy 7 cells to determine whether this chromosomal abnormality developed de novo or arose as a result of favored expansion of a preexisting clone. Fluorescence in situ hybridization (FISH) of chromosome 7 was used to identify small populations of aneuploid cells. When bone marrow mononuclear cells from patients with monosomy 7 were cultured with 400 ng/ml GCSF, all samples showed significant increases in the proportion of monosomy 7 cells. In contrast, bone marrow from karyotypically normal aplastic anemia, myelodysplastic syndrome, or healthy individuals did not show an increase in monosomy 7 cells in culture. In bone marrow CD34 cells of patients with myelodysplastic syndrome and monosomy 7, GCSF receptor (GCSFR) protein was increased. Although no mutation was found in genomic GCSFR DNA, CD34 cells showed increased expression of the GCSFR class IV mRNA isoform, which is defective in signaling cellular differentiation. GCSFR signal transduction via the Jak/Stat system was abnormal in monosomy 7 CD34 cells, with increased phosphorylated signal transducer and activation of transcription protein, STAT1-P, and increased STAT5-P relative to STAT3-P. Our results suggest that pharmacologic doses of GCSF increase the proportion of preexisting monosomy 7 cells. The abnormal response of monosomy 7 cells to GCSF would be explained by the expansion of undifferentiated monosomy 7 clones expressing the class IV GCSFR, which is defective in signaling cell maturation.

Disclosure of candidate genes in acute myeloid leukemia with complex karyotypes using microarray-based molecular characterization

PURPOSE

To identify novel genomic regions of interest in acute myeloid leukemia (AML) with complex karyotypes, we applied comparative genomic hybridization to microarrays (array-CGH), allowing high-resolution genome-wide screening of genomic imbalances.

PATIENTS AND METHODS

Sixty AML cases with complex karyotypes were analyzed using array-CGH; parallel analysis of gene expression was performed in a subset of cases.

RESULTS

Genomic losses were found more frequently than gains. The most frequent losses affected 5q (77%), 17p (55%), and 7q (45%), and the most frequent genomic gains 11q (40%) and 8q (38%). Critical segments could be delineated to genomic fragments of only 0.8 to a few megabase-pairs of DNA. In lost/gained regions, gene expression profiling detected a gene dosage effect with significant lower/higher average gene expression levels across the genes located in the respective regions. Furthermore, high-level DNA amplifications were identified in several regions: 11q23.3-q24.1 (n = 7), 21q22 (n = 6), 11q23.3 (n = 5), 13q12 (n = 3), 8q24 (n = 3), 9p24 (n = 2), 12p13 (n = 2), and 20q11 (n = 2). Parallel analysis of gene expression in critical amplicons displayed overexpressed candidate genes (eg, C8FW and MYC in 8q24).

CONCLUSION

In conclusion, a large spectrum of genomic imbalances, including novel recurring changes in AML with complex karyotypes, was identified using array-CGH. In addition, the combined analysis of array-CGH data with gene expression profiles allowed the detection of candidate genes involved in the pathogenesis of AML.

Array CGH of fusion gene-positive leukemia-derived cell lines reveals cryptic regions of genomic gain and loss

Human leukemia-derived cell lines containing characteristic chromosomal translocations and inversions have been instrumental in identifying fusion genes implicated in the pathogenesis of the corresponding leukemia. Although chimeric fusion genes usually provide early and essential steps in the development of leukemia, they are not in themselves sufficient, requiring additional genetic events. The nature of these secondary, cooperating genetic events is not known. The advent of genome wide microarray-based methods for assessing copy number changes made it possible to search for cytogenetically invisible regions of chromosome imbalance. We used BAC microarrays with a resolution of 1 Mb to determine whether cryptic regions of deletion or gain were associated with specific leukemia-associated fusion genes in a series of cell lines. To complement the array analysis, we also applied 24-color karyotyping by M-FISH. This revealed cryptic chromosomal translocations and regions of loss or gain in all the cell lines studied. The chromosomal origin of previously unidentified marker chromosomes was revealed. In all cases, chromosomes described as monosomic were shown to be involved in unbalanced translocations with concurrent loss and/or gain of chromosomal material. The extent of these amplified and deleted regions was more accurately defined. Finally, small regions of deletion and amplification, often including genes known to be involved in leukemia progression (for example MYC, TP53, CDKN2A, and KIT), were identified.

High-resolution genome-wide array-based comparative genome hybridization reveals cryptic chromosome changes in AML and MDS cases with trisomy 8 as the sole cytogenetic aberration

Although trisomy 8 as the sole chromosome aberration is the most common numerical abnormality in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), little is known about its pathogenetic effects. Considering that +8 is a frequent secondary change in AML/MDS, cryptic--possibly primary--genetic aberrations may occur in cases with trisomy 8 as the apparently single anomaly. However, no such hidden anomalies have been reported. We performed a high-resolution genome-wide array-based comparative genome hybridization (array CGH) analysis of 10 AML/MDS cases with isolated +8, utilizing a 32K bacterial artificial chromosome array set, providing >98% coverage of the genome with a resolution of 100 kb. Array CGH revealed intrachromosomal imbalances, not corresponding to known genomic copy number polymorphisms, in 4/10 cases, comprising nine duplications and hemizygous deletions ranging in size from 0.5 to 2.2 Mb. A 1.8 Mb deletion at 7p14.1, which had occurred prior to the +8, was identified in MDS transforming to AML. Furthermore, a deletion including ETV6 was present in one case. The remaining seven imbalances involved more than 40 genes. The present results show that cryptic genetic abnormalities are frequent in trisomy 8-positive AML/MDS cases and that +8 as the sole cytogenetic aberration is not always the primary genetic event.