Table 1.
A summary of the copy number changes in glioblastoma multiforme for a panel of genes involved in phosphoinositide signalling and trafficking
| Gene | Chromosome | Gain | Loss | Main effect on lipids | Previous report in glioma |
|---|---|---|---|---|---|
| INPP5B (1p34) | 1 | 8.80 | 2.70 | PI(4,5)P2 ↓ | No |
| PIK3R3 (1p36.2) | 1 | 8.80 | 2.20 | PI(3,4,5)P3 ↑ | Yes [88] |
| PI4KB (1q21) | 1 | 11.30 | 0.60 | PI4P ↑ | No |
| PIP5K1A (1q21.3) | 1 | 11.30 | 0.60 | PI(4,5)P2 ↑ | No |
| AKT3 (1q44) | 1 | 12.20 | 2.00 | – | Yes [89] |
| PIK3C2B (1q32) | 1 | 19.80 | 0.60 | PI(3,4)P2 ↑ | Yes [45, 90, 91] |
| INPP1 (2q32) | 2 | 2.50 | 3.80 | IP2 ↑ | No |
| INPP4A (2q11.2) | 2 | 4.50 | 1.60 | PI3P ↑ | No |
| PIKFYVE (2q34) | 2 | 3.50 | 2.40 | PI5P/PI(3,5)P2 ↑ | No |
| SACM1L (3p21.3) | 3 | 5.80 | 7.80 | PI4P ↑ | No |
| PIK3R4 (3q22.1) | 3 | 7.00 | 6.00 | PI3P ↑ | No |
| PIK3CB (3q22.3) | 3 | 6.90 | 5.20 | PI(3,4,5)P3 ↑ | Yes [92] |
| PIK3CA (3q26.3) | 3 | 11.80 | 3.50 | PI(3,4,5)P3 ↑ | Yes [93] |
| INPP4B (4q31.21) | 4 | 3.60 | 5.80 | PI(3,4)P2 ↑ | No |
| PIK3R1 (5q13.1) | 5 | 4.40 | 6.60 | PI(3,4,5)P3 ↓ | Yes [94] |
| FIG 4 (6q21) | 6 | 1.60 | 18.80 | PI(3,5)P2 ↑ | No |
| MTMR7 (8p22) | 8 | 6.30 | 8.00 | PI3P ↑ | No |
| PIP4K2A (10p12.2) | 10 | 2.20 | 77.60 | PI(4,5)P2 ↓ | No |
| MINPP1 (10q23) | 10 | 0.30 | 83.90 | IP6 ↑ | No |
| PTEN (10q23.3) | 10 | 2.00 | 84.80 | PI(3,4,5)P3 ↑ | Yes |
| PIK3AP1 (10q24.1) | 10 | 0.30 | 83.40 | PI(3,4,5)P3 ↓ | No |
| INPP5F (10q26.11) | 10 | 84.30 | PI(3,4,5)P3 ↑ | No | |
| INPP5A (10q26.3) | 10 | 83.40 | IP3 ↑ | Yes [66] | |
| PIK3C2A (11p15.5-p14) | 11 | 2.50 | 12.10 | PI3P/PI(3,4)P2 ↓ | No |
| PLCB3 (11q13) | 11 | 1.60 | 11.30 | PI(4,5)P2 ↑ | No |
| MTMR2 (11q22) | 11 | 2.70 | 9.70 | PI3P ↑ | No |
| PIK3C2G (12p.12) | 12 | 8.90 | 9.90 | PI(3,4,5)P3 ↑ or ↓ | Yes [95] |
| MTMR6 (13q12) | 13 | 1.60 | 26.50 | PI3P/PI(3,5)P2 ↑ | No |
| AKT1 (14q32.32) | 14 | 4.50 | 23.00 | – | Yes |
| PLCB2 (15q15) | 15 | 1.10 | 21.90 | PI(4,5)P2 ↑ | No |
| PLCG2 (16q24.1) | 16 | 3.10 | 11.60 | PI(4,5)P2 ↑ | No |
| PIK3R5 (17p13.1) | 17 | 2.70 | 10.70 | PI(3,4,5)P2 ↑ | No |
| PIP4K2B (17q12) | 17 | 2.80 | 10.70 | PI(4,5)P2 ↓ | No |
| MTMR4 (17q22–q23) | 17 | 6.40 | 5.50 | PI3P ↑ | No |
| PIK3C3 (18q12.3) | 19 | 4.90 | 7.50 | PI3P ↓ | No |
| PIP5K1C (19p13.3) | 19 | 30.20 | 5.00 | PI(4,5)P2 ↑ | No |
| PIP5K1B (19; 19 C1) | 19 | 8.00 | 9.70 | PI(4,5)P2 ↑ | No |
| AKT2 (19q13.1–q13.2) | 19 | 25.60 | 5.80 | – | Yes [89, 96] |
| PIK3R2 (19q13.2–q13.4) | 19 | 30.60 | 3.30 | PI(3,4,5)P3 ↑ | No |
| PLCB4 (20p12) | 20 | 31.80 | 2.40 | PI(4,5)P2 ↓ | No |
| PLCB1 (20p12) | 20 | 34.60 | 2.20 | PI(4,5)P2 ↓ | No |
| PLCG1 (20q12–q13.1) | 20 | 30.30 | 2.20 | PI(4,5)P2 ↓ | Yes[97] |
| PIK3IP1 (22q12.2) | 22 | 1.90 | 27.90 | PI(3,4,5)P3 ↑ | Yes [98] |
| MTMR8 (Xq11.2) | X | 5.60 | 65.70 | PI3P/PI(3,5)P2 ↑ | No |
| OCRL (Xq25) | X | 4.50 | 66.60 | PI(4,5)P2 ↑ | No |
| MTM1 (Xq28) | X | 4.50 | 66.00 | PI3P/PI(3,5)P2 ↑ | No |
The chromosomal localisation of each gene appears in brackets after its name. The “main effect on lipid” column refers to the predicted effect on either phosphoinositide lipid or inositol phosphate levels depending on whether gene copy number loss or gain predominates. The “previously reported in glioma” column indicates where there has been a previous publication demonstrating that a gene or gene product is involved in glioblastoma multiforme.