Article Figures & Data
Figures
- Fig. 1.
A, venn diagram showing probe sets identified by GeneSpring GX analysis with a cut off of FC ≥ 2 (P < 0.05) after either RMA or GC-RMA normalization and by rank product analysis. B, supervised hierarchical clustering using Eucledian distance for 23 genes differentially expressed (P < 0.05) in PV CD34+ cells compared with controls cells as identified by oligonucleotide microarray and verified by TLDAs between normal and PV samples. Red, upregulated genes; green, downregulated genes.
- Fig. 2.
A, erythroid differentiation of CD34+ cells transduced with JAK2. Fluorescence-activated cell sorting analysis for GpA and CD71 cell surface antigenes was done at 10 d posttransduction with WT JAK2, JAK2V617F, or Tel-JAK2. Cells were grown in full erythroid media +/− EPO or maintenance media. The experiment was repeated thrice with similar results obtained. B, cells were grown in methylcellulose containing or lacking EPO for 12 d after transduction with the indicated JAK2 allele. The average (±SEM) of erythroid or myeloid colonies was determined from counts of eight replicate plates of cells. Statistical significance was calculated (Student's t test) comparing JAK2V617F and JAK2wt. The experiment was repeated thrice with similar results obtained.
- Fig. 3.
A, venn diagram showing the overlap between the set of genes found differentially expressed in CD34+ cells transduced with WT JAK2 when compared with control cells and in cells transduced with JAK2V617F when compared with controls. B, hierarchical clustering of the genes differentially expressed in cells transduced with either JAK2 or JAK2V617F when compared with untransduced cells: genes found in common (left), genes specific to JAK2 (middle), genes specific to JAK2V617F (right).
- Fig. 4.
A, expression of WT1, BCL6, and FLT3 mRNA in HEL and UKE-1 cells (mutant JAK2) and K562 (wt JAK2; BCR/ABL positive) as measured by reverse transcription-PCR, at 24 h posttreatment with 1 or 2 μmol/L JAK inhibitor I. B, expression levels of EVI1, SEPT6 after treatment as in A.
- Fig. 5.
A, cross-classification plots generated by prediction analysis for microarrays R software (16) for PV versus normal and ET versus normal specimens. Red and green dots, the specimens analyzed with different list of genes: the JAK2 inhibition signature, JAK2 overexpression signature, and PV signature. B, venn diagram showing the relationship between the PV expression signature, genes regulated in response to JAK2 overexpression in CD34+ cells, and genes regulated in JAK2V617F harboring cell lines treated with JAK inhibitor. The 287 probe sets remaining from the PV signature can still be used to distinguish PV from normal specimens. C and D, the GSE3410 data set (C) and GSE9827 (D) were imported onto GeneSpring GX11, and both JAK2-dependent and JAK2-independent gene sets were used to classify samples by unsupervised hierarchical clustering.
Tables
- Table 1.
JAK2-dependent and JAK2-independent gene sets
Name Affymetrix ID Log ratio (normal/PV) P Entrez gene ID A. JAK2-dependent PV signature genes* AIM1 212543_at 2.6 0.021 202 ANXA5 200782_at 2.3 0.0424 308 BACH2 221234_s_at 3.7 0.0007 60468 BCL6 203140_at 3.9 0.0003 604 BLNK 207655_s_at 4.3 0 29760 GALNAC4S-6ST 203066_at 3.7 0.0009 51363 HLA-DMB 203932_at 2.5 0.0257 3109 IRF8 204057_at 4.6 0 3394 KLF4 221841_s_at 2.2 0.0485 9314 LOC100133941 266_s_at 3 0.007 100133941 LY86 205859_at 2.4 0.036 9450 PLAC8 219014_at 3.4 0.0023 51316 RNASE6 213566_at 2.5 0.0233 6039 TIPARP 212665_at 2.5 0.0253 25976 B. JAK2-independent PV signature genes† DEFA1 205033_s_at −2.3 0 1667 MCL1 214057_at 1.5 0.0001 4170 P2RY14 206637_at 1.7 0 9934 C13orf15 218723_s_at 2 0 28984 INHBC 207688_s_at 1.6 0.0001 3626 SAMHD1 204502_at 1.4 0.0003 25939 ARL4C 202207_at 1.5 0.0002 10123 TGFB1 201506_at 1.5 0 7045 DEFA4 207269_at −1.6 0 1669 ILF2 200052_s_at 1.1 0.0164 3608 SNRPE 215450_at 1.4 0.0006 6635 YBX1 208627_s_at 1.2 0.006 4904
Supplementary Data
Supplementary Figures S1-S2 and Supplementary Tables S1-S9.
Files in this Data Supplement:
- Supplementary Figure S1 - Supplementary Figure S1.
- Supplementary Figure S2 - Supplementary Figure S2.
- Supplementary Legends - Supplementary Legends.
- Supplementary Table S5 - Supplementary Table S5.
- Supplementary Table S6 - Supplementary Table S6.
- Supplementary Table S7 - Supplementary Table S7.
- Supplementary Table S8 - Supplementary Table S8.
- Supplementary Table S9 - Supplementary Table S9.
- Supplementary Table S1 - Supplementary Table S1.
- Supplementary Table S2 - Supplementary Table S2.
- Supplementary Table S3 - Supplementary Table S3.
- Supplementary Table S4 - Supplementary Table S4.
Volume 16, Issue 17
