Deregulated microRNAs in neurofibromatosis type 1 derived malignant peripheral nerve sheath tumors

Malignant peripheral nerve sheath tumors (MPNST) are aggressive cancers that occur spontaneously (sporadic MPNST) or from benign plexiform neurofibromas in neurofibromatosis type 1 (NF1) patients. MPNSTs metastasize easily, are therapy resistant and are frequently fatal. The molecular changes underlying the malignant transformation in the NF1 setting are incompletely understood. Here we investigate the involvement of microRNAs in this process. MicroRNA expression profiles were determined from a series of archival, paired samples of plexiform neurofibroma and MPNST. Ninety differentially expressed microRNAs were identified between the paired samples. Three downregulated microRNAs (let-7b-5p, miR-143-3p, miR-145-5p) and two upregulated microRNAs (miR135b-5p and miR-889-3p) in MPNST were selected for functional characterization. In general, their differential expression was validated in a relevant cell line panel but only partly in a series of unpaired, fresh frozen tumor samples. As part of the validation process we also analyzed microRNA expression profiles of sporadic MPNSTs observing that microRNA expression discriminates NF1-associated and sporadic MPNSTs. The role of microRNAs in cancer progression was examined in NF1-derived MPNST cell lines by transiently modulating microRNA levels. Our findings indicate that some microRNAs affect migratory and invasive capabilities and Wnt signaling activity but the effects are distinct in different cell lines. We conclude that miRNAs play essential regulatory roles in MPNST facilitating tumor progression.

Abstract 4345: Molecular comparison of imatinib-naïve and resistant gastrointestinal stromal tumors: Differentially expressed microRNAs and mRNAs

Background and aim: Gastrointestinal stromal tumors (GISTs) are rare mesenchymal tumors of the gastrointestinal tract. Gain-of-function mutations in KIT or, less frequently, PDGFRA underlie the pathogenