High-resolution analysis of aberrant regions in autosomal chromosomes in human leukemia THP-1 cell line

Abstract

Background: THP-1 is a human monocytic leukemia cell line derived from a patient with acute monocytic leukemia. The cell line differentiates into macrophage-like cells by stimulation with phorbol myristate acetate (PMA). Although it has been used frequently as a model for macrophage differentiation in research including the FANTOM4/Genome Network Project, there are few reports on its genomic constitution. Therefore, we attempted to reveal the genomic aberrations in these cells with the microarray-based comparative genomic hybridization (aCGH) technique.

Findings: We report large aberrations, including deletions 6p, 12p, 17p, and trisomy 8, and revealed breakpoints in the MLL and MLLT3 genes. Moreover, we found novel genomic aberrations such as a hemizygous narrow deletion partially containing the TP73 gene and homozygous deletions, including the CDKN2A, CDKN2B and PTEN genes.

Conclusion: In this study, we identified 119 aberrant regions in autosomal chromosomes, and at least 16 of these aberrations were less than 100 kb, most of which were undetectable in the previous works. We also revealed a total of 4.6 Mb of homozygous deleted regions. Our results will provide a base to precisely understand studies involving the THP-1 cell line, especially the huge amount of data generated from the FANTOM4/Genome Network Project.

Figure 1

Chromosomal aberrations detected in the THP-1 cell sample. Moving averages of signal log ratio for each chromosome (window size = 10 points) are represented as a line plot. Each chromosome is represented on the left. Signal log ratio increases to the right and decreases to the left of centerline. Losses and gains identified by the software are represented by the shaded region and the vertical line.

Figure 2

Regional loss on the chromosome X. A loss of signals was detected across chromosome X, because the THP-1 cell line derived from a human male patient was compared with the reference human female genome. Two local deletions were also found (arrows). Weighted log ratio data appear as a scatter plot. Green points represent subthreshold values. The identified aberrant region is plotted as a bar graph and shaded in red, and the height of each bar corresponds to the average log ratio for that interval.

Figure 3

Breakpoints on the MLL and MLLT3 genes. (A) MLL gene on chromosome 11. (B) MLLT3 gene on chromosome 9. The MLL and MLLT3 genes had a breakpoint in their gene regions. Weighted log ratio data appear as a scatter plot. Red points represent suprathreshold values. The identified aberrant region is plotted as a bar graph shaded in red, and height of each bar corresponds to the average log ratio for that interval.

Figure 4

Regions of homozygous deletion. (A) Loss of region containing the CDKN2A and CDKN2B genes. A continuous region containing CDKN2A and CDKN2B on chromosome 9 was deleted. (B) Partial loss in the PTEN gene. PTEN lost a part of its gene region. Weighted log ratio data appear as a scatter plot. Green points represent subthreshold values. The identified aberrant regions are plotted as a bar graph shaded in red, and the height of each bar corresponds to the average log ratio for that interval. (C) Deleted regions displayed on the UCSC Genome Browser. Black boxes represent the identified aberration Nos. 78 and 79, and lower row shows schematic structure of the RefSeq genes in this region.

Figure 5

Deletion in the region containing the TP73 gene. One narrow deletion on chromosome 1 included the KIAA0495 and TP73 genes. Weighted log ratio data appear as a scatter plot. Green points represent subthreshold values. The identified aberrant region is plotted as a bar graph shaded in red, and the height of each bar corresponds to the average log ratio for that interval.