Definitive molecular cytogenetic characterization of 15 colorectal cancer cell lines

Abstract

In defining the genetic profiles in cancer, cytogenetically aberrant cell lines derived from primary tumors are important tools for the study of carcinogenesis. Here, we present the results of a comprehensive investigation of 15 established colorectal cancer cell lines using spectral karyotyping (SKY), fluorescence in situ hybridization, and comparative genomic hybridization (CGH). Detailed karyotypic analysis by SKY on five of the lines (P53HCT116, T84, NCI-H508, NCI-H716, and SK-CO-1) is described here for the first time. The five lines with karyotypes in the diploid range and that are characterized by defects in DNA mismatch repair had a mean of 4.8 chromosomal abnormalities per line, whereas the 10 aneuploid lines exhibited complex karyotypes and a mean of 30 chromosomal abnormalities. Of the 150 clonal translocations, only eight were balanced and none were recurrent among the lines. We also reviewed the karyotypes of 345 cases of adenocarcinoma of the large intestine listed in the Mitelman Database of Chromosome Aberrations in Cancer. The types of abnormalities observed in the cell lines reflected those seen in primary tumors: there were no recurrent translocations in either tumors or cell lines; isochromosomes were the most common recurrent abnormalities; and breakpoints occurred most frequently at the centromeric/pericentromeric and telomere regions. Of the genomic imbalances detected by array CGH, 87% correlated with chromosome aberrations observed in the SKY studies. The fact that chromosome abnormalities predominantly result in copy number changes rather than specific chromosome or gene fusions suggests that this may be the major mechanism leading to carcinogenesis in colorectal cancer.

Figure 1

SKYGRAM ideograms in COLO320DM demonstrating complex chromosomal aberrations, including involvement of chromosomes 8 (orange, MYC+) and 13 (red, CDX2+): (A) double minutes and translocations/insertions (arrows) in clone A1. (B) hrs in der(19) in clone B1. (C) hrs in der(8) in clone B2. Clones A1 and A2 contained 50~100 dmin per cell. See Table 1 for full written karyotypes. (D) FISH in COLO320DM: insertions of MYC (orange) and CDX2 (green) into chromosome 2.

Figure 2

Chromosomal CGH in nine CRC cell lines: A, DLD1; B, HCT116; C, p53HCT116; D, HT-29; E, SW48; F, SW480; G, SW837; H, T84; and I, LoVo. Vertical lines to the left of the chromosome ideogram indicate loss and lines to the right indicate gain; heavy lines indicate amplification.

Figure 3

Recurrent breakpoints in 15 CRC cell lines. Each mark indicates one cell line (each particular breakpoint was counted only once per cell line). Color code: blue, translocation; red, deletion; pink, interstitial deletion; brown, duplication; plum, insertion; green, isochromosome; orange, hsr; light blue, multiple types of breakpoint per band in one cell line (e.g., translocation and deletion).

Figure 4

Cell line SW480. (A) Partial SKYGRAM demonstrating der(19)t(8;19)t(5;19); the arrow indicates chromosome 8. (B) FISH demonstrating copies of MYC in a normal chromosome 8 and a der(9), and MYC amplification in the der(19). (C, D) Jumping translocations involving chromosome 15 in LS411N: C. SKY analysis and D. aCGH demonstrating amplification of the JT segment 15q21.2->15qter.