Interphase FISH results in DLCL and comparison with HLA protein expression
| . | Homozygous deletion . | Hemizygous deletion . | Expression* . | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 619pWE1 DPB . | 223H1 TAP . | 93N13 DQA1 . | 172K2 DRA . | M31A TNF-α . | C109K2118 HLA-A . | 619pWE1 DPB . | 223H1 TAP . | 93N13 DQA1 . | 172K2 DRA . | M31A TNF-α . | C109K2118 HLA-A . | HLA-DQ . | HLA-DR . | HLA-A . | |
| T2 | 3.0 | 1.5 | 48.5 | 49.0 | 1.0 | 3.0 | 27.0 | 12.5 | 16.0 | 14.0 | 19.0 | 14.0 | H | H | − |
| T3* | 0.0 | 1.0 | 5.0 | 1.5 | 3.0 | 1.0 | 5.0 | 15.0 | 30.0 | 10.0 | 10.0 | 2.0 | + | + | + |
| T11 | 1.5 | 0.0 | 9.0 | 15.5 | 3.5 | 1.0 | 13.0 | 5.5 | 58.0 | 49.5 | 35.0 | 20.0 | − | + | − |
| T13 | 1.5 | 2.5 | 0.5 | 16.0 | 1.0 | 0.0 | 24.0 | 25.5 | 26.5 | 40.0 | 42.0 | 35.5 | − | − | − |
| T14 | 1.5 | 2.5 | 69.0 | 58.5 | 2.5 | 0.0 | 15.0 | 48.0 | 13.5‡ | 5.0‡ | 57.5 | 58.5 | − | − | − |
| T16 | 0.0 | 0.0 | 22.5 | 8.0 | 2.5 | 3.0 | 23.5 | 18.5 | 15.0 | 25.5 | 27.0 | 27.5 | − | − | − |
| T18† | 0.0 | 7.0 | 64.5 | 71.5 | 1.0 | 2.5 | 18.5 | 17.0 | 2.0 | 2.0 | 7.5 | 23.5 | − | − | H |
| T19 | 2.5 | 3.0 | 16.5 | 3.0 | 0.5 | 1.5 | 19.0 | 15.0 | 11.0 | 11.0 | 13.5 | 14.0 | − | − | − |
| T20† | 0.0 | 0.0 | 59.5 | 3.0 | 2.0 | 6.5 | 70.0 | 70.0 | 25.5 | 79.5 | 75.5 | 53.0 | − | − | − |
| T22 | 1.0 | 0.5 | 1.5 | 6.0 | 1.0 | 0.0 | 8.5 | 1.0 | 11.5 | 10.0 | 6.0 | 7.0 | − | W | + |
| T23† | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 2.5 | 4.0 | 14.5 | 14.5 | 21.0 | 4.0 | − | W | + |
| T25† | 0.0 | 6.0 | 60.5 | 11.5 | 2.5 | 12.0 | 58.0 | 33.5 | 9.0 | 45.0 | 52.0 | 26.0 | − | − | − |
| T26 | 0.0 | 0.0 | 2.0 | 5.5 | 1.0 | 0.0 | 11.0 | 10.0 | 2.5 | 6.5 | 9.5 | 12.5 | ND | H | H |
| T30 | 2.0 | 1.5 | 0.5 | 0.5 | 0.5 | 0.0 | 16.0 | 12.0 | 10.0 | 15.5 | 9.0 | 30.5 | − | + | − |
| C1 | 0.0 | 0.5 | 27.5 | 26.0 | 1.0 | 2.0 | 3.0 | 16.0 | 32.5 | 15.0 | 22.0 | 17.0 | − | − | − |
| C2 | 0.0 | 0.0 | 0.0 | 0.0 | 3.0 | 1.0 | 8.5 | 9.5 | 72.0 | 72.5 | 68.5 | 68.5 | − | − | − |
| C9 | 0.0 | 30.0 | 44.0 | 52.0 | 1.0 | 0.0 | 10.0 | 13.5 | 27.0 | 22.0 | 56.0 | 8.5 | ND | − | − |
| C11† | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 6.0 | 14.0 | 15.0 | 3.5 | 5.0 | 6.0 | + | + | − |
| N3 | 2.0 | 0.0 | 0.0 | 0.5 | 2.0 | 0.0 | 5.0 | 12.5 | 12.0 | 24.0 | 16.5 | 9.0 | − | − | − |
