FIGURES AND TABLES

Figure 1.

Representative genomic profiles for individual tumors. Whole genomic profiles are shown for a representative patient sample (a) and the SP-53 cell line (b). Log₂ ratios were plotted for all clones on the basis of chromosome position, with the vertical lines showing separation of chromosomes. The BACs and PACs are ordered according to their position in the genome from the 1p telomere on the left to the Xq telomere on the right. (a) Regions of copy number gain: 5p, 7p21.3, 17q21.31−q24.3 and X. Regions of copy number loss: 1p32, 2p11.2, 2q13, 8p12−p23.3, 8q12.3−q13.1, 9p24.3−q31.2, 11q22.3−q23.2, 13q14.3−q21.1 and 15. (b) Regions of copy number gain: 7p11.2−p22.3. Regions of copy number loss: 1p36.23−p36.32, 1p13.3−p31.2, 1q13.2−q44, 2p11.2−q14.3, 4p15.1−p16.1, 6q14.1−q21, 6q23.2−q26, 7q22.1−q32.3, 9p21.3−p22.1, 11q22.3−q23.2, 18q22.1 and 20q13.13−q13.2

Figure 2.

Genome-wide frequency of copy number alterations for 29 patients. (a) Frequency of copy number gains. (b) Frequency of copy number losses. Clones are ordered from chromosome 1 to 22 and within each chromosome according to their Sanger Center mapping position, May 2004 version

Figure 3.

Genomic profiles of chromosome 2q from a patient sample (G468) and from three MCL cell lines (SP-53, Z-138 and Jeko-1). Log₂ ratio over +0.2 represents genomic copy number gain, and a log₂ ratio below -0.2 genomic copy number loss. Physical distances (Mb) from the 2q centromere are indicated. The vertical lines indicate the lowest locus of chromosome 2 at BAC438K19 containing the BIM gene. Log₂ ratios were -0.59 (G468), -2.75 (SP-53), -1.71 (Z-138) and -1.76 (Jeko-1) at BAC438K19, suggesting that homozygous loss occurs at the BIM gene locus

Figure 4.

Minimum common region of homozygous loss at 2q13 and expression of BIM. (a) Schematic illustration of BAC438K19, the BIM gene exons, and loss patterns of three cell lines (SP-53, Z-138 and Jeko-1). Gray boxes: exons (open reading frames) of BIM EL and BIM L. The open reading frame of BIM EL (597 bp) consists of three exons: exon 1 from 75 082 to 75 475 bp (394 bp) including the initiating codon (ATG), exon 2 from 49 074 to 49 177 bp (104 bp), and exon 3 from 34 990 to 35 088 bp (99 bp) including the termination codon (TGA), all on BAC438K19. Black and white circles: probes used for Southern blot analyses. Broken horizontal lines with white circles: homozygous loss (bands negative). Thick horizontal lines with black circles: no homozygous loss (bands positive). Thin horizontal lines: not confirmed whether homozygous loss or not. Bold broken horizontal arrows between probes 2 and 3 indicate the minimum common region of homozygous loss of 2q13. (b) Southern blot analyses using probes 1−6 for genomic DNAs of MCL cell lines. Lane 1, human placenta; lane 2, SP-53; lane 3, Granta 519 (G519); lane 4, Z-138; lane 5, REC-1; lane 6, NCEB-1; lane 7, Jeko-1; lane 8, JVM2. Bands of probe 1: human placenta (+), SP-53 (-), Granta 519 (+), Z-138 (+), REC-1 (+), NCEB-1 (+), Jeko-1 (-), and JVM2 (+). Bands of probes 2 and 3: human placenta (+), SP-53 (-), Granta 519 (+), Z-138 (-), REC-1 (+), NCEB-1 (+), Jeko-1 (-), and JVM2 (+). Bands of probe 4: human placenta (+), SP-53 (-), Granta 519 (+), Z-138 (-), REC-1 (+), NCEB-1 (+), Jeko-1 (+/-), and JVM2 (+). Bands of probes 5 and 6: human placenta (+), SP-53 (-), Granta 519 (+), Z-138 (-), REC-1 (+), NCEB-1 (+), Jeko-1 (+), and JVM2 (+). 'Control' indicates the representative control band of probe 3 (TCR probe) located under the bands of probe 6. (c) Northern blot analysis of BIM with seven MCL cell lines, B-cell lymphoma (Karpas 231) and Burkitt's lymphoma (Raji) cell lines. Control is -actin

Figure 5.

Southern blot and FISH analysis of a patient sample (G468). (a) Southern blot analysis. Lane 1: human placenta. Lanes 2, 3, 5: Patient samples without 2q13 deletion. Lane 4: G468 showing 2q13 loss by array CGH (see Figure 3). Lane 6: Jeko-1 cell line showing homozygous deletion at BIM locus. Probe 2 that contain BIM exon was used in this experiment. (b) Dual-color FISH analysis with probes A and B of G468. Probe A: BAC438K19; probe B: BAC368A17. Probe B is 1.55 Mb telomeric to probe A, and BAC438K19 contains the BIM gene. Interphase chromosomes have two pairs of red signals (probe B, red), and one pair of green signals (probe A, green), indicating heterozygous loss of probe A

Table 1 - Recurrent and most frequent regions of genomic gain and loss.