Microarray-based copy number analysis of neurofibromatosis type-1 (NF1)-associated malignant peripheral nerve sheath tumors reveals a role for Rho-GTPase pathway genes in NF1 tumorigenesis

Abstract

Neurofibromatosis type-1 (NF1) is associated with the growth of benign and malignant tumors. Approximately 15% of NF1 patients develop malignant peripheral nerve sheath tumors (MPNSTs), underlining the need to identify specific diagnostic/prognostic biomarkers associated with MPNST development. The Affymetrix Genome-Wide Human single-nucleotide polymorphism (SNP) Array 6.0 was used to perform SNP genotyping and copy number alteration (CNA), loss-of-heterozygosity (LOH), and copy number neutral-LOH (CNN-LOH) analyses of DNA isolated from 15 MPNSTs, five benign plexiform neurofibromas (PNFs), and patient-matched lymphocyte DNAs. MPNSTs exhibited high-level CNN-LOH, with recurrent changes occurring in MPNSTs but not PNFs. CNN-LOH was evident in MPNSTs but occurred less frequently than genomic deletions. CNAs involving the ITGB8, PDGFA, Ras-related C3 botulinum toxin substrate 1 (RAC1) (7p21-p22), PDGFRL (8p22-p21.3), and matrix metallopeptidase 12 (MMP12) (11q22.3) genes were specific to MPNSTs. Pathway analysis revealed the MPNST-specific amplification of seven Rho-GTPase pathway genes and several cytoskeletal remodeling/cell adhesion genes. In knockdown experiments employing short-hairpin RAC1, ROCK2, PTK2, and LIMK1 RNAs to transfect both control and MPNST-derived cell lines, cell adhesion was significantly increased in the MPNST cell lines, whereas wound healing, cell migration, and invasiveness were reduced, consistent with a role for these Rho-GTPase pathway genes in MPNST development and metastasis. These results suggest new targets for therapeutic intervention in relation to MPNSTs.

STAT3 and HIF1α Signaling Drives Oncogenic Cellular Phenotypes in Malignant Peripheral Nerve Sheath Tumors

“…Interestingly, we observed that PDGF stimulation also caused robust activation of MET, this is suggestive of signaling cross-talk between PDGF-R and MET. PDGFR-b expression is known to transform Schwann cells lacking NF1 (15,35), implying that PDGF-Rb amplification might be involved in Schwann cell hyperplasia. In a more recent study using a panel of 11 MPNST tumors, PDGF-Ra, PDGF-Rb, and EGF-R were shown to be overexpressed when compared with benign controls correlating with a higher level of PI3K/Akt/mTORC1 signal transduction (24,34).…”

“…Recently, Upadhyaya and colleagues (2012) used Affymetrix SNP 6.0 Array analysis to examine the genetic profile of MPNSTs compared with benign neurofibromas (15). The study reported MPNST-specific upregulation of seven Rho-GTPase pathway genes that are thought to be critically involved in MPNST development and metastasis.…”

“…High-throughput whole-genome analysis with microarrays has provided the most insight into new therapeutic options by revealing patterns or molecular signatures common in MPNSTs that are not present in benign neurofibromas, that is, copy number variations and gene expression changes (15,16). It has been previously determined that the HGF, MET, and PDGFRA genes are frequently amplified in MPNSTs (15,17). The MET proto-oncogene, receptor tyrosine kinase (MET) is activated through its sole ligand, hepatocyte growth factor (HGF).…”

Protein Tyrosine Phosphatase-PEST and β8 Integrin Regulate Spatiotemporal Patterns of RhoGDI1 Activation in Migrating Cells

“…Single nucleotide polymorphisms in the human ␤8 integrin (ITGB8) gene that diminish protein expression have been identified in patients with brain vascular malformations (21). ITGB8 expression levels are upregulated in nervous system malignancies, including glioblastoma (22,23) and peripheral nerve sheath tumors (24).…”

Expression profiling of 519 kinase genes in matched malignant peripheral nerve sheath tumor/plexiform neurofibroma samples is discriminatory and identifies mitotic regulators BUB1B, PBK and NEK2 as overexpressed with transformation

“…1,2 Malignant peripheral nerve sheath tumors often show complex karyotypes with losses and gains of chromosome arms as well as focal amplifications and deletions. [3][4][5][6] A number of miRNAs, cell cycle regulators, signaling molecules and transcription factors have been shown to be differentially expressed between neurofibromas and malignant peripheral nerve sheath tumors including CDKN2A, TP53, RB1, EGFR, CD44, PDGFRB, PDGFRA, HGF, MET, IGFR1, SOX9, SOX10, miR-34a and miR-21. 3,[7][8][9][10][11][12][13][14] Neurofibromatosis type 1 patients often have multiple plexiform neurofibromas.…”