Table 2.
Partial list of dysregulated genes that were originally present in patient tumor and maintained in the xenografts during serial subtransplantations
| Accession | Target ID | Definition | Log 2 ratio (tumor/normal) |
||
|---|---|---|---|---|---|
| Patient tumor | Xeno (P-I) | Xeno (P-III) | |||
| NOTCH pathway | |||||
| NM_017617.3 | NOTCH1 | Notch homolog 1, translocation-associated | 2.89 | 3.01 | 2.35 |
| NM_203458.3 | NOTCH2NL | Notch homolog 2 (Drosophila) N-terminal like | 1.35 | 1.38 | 1.35 |
| NM_005524.2 | HES1 | Hairy and enhancer of split 1 (Drosophila) | 1.85 (1.13)a | 1.90 (1.5) | 2.08 (1.25) |
| NM_001024598 | HES3 | Hairy and enhancer of split 3 (Drosophila) | 1.61 | 2.21 | 2.75 |
| NM_021170.2 | HES4 | Hairy and enhancer of split 4 (Drosophila) | 5.41 (1.26) | 5.65 (1.13) | 5.59 (1.49) |
| NM_000214.1 | JAG1 | Jagged 1 (Alagille syndrome) | 2.03 | 1.31 | 0.79 |
| NM_002226.3 | JAG2 | Jagged 2 (JAG2), transcript variant 1 | 1.64 (1.47) | 2.57 (1.96) | 2.83 (1.64) |
| NM_001040167 | LFNG | Lunatic fringe homolog (Drosophila) | 5.51 | 5.32 | 5.22 |
| NM_172341.1 | PSENEN | Presenilin enhancer 2 homolog (Caenorhabditis elegans) | 1.02 (1.77) | 0.96 (2.26) | 2.41 (1.62) |
| NM_001005744 | NUMB | Numb homolog (Drosophila) | −1.14 (−0.97) | −1.11 (−0.66) | −1.01 (−1.24) |
| PTCH-SHH pathway | |||||
| NM_005270.3 | GLI2 | GLI-Kruppel family member GLI2 | 1.56 | 2.08 | 1.94 |
| NM_000168.3 | GLI3 | GLI-Kruppel family member GLI3 | 2.60 (20.5) | 2.94 (2.38) | 2.86 (0.93) |
| NM_152629.3 | GLIS3 | GLIS family zinc finger 3 | 2.02 | 1.34 | 1.29 |
| NM_005631.3 | SMO | Smoothened homology (Drosophila) | 1.91 | 2.32 | 2.32 |
| NM_002442.2 | MSI1 | Musashi homolog 1 (Drosophila) | 2.33 (1.74) | 2.49 (2.54) | 2.98 (1.27) |
| NM_170721.1 | MSI2 | Musashi homolog 2 (Drosophila) | 1.24 | 1.30 | 0.98 |
| WNT pathway | |||||
| NM_004655.2 | AXIN2 | Axin 2 (conductin, axil) | 2.36 | 1.89 | 2.27 |
| NM_024494.1 | WNT2B | Wingless-type MMTV integration site family, member 2B | 3.50 | 3.12 | 2.45 |
| NM_012242.2 | DKK1 | Dickkopf homolog 1 (Xenopus laevis) | 2.29 | 0.72 | 1.31 |
| NM_014421.2 | DKK2 | Dickkopf homolog 2 (Xenopus laevis) | 2.65 | 2.58 | 2.90 |
| NM_004422.2 | DVL2 | Dishevelled, dsh homolog 2 (Drosophila) | 1.07 | 0.92 | 0.97 |
| NM_001463.2 | FRZB | Frizzled-related protein | 4.82 (3.64) | 4.77 (2.45) | 4.65 (3.05) |
| NM_003505.1 | FZD1 | Frizzled homolog 1 (Drosophila) | 2.19 (2.14) | 2.44 (2.35) | 2.35 (2.54) |
| NM_007197.2 | FZD10 | Frizzled homolog 10 (Drosophila) | 1.70 | 2.11 | 2.16 |
| NM_001466.2 | FZD2 | Frizzled homolog 2 (Drosophila) | 3.26 | 3.48 | 3.02 |
| NM_003506.2 | FZD6 | Frizzled homolog 6 (Drosophila) | 1.84 | 1.99 | 1.94 |
| NM_003507.1 | FZD7 | Frizzled homolog 7 (Drosophila) | 1.61 | 1.49 | 1.28 |
| Stem cell marker | |||||
| NM_006017.1 | PROM1 | Prominin 1 | 3.44 (3.83) | 2.81 (6.05) | 3.39 (2.40) |
| NM_006617.1 | NES | Nestin | 3.11 (1.99) | 3.39 (3.15) | 3.15 (0.55) |
| NM_000693.2 | ALDH1A3 | Aldehyde dehydrogenase 1 family, member A3 | 1.97 | 2.17 | 1.37 |
| NM_000691.3 | ALDH3A1 | Aldehyde dehydrogenase 3 family, member A1 | 1.78 | 1.81 | 2.12 |
| NM_170726.1 | ALDH4A1 | Aldehyde dehydrogenase 4 family, member A1 | 2.02 | 2.25 | 1.57 |
| NM_002211.2 | ITGB1 | Integrin, beta 1, transcript variant 1A | 2.43 (0.72) | 2.57 (1.73) | 2.41 (0.51) |
| NM_033668.1 | ITGB1 | Integrin, beta 1, transcript variant 1D | 2.20 | 2.16 | 2.22 |
| Oncogenes | |||||
| NM_005157.3 | ABL1 | v-abl Abelson murine leukemia viral oncogene | 2.24 | 2.37 | 1.82 |
| NM_031934.3 | RAB34 | RAB34, member RAS oncogene family | 3.41 | 3.37 | 3.63 |
| NM_012250.3 | RRAS2 | Related RAS viral (r-ras) oncogene homolog 2 | 1.48 | 1.32 | 1.43 |
| Drugable targets | |||||
| NM_004964.2 | HDAC1 | Histone deacetylase 1 | 2.23 | 1.91 | 1.53 |
| NM_006037.3 | HDAC4 | Histone deacetylase 4 | 2.28 | 2.23 | 1.95 |
| NM_001067.2 | TOP2A | Topoisomerase (DNA) II alpha 170 kDa | 5.56 | 5.67 | 6.03 |
| NM_006437.3 | PARP4 | Poly(ADP-ribose) polymerase family, member 4 | 2.40 | 2.27 | 2.50 |
| NM_031458.1 | PARP9 | Poly(ADP-ribose) polymerase family, member 9 | 2.10 | 1.40 | 1.68 |
| NM_022750.2 | PARP12 | Poly(ADP-ribose) polymerase family, member 12 | 2.05 | 1.44 | 1.61 |
| NM_017554.1 | PARP14 | Poly(ADP-ribose) polymerase family, member 14 | 2.16 | 2.29 | 2.49 |
| Differentiation marker | |||||
| NM_003380.2 | VIM | Vimentin | 5.54 | 5.31 | 5.12 |
| NM_003179.2 | SYP | Synaptophysin | −3.17 | −2.97 | −2.59 |
| NM_031845.2 | MAP2 | Microtubule-associated protein 2 | −1.83 | −1.99 | −2.44 |
| NM_002055.2 | GFAP | Glial fibrillary acidic protein | −1.41 | −4.95 | −4.97 |
aRatio of quantitative reverse transcriptase–polymerase chain reaction.