Table 3.
Validation of twenty one differentially expressed genes in CLL. Data from RNA seq analysis (n = 10), qRT-PCR of identical specimens (n = 10) and qRT-PCR from a test cohort (n = 22) of CLL specimens
| CLL downregulated genes | Fold downregulation based on RNA-seq data (n =10) | Fold downregulation RNA-seq cohort (qRT-PCR data, n = 10) | Fold downregulation in test cohort qRT-PCR, n = 22) |
| UACA, uveal autoantigen with coiled-coil domains and ankyrin repeats | 44 | 9.8 ± 3.9 | 135 ± 3.7 |
| PTPRK, protein tyrosine and phosphatase, receptor type, K | 24.2 | * | * |
| JUP, junction plakoglobin | 13.4 | 44 ± 8.1 | 32 ± 5 |
| ITGA4, integrin, alpha 4 (CD49D, alpha 4 subunit of VLA-4 receptor) | 10.3 | 6 ± 2.9 | 12.9 ± 2.5 |
| BANK1, B-cell scaffold protein with ankyrin repeats 1 | 7.2 | 1.23 ± 2 | 10.1 ± 1.86 |
| RHOB, ras homolog family member B | 5.9 | 6.5 ± 2 | 1.97 ± 2.1 |
| Jam3, junctional adhesion molecule 3 | 5.59 | 3.5 ± 2.5 | 75.5 ± 3.6 |
| CD69, CD69 molecule | 4.7 | 4.6 ± 1.7 | 1.07 ± 2.6 (upregulation) |
| GRASP, (receptor for phosphoinositides 1)-associated scaffold protein | 2.6 | 36.7 ± 6 | 9.8 ± 3.8 |
| CLL upregulated genes | Fold downregulation based on RNA-seq data (n =10) | Fold downregulation RNA-seq cohort (qRT-PCR data, n = 10) | Fold downregulation in test cohort qRT-PCR, n = 22) |
| THBS1, thrombospondin 1 | 528 ± 640 | 9.8 ± 15.8 | 12.9 ± 30.8 |
| TGFBR3, transforming growth factor, beta receptor III | 373 ± 205 | 6.6 ± 1.6 | 30.5 ± 42 |
| GIMAP7, GTPase, IMAP family member 7 | 340 ± 305 | 34.2 ± 3.4 | 9.7 ± 7.7 |
| LYZ, lysozyme | 41.8 ± 69 | 1.5 ± 5.6 | 10 ± 9.9 |
| PDE4a, phosphodiesterase 4A, cAMP-specific | 26.5 ± 33.9 | 3 ± 3 | 4 ± 2.3 |
| MYL9, myosin, light chain 9, regulatory | 24.9 ± 34 | 3.5 ± 3.4 | 8.7 ± 8.9 |
| RAPGEF 3, Rap guanine nucleotide exchange factor (GEF) 3 | 24 ± 14.7 | 17.1 ± 2.9 | 13.6 ± 11.3 |
| PIM1, pim-1 oncogene | 13.9 ± 17 | 9.4 ± 7.9 | 6.75 ± 4.6 |
| RXRA, retinoid X receptor, alpha | 13.2 ± 12.8 | 215 ± 196 | 9.4 ± 9 |
| LCK, lymphocyte specific protein tyrosine kinase | 4 ± 2.4 | 3.2 ± 2.68 | 4.59 ± 2 |
| CLNK, cytokine-dependent hematopoietic cell linker | 3.3 ± 1.8 | 26 ± 22 | 36.8 ± 45.2 |
| TGFbeta 1, transforming growth factor, beta 1 | 1.6 ± 1.1 | 1.07 ± 2.8 | 1.4 ± 2.7 |
*PTPRK expression was not detected in normal B cells therefore fold change could not be calculated
**downregulation of CD69 not validated in test cohort