New insights into ADPKD molecular pathways using combination of SAGE and microarray technologies

• Published in: Genomics (San Diego, Calif.) Calif.), 2004-09, Vol.84 (3), p.497-510
• Main Authors: Husson, Hervé, Manavalan, Partha, Akmaev, Viatcheslav R., Russo, Ryan J., Cook, Brian, Richards, Brenda, Barberio, Dana, Liu, Dongyu, Cao, Xiaohong, Landes, Gregory M., Wang, Clarence J., Roberts, Bruce L., Klinger, Katherine W., Grubman, Shelley A., Jefferson, Douglas M., Ibraghimov-Beskrovnaya, Oxana
• Format: Article
• Language: English
• Subjects: Analysis of Variance; Autosomal-dominant polycystic kidney disease; Biological and medical sciences; DNA Primers; Epithelium - metabolism; Fundamental and applied biological sciences. Psychology; Gene expression profiling; Gene Expression Profiling - methods; Gene Expression Regulation; Gene Library; Genes - genetics; Genes. Genome; Genetics of eukaryotes. Biological and molecular evolution; Humans; Kidney - metabolism; Kidneys; Liver - metabolism; Malformations of the urinary system; Medical sciences; Microarray; Molecular and cellular biology; Molecular genetics; Nephrology. Urinary tract diseases; Oligonucleotide Array Sequence Analysis - methods; PKD1; PKD2; Polycystic Kidney, Autosomal Dominant - genetics; Polycystin; Reverse Transcriptase Polymerase Chain Reaction; RT-PCR; SAGE
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2004.03.009

Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in the PKD1 or PKD2 gene, but cellular mechanisms of cystogenesis remain unclear. In an attempt to display the array of cyst-specific molecules and to elucidate the disease pathway, we have performed comprehensive high-throughput expression analysis of normal and ADPKD epithelia in a two-step fashion. First, we generated expression profiles of normal and cystic epithelia derived from kidney and liver using serial analysis of gene expression (SAGE). We found 472 and 499 differentially expressed genes with fivefold difference in liver and kidney libraries, respectively. These genes encode growth factors, transcription factors, proteases, apoptotic factors, molecules involved in cell–extracellular matrix interactions, and ion channels. As a second step, we constructed a custom cDNA microarray using a subset of the differentially regulated genes identified by SAGE and interrogated ADPKD patient samples. Subsequently, a set of differentially expressed genes was refined to 26 up-regulated and 48 down-regulated genes with a p value of