BMC Genomics 2009, 10:442 http://www.biomedcentral.com/1471-2164/10/442 Background Protein synthesis is essential to the survival and growth of cells. Ribosomes, the sites where translation occurs, there- fore play a fundamental role in cell biology. In human cells, ribosome biogenesis occurs in the nucleolus: it requires the transcription of four ribosomal RNA (rRNA) species and their assembly with 79 ribosomal proteins (RPs) in order to produce the small (40S) and large (60S) ribosomal subunits. These subunits are independently exported to the cytoplasm and joined to obtain mature ribosomes [1]. Several inherited or acquired bone marrow failure syn- dromes are due to mutations in genes encoding proteins involved in ribosome biogenesis. They include Diamond- Blackfan anaemia (DBA, MIM#105650), Shwachman- Diamond syndrome (SDS, MIM#260400), dyskeratosis congenita (DC, MIM#127550, #305000, #224230) and 5q- syndrome (MIM#153550) [2,3]. DBA is an inherited erythroid hypoplasia which usually develops within the first year of life and is characterised by a severe normo- chromic macrocytic anaemia caused by a defect in the maturation of erythroid progenitors. Haematological signs include paucity of bone marrow progenitors, reticu- locytopenia, elevated erythrocyte adenosine deaminase (eADA) activity and high levels of foetal haemoglobin. Patients are prone to develop malignancies and one third of them present congenital abnormalities [4,5]. Mutations causing DBA have been found so far in six RP genes, encoding both small and large subunit components: RPS19 (in 25% of cases), RPS24 (2%), RPS17 (one case), RPL35A (2%), RPL5 (9%) and RPL11 (6.5%), overall accounting for about 50% of cases [6-10]. All patients are heterozygous with respect to mutations and haplo-insuf- ficiency is thought to be responsible for the pathogenetic mechanism of the disease. The main hypothesis to explain DBA implies that a defect in ribosome biogenesis and pro- tein synthesis would trigger apoptotic processes in eryth- roid progenitors. This is supported by several studies showing that mutations in RPs impair rRNA processing, both in CD34+ cells from DBA patients and in erythroid cells with knock-down of the known DBA genes [8-13]. Mutations in different genes impair different steps of rRNA maturation, but they all lead to the accumulation of rRNA precursors and to a reduction in mature ribosomes. Similar alterations have also been demonstrated in yeast and human cells deficient for other RPs, not yet found mutated in DBA [2,14,15]. However, the link between the haplo-insufficiency of an RP and the erythroid defect occurring in DBA has not been clarified yet. DBA has been considered a disease that affects only eryth- roid progenitors and thus the prototype of a pure eryth- roid aplasia. However, several lines of evidence suggest that erythroid progenitors, though apparently more sensi- tive to RP haplo-insufficiency than other cell types, are not the only cell type affected in DBA. Some patients evolve trilinear aplasia [16], showing that haematopoiesis in general can be affected, while the presence of congenital malformations demonstrates that some organogenetic processes are affected by DBA mutations. Moreover, patients show short statures well below their genetic potentials [5]. To gain a better insight into the biological processes and functions involved in the pathogenesis of DBA, we per- formed a global gene expression analysis of fibroblasts isolated from DBA patients carrying mutations in RPS19. Our data reveal for the first time the presence of abnormal gene expression in non-haematopoietic DBA cells. Protein synthesis, nucleotide and amino acid metabolism and apoptosis are the most affected biological processes. Results Gene expression profiling of cells from DBA patients To identify genes associated with a defect of RPS19, a whole genome expression profiling study was performed using Affymetrix GeneChip Human Genome U133A 2.0 Arrays which allow the screening of 18,400 transcripts, including 14,500 well-characterised genes. We analysed the gene expression profiles of dermal fibroblasts isolated from four DBA patients carrying mutations in RPS19, in comparison to those obtained from six healthy individu- als. Of the 22,227 probes present on the chip, 13,396 had Affymetrix "Present" detection calls and intensity values more than 100 in all arrays and have been used for data analysis. A list of 490 statistically significantly differen- tially expressed probes was generated, 215 of which are up-regulated and 275 down-regulated in DBA patients (see additional file 1: Genes differentially expressed in DBA patients identified by microarray profiling). These probes correspond to 421 differentially expressed genes (176 up-regulated and 245 down-regulated) in patients compared to controls. We also evaluated whether the observed differences in gene expression may be due to a gender-dependent bias. The comparison between the array data of female to male individuals irrespective of the health status yielded a list of 33 differentially expressed probes (six up-regulated and 27 down-regulated in females), corresponding to genes mainly located on chromosomes X or Y (see additional file 2: Differentially expressed genes in females relative to males). Moreover, we identified only five differentially expressed genes in female DBA patients relative to male DBA patients (see additional file 3: Differentially expressed genes in female patients relative to male patients). These results rule out the presence of gender- dependent defects in DBA patients. Page 2 of 12 (page number not for citation purposes)