BMC Genomics 2009, 10:442 http://www.biomedcentral.com/1471-2164/10/442 Table 5: Ingenuity Pathways Analysis: Top Bio Functions - Physiological System Development and Function Category Connective Tissue Development and Function Embryonic Development P-value* Molecules 2.14E-04 to 3.06E-02 RPL22, ICAM1, LIF, KLF10, BMP2, MMP14, METTL8, HAX1, TNFAIP3, NFKB1, MSX2, EIF4EBP1, PTEN, PGF, LIMK1, EDN1, CHST3, FOSL2, SSBP3, MMP1 (includes EG:4312), SRC, PXN, MITF, BGN, JUNB, IRAK3, CEBPB, NFKB2, IGF2R, NDN, NOV, RUNX1, PLAU 2.14E-04 to 3.06E-02 LIF, ICAM1, BMP2, EXT1, NUP50, MSX2, PTEN, NR4A3, 26 NFKBIA, RASSF1, EDN1, POSTN, FOSL2, SRC, PXN, MITF, FGFR1, THRA, L1CAM, JUNB, CEBPB, AFF1, BTG2, RBPJ, IFT52, PLAU Skeletal and Muscular System Development and Function 2.14E-04 to 3.06E-02 MSC, VAMP5, LIF, MMP14, BMP2, KLF10, METTL8, FKBP1A, EXT1, NFKB1, COMP, MSX2, PGF, PTEN, SATB2, NFKBIA, EDN1, CDON, FOXO3, CHST3, POSTN, FOSL2, ACTC1, SSBP3, CACNA1G, SRC, NOX4, BMP2K (includes EG:55589), NAB1, SGCG, MITF, FGFR1, BGN, ADCY3, THRA, NFKB2, IRAK3, JUNB, SMA4, RBPJ, PLAU, RUNX1 Tissue Morphology Respiratory System Development and Function 2.14E-04 to 3.06E-02 ICAM1, LIF, BMP2, NFKB1, MSX2, ABCA1, PGF, PTEN, EIF4EBP1, CASP9, NFKBIA, EDN1, CTSS, PHGDH, FOSL2, SSBP3, SRC, RELB, BGN, ZIC1, APAF1, L1CAM, THRA, JUNB, NFKB2, CEBPB, OGG1, AFF1, CCND2, RBPJ, CYLD, PLAU, ATP2B4 1.44E-03 to 3.06E-02 SRC, NFKBIA, CCND2, COX11, EDN1, MAN2A1, MAFB, ABCA1, NDN, PTEN *Fischer's exact test was used to calculate a p-value determining the probability that each biological function assigned to that data set is due to chance alone. cofactors, i.e. proteins p18, p38 and p43, and interacting core proteins are required to form a functional multisyn- thetase complex [25]. The gene encoding p18 (CDKN2C) is also down-regulated in DBA fibroblasts. Moreover, ARS contribute to the regulation of amino acid metabolism, which is tightly regulated and essential for ribosome bio- genesis and function. Human tryptophanyl-tRNA syn- thetase (WARS) is up-regulated after IFN-gamma treatment, together with indoleamine 2,3-dioxygenase (IDO), the enzyme responsible for tryptophan degrada- tion, thus creating a pool of Trp-tRNA and providing a res- ervoir of Trp available for protein synthesis [26-28]. Interestingly, haem stimulates Trp catabolism enhancing both IDO and WARS enzymatic activities [29,30]. An abnormal haem catabolism has been suggested to occur in DBA [31]. Finally, non canonical functions have been proposed for glutamyl-prolyl-tRNA synthetase (EPRS) in the translational regulation of specific genes containing a GAIT element in the 3'UTR [32]. We demonstrate here that these key regulators are defective in fibroblasts from DBA patients. This suggests that a differential regulation of specific mRNAs may have a role in DBA. High levels of erythrocyte adenosine deaminase (eADA) activity are a common clinical feature in DBA patients, suggesting that adenine catabolism is stimulated. This most likely happens since DBA cells show the impaired processing of rRNA precursor species, which markedly accumulate in the nucleoli and need to be degraded [14]. Interestingly, we observed an increased expression of ade- nosine monophosphate deaminase (AMPD3), an enzyme of nucleotide break-down involved in the regulation of energetic metabolism in mammalian cells. It catalyses the irreversible deamination of adenylic acid and represents a branchpoint of adenylate nucleotides catabolism, regulat- ing the size of the purine nucleotide pool [33,34]. The maintenance of an appropriate intracellular purine nucle- otide concentration range is necessary for cell survival. The increased expression of AMPD3 may indicate the need to dispose of an excess purine pool in DBA fibrob- lasts. About 4% of DBA patients develop cancer, most fre- quently acute myeloid leukemia, myelodysplastic syn- drome and osteosarcoma [5]. This prevalence is much higher than that in the general population. Thus DBA patients seem to have an increased risk of developing malignancies. Gene expression analysis performed on fibroblasts from DBA patients revealed dysregulation of genes involved in cell death and cancer. The decrease in pro-apoptotic (CASP9, APAF1) and oncosuppressor genes (PTEN), coupled to the increased expression of some Page 7 of 12 (page number not for citation purposes) N° 33 42 33 10