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Blood, Vol. 113, Issue 26, 6681-6690, June 25, 2009
Copy number abnormalities, MYC activity, and the genetic fingerprint of normal B cells mechanistically define the microRNA profile of diffuse large B-cell lymphoma
Blood Li et al.
113: 6681
Supplemental materials for: Li et al
Files in this Data Supplement:
- Table S5. Fisher’s Exact Test of LN vs. XN samples (PDF, 24 KB)
- Table S6. Fisher’s Exact Test of primarytumors vs. cell lines (PDF, 60 KB)
- Table S7. Components of miRNA clusters with 98, 38, and 16 miRNA genes (PDF, 49.5 KB)
- Table S8. miRNAs directly regulated by MYC* and MG cluster assignment (PDF, 29 KB)
- Table S9. miRNA signature from normal B cells* and MG cluster assignment (PDF, 52.9 KB)
- Figure S1. Heat map of copy number data for miRNA mapping on chromosome 13 in DLBCL cell lines (JPG, 565 KB)
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Highlighted on the right side are three DLBCL cell lines, two of each (Ly4 and Ly7) are known to have amplification of miR-17-92 cluster locus. The left side red line indicates the extension of our platform coverage in this locus. Noticeable as well is the high frequency (~50%) of gain/amplification targeting the entire chromosome 13, or preferentially the miR-17-92 locus, in DLBCL cell lines. Loss of miR-15a/16-1 miRNAs (green line) was detected in five cell lines.
- Figure S2. Heat map of copy number data for miR-650 and its relationship to light chain immunophenotyping in DLBCL cell lines (JPG, 395 KB)
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MiRNA-650 maps within the light chain lambda locus (λ) and it is frequently deleted following rearrangement of this locus in lambda but not in kappa light chain expressing DLBCLs (p<0.0, Fisher exact test). Importantly, we used northern blots to extensively investigate the expression of this miRNA in multiple DLBCL cell lines and found it to not be detectable in this tissue type, regardless of the copy number status.
- Figure S3. Fluorescence in situ hybridization (FISH) of miR-26a-2 and miR-15a/16-1 loci (JPG, 93.4 KB)
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FISH analyses were used to validate our copy number calling algorithm. In panel A, three independent DLBCL cell lines with gain of miR-26a-2 were hybridized to two differentially labeled BAC clones (RP11-571M6 and RP11-155I23 on chromosome 12q13) and three or more signals were promptly detected. In the same panel, the cell line DHL8 was investigated with BAC clone RP11-34F20 (chromosome 13q14), encompassing the miR-15a/16-1 locus, and the copy number gain readily confirmed. In panel B, the array CGH defined copy number loss of the miR-16-1/15a locus was validated in a DLBCL cell line and primary tumors (interphase-FISH).
- Figure S4. Heat map of copy number data for primary DLBCL classified as GCB (G) or non-GCB (N) (JPG, 126 KB)
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MiRNA loci shown were more frequently gained (top) or lost (bottom) in GCB than non-GCB DLBCLs (p <=.05, Fisher’s exact test). Note the predominant gain of a series of miRNAs mapping to chromosome 12 in GCB classified tumors. These data agree with a previous report of copy number gain in DLBCL molecularly classified as GCB (Refs. 12–14, main article), validating our immunohistochemical-based tumor assignment (Table S1).
- Figure S5. Heat map of copy number data for nodal vs. extranodal DLBCL (JPG, 122 KB)
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MiRNA loci shown were more frequently gained (top) or lost (bottom) in extra-nodal (X) than nodal (L) DLBCLs (p <=.05, Fisher’s exact test).
- Figure S6. Heat map of copy number data for primary DLBCL vs. cell lines (JPG, 579 KB)
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MiRNA loci shown were more frequently gained (top) or lost (bottom) in cell lines than primary DLBCLs (p <=.05, Fisher’s exact test). As displayed above, there is a striking difference in the integrity of the microRNA genome between cell lines and primary tumors, whereas the differences between GCB and non-GCB or nodal and extra-nodal tumors are relatively modest (Figs. S4 and S5). Considering the relevance of copy number changes in gene expression, these findings indicate that cell lines may not represent an authentic model to study miRNAs in DLBCL.
Additional supplemental figures can be found here.
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