Rhabdoid tumors: The cell of origin and the role of INI1

Abstract

INI1/hSNF5 is a tumor suppressor that encodes a core component of the human SWI/SNF complex. A germline INI1 mutation predisposes individuals to rhabdoid tumors, rare aggressive pediatric tumors of the brain, kidney and other sites. The precise cell of origin of rhabdoid tumors, and the role of INI1 loss in their development, remains unknown. We hypothesized that loss of INI1 in a susceptible cell results in a transcriptional defect which leads to tumor formation. To determine the cell of origin of rhabdoid tumors, and to understand the nature of the transcriptional defect in these cells, we studied the gene expression changes following re-introduction of INI1 into rhabdoid cell lines using cDNA microarrays.;We found that even 11 days following re-expression of INI1 in a rhabdoid cell line called MON by transient transfection, with the resultant flat cell phenotype, only about 50 genes (0.05%) are consistently upregulated or downregulated in three independent experiments. By a systematic keyword analysis, we found that most of the downregulated genes are cell-cycle related (p < 0.024). In contrast, most of the upregulated genes are differentiation-related or tissue-specific (p < 0.0003), specifically pointing to endothelial and smooth muscle lineages. Consistent with these findings, angioblast markers CD34 and Flk-1 are highly expressed in MON cells by microarray intensity analysis, by FACS analysis, and by real-time RT-PCR. Other endothelial markers we examined, LDLR/MSR1, CD34, KDR, Flt-1, Tie-1, Tie-2, CD31, ACE, VE-Cadherin, Sca-1, and Flt-4, were expressed at high levels in MON cells by real-time RT-PCR, and many were further induced by INI1. As expected, MSR1 upregulation resulted in increased acetylated LDL uptake, another marker of endothelial lineage. To confirm these findings, we show for the first time that rhabdoid tumors are positive for angioblast markers CD34 and Flk-1 and negative for a late endothelial marker, Factor VIII. We conclude that some rhabdoid tumors are derived from vascular progenitor cells that are unable to differentiate due to the loss of INI1.;To explore the early transcriptional events following INI1 re-introduction into MON cells, we performed cDNA microarray analysis within 3 days of transient transfection, using puromycin to achieve fast selection. We found that only 40 genes were consistently upregulated, and none downregulated, in three independent experiments. Several of the upregulated genes were the same as those upregulated at 11 days (p < 0.00005), validating both results. In addition, we found that many genes upregulated at 3 days were interferon target genes (p < 10-19). (Abstract shortened by UMI.).