| N4 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 1.5 | 9.5 | 5.0 | 32.0 | 16.5 | 9.5 | 9.0 | − | + | − |
| N8† | 0.0 | 1.0 | 0.0 | 0.0 | 0.5 | 1.0 | 15.0 | 9.5 | 7.0 | 7.0 | 17.0 | 16.0 | + | + | + |
| N9 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 4.5 | 12.0 | 8.5 | 8.5 | 21.0 | 20.0 | 13.0 | + | + | + |
| N13 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 10.0 | 9.0 | 10.5 | 9.0 | 13.0 | 8.0 | + | + | H |
| N15 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 11.0 | 12.0 | 6.0 | 5.0 | 4.5 | 7.0 | + | + | + |
| N18 | 0.0 | 0.0 | 0.5 | 0.0 | 2.0 | 0.0 | 9.0 | 7.0 | 5.0 | 4.0 | 16.5 | 9.0 | ? | H | + |
| Co1 | 0.0 | 0.5 | 0.0 | 0.0 | 1.0 | 0.0 | 2.0 | 1.5 | 8.0 | 5.0 | 9.0 | 2.0 | ND | ND | ND |
| Co2 | 0.0 | 5.0 | 0.0 | 0.0 | 0.0 | 0.0 | 4.0 | 8.0 | 1.5 | 3.5 | 8.5 | 7.5 | ND | ND | ND |
| Co3 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 4.0 | 4.0 | 9.0 | 8.0 | 9.0 | 4.0 | ND | ND | ND |
| Co4 | 0.0 | 0.0 | 0.5 | 0.0 | 0.0 | 0.0 | 4.0 | 5.0 | 9.0 | 5.0 | 7.0 | 5.0 | ND | ND | ND |
| Co5 | 0.0 | 0.0 | 1.0 | 7.0 | 0.0 | 0.0 | 5.5 | 5.0 | 2.0 | 1.0 | 4.5 | 5.5 | ND | ND | ND |
| Co6 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 2.5 | 3.5 | 6.0 | 7.0 | 4.0 | 4.0 | ND | ND | ND |
| Co7 | 0.0 | 3.0 | 1.0 | 1.0 | 1.0 | 0.0 | 6.0 | 7.0 | 5.0 | 4.0 | 3.5 | 6.0 | ND | ND | ND |
| Co8 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 4.0 | 5.0 | 5.5 | 1.0 | 6.5 | 10.5 | ND | ND | ND |
| Co9 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 6.0 | 3.0 | 5.0 | 8.0 | 8.0 | 9.5 | ND | ND | ND |
| Co10 | 0.0 | 1.0 | 0.0 | 0.0 | 0.5 | 0.0 | 1.5 | 3.0 | 3.0 | 10.5 | 19.0 | 9.5 | ND | ND | ND |
| . | Homozygous deletion . | Hemizygous deletion . | Expression* . | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 619pWE1 DPB . | 223H1 TAP . | 93N13 DQA1 . | 172K2 DRA . | M31A TNF-α . | C109K2118 HLA-A . | 619pWE1 DPB . | 223H1 TAP . | 93N13 DQA1 . | 172K2 DRA . | M31A TNF-α . | C109K2118 HLA-A . | HLA-DQ . | HLA-DR . | HLA-A . | |
| T2 | 3.0 | 1.5 | 48.5 | 49.0 | 1.0 | 3.0 | 27.0 | 12.5 | 16.0 | 14.0 | 19.0 | 14.0 | H | H | − |
| T3* | 0.0 | 1.0 | 5.0 | 1.5 | 3.0 | 1.0 | 5.0 | 15.0 | 30.0 | 10.0 | 10.0 | 2.0 | + | + | + |
| T11 | 1.5 | 0.0 | 9.0 | 15.5 | 3.5 | 1.0 | 13.0 | 5.5 | 58.0 | 49.5 | 35.0 | 20.0 | − | + | − |
| T13 | 1.5 | 2.5 | 0.5 | 16.0 | 1.0 | 0.0 | 24.0 | 25.5 | 26.5 | 40.0 | 42.0 | 35.5 | − | − | − |
| T14 | 1.5 | 2.5 | 69.0 | 58.5 | 2.5 | 0.0 | 15.0 | 48.0 | 13.5‡ | 5.0‡ | 57.5 | 58.5 | − | − | − |
| T16 | 0.0 | 0.0 | 22.5 | 8.0 | 2.5 | 3.0 | 23.5 | 18.5 | 15.0 | 25.5 | 27.0 | 27.5 | − | − | − |
| T18† | 0.0 | 7.0 | 64.5 | 71.5 | 1.0 | 2.5 | 18.5 | 17.0 | 2.0 | 2.0 | 7.5 | 23.5 | − | − | H |
| T19 | 2.5 | 3.0 | 16.5 | 3.0 | 0.5 | 1.5 | 19.0 | 15.0 | 11.0 | 11.0 | 13.5 | 14.0 | − | − | − |
| T20† | 0.0 | 0.0 | 59.5 | 3.0 | 2.0 | 6.5 | 70.0 | 70.0 | 25.5 | 79.5 | 75.5 | 53.0 | − | − | − |
| T22 | 1.0 | 0.5 | 1.5 | 6.0 | 1.0 | 0.0 | 8.5 | 1.0 | 11.5 | 10.0 | 6.0 | 7.0 | − | W | + |
| T23† | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 2.5 | 4.0 | 14.5 | 14.5 | 21.0 | 4.0 | − | W | + |
| T25† | 0.0 | 6.0 | 60.5 | 11.5 | 2.5 | 12.0 | 58.0 | 33.5 | 9.0 | 45.0 | 52.0 | 26.0 | − | − | − |
| T26 | 0.0 | 0.0 | 2.0 | 5.5 | 1.0 | 0.0 | 11.0 | 10.0 | 2.5 | 6.5 | 9.5 | 12.5 | ND | H | H |
| T30 | 2.0 | 1.5 | 0.5 | 0.5 | 0.5 | 0.0 | 16.0 | 12.0 | 10.0 | 15.5 | 9.0 | 30.5 | − | + | − |
| C1 | 0.0 | 0.5 | 27.5 | 26.0 | 1.0 | 2.0 | 3.0 | 16.0 | 32.5 | 15.0 | 22.0 | 17.0 | − | − | − |
| C2 | 0.0 | 0.0 | 0.0 | 0.0 | 3.0 | 1.0 | 8.5 | 9.5 | 72.0 | 72.5 | 68.5 | 68.5 | − | − | − |
| C9 | 0.0 | 30.0 | 44.0 | 52.0 | 1.0 | 0.0 | 10.0 | 13.5 | 27.0 | 22.0 | 56.0 | 8.5 | ND | − | − |
| C11† | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 6.0 | 14.0 | 15.0 | 3.5 | 5.0 | 6.0 | + | + | − |
| N3 | 2.0 | 0.0 | 0.0 | 0.5 | 2.0 | 0.0 | 5.0 | 12.5 | 12.0 | 24.0 | 16.5 | 9.0 | − | − | − |
| N4 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 1.5 | 9.5 | 5.0 | 32.0 | 16.5 | 9.5 | 9.0 | − | + | − |
| N8† | 0.0 | 1.0 | 0.0 | 0.0 | 0.5 | 1.0 | 15.0 | 9.5 | 7.0 | 7.0 | 17.0 | 16.0 | + | + | + |
| N9 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 4.5 | 12.0 | 8.5 | 8.5 | 21.0 | 20.0 | 13.0 | + | + | + |
| N13 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 10.0 | 9.0 | 10.5 | 9.0 | 13.0 | 8.0 | + | + | H |
| N15 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 11.0 | 12.0 | 6.0 | 5.0 | 4.5 | 7.0 | + | + | + |
| N18 | 0.0 | 0.0 | 0.5 | 0.0 | 2.0 | 0.0 | 9.0 | 7.0 | 5.0 | 4.0 | 16.5 | 9.0 | ? | H | + |
| Co1 | 0.0 | 0.5 | 0.0 | 0.0 | 1.0 | 0.0 | 2.0 | 1.5 | 8.0 | 5.0 | 9.0 | 2.0 | ND | ND | ND |
| Co2 | 0.0 | 5.0 | 0.0 | 0.0 | 0.0 | 0.0 | 4.0 | 8.0 | 1.5 | 3.5 | 8.5 | 7.5 | ND | ND | ND |
| Co3 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 4.0 | 4.0 | 9.0 | 8.0 | 9.0 | 4.0 | ND | ND | ND |
| Co4 | 0.0 | 0.0 | 0.5 | 0.0 | 0.0 | 0.0 | 4.0 | 5.0 | 9.0 | 5.0 | 7.0 | 5.0 | ND | ND | ND |
| Co5 | 0.0 | 0.0 | 1.0 | 7.0 | 0.0 | 0.0 | 5.5 | 5.0 | 2.0 | 1.0 | 4.5 | 5.5 | ND | ND | ND |
| Co6 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 2.5 | 3.5 | 6.0 | 7.0 | 4.0 | 4.0 | ND | ND | ND |
| Co7 | 0.0 | 3.0 | 1.0 | 1.0 | 1.0 | 0.0 | 6.0 | 7.0 | 5.0 | 4.0 | 3.5 | 6.0 | ND | ND | ND |
| Co8 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 4.0 | 5.0 | 5.5 | 1.0 | 6.5 | 10.5 | ND | ND | ND |
| Co9 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 6.0 | 3.0 | 5.0 | 8.0 | 8.0 | 9.5 | ND | ND | ND |
| Co10 | 0.0 | 1.0 | 0.0 | 0.0 | 0.5 | 0.0 | 1.5 | 3.0 | 3.0 | 10.5 | 19.0 | 9.5 | ND | ND | ND |
FISH indicates fluorescent in situ hybridization; DLCL, diffuse large B-cell lymphomas; HLA, human leukocyte antigen; TNFα, tumor necrosis factor α; T, testicular DLCL; C, central nervous system DLCL; N, nodal DLCL; Co, normal control (tonsil) tissue.
The table shows the percentages of nuclei with loss of one or two HLA region-specific signals in combination with retention of the centromeric signals for chromosome 6. In each experiment, 200 nuclei were counted. Shaded boxes indicate loci with an abnormal percentage of cells with homozygous or hemizygous deletions. These percentages were significantly higher than those obtained in the 10 normal controls. For homozygous deletions, the cut-off level was > 6% cells, for hemizygous deletions > 21% (see text).
Immunohistochemistry (see also Table 1) was performed on frozen sections (HLA-DR and HLA-DQ) or paraffin-embedded tissue sections (HLA-A), whereas FISH analysis was done on nuclei obtained from frozen tissue sections. The − indicates negative; +, positive; W: weakly positive; H: tumor heterogeneity with distinct tumor parts being completely negative; ?, undeterminable; ND, not done.
In case of aneuploidy for chromosome 6, this was corrected per cell for the number of centromere 6 specific signals.
These and many other percentages are relatively low because the tumor was also affected by a homozygous deletion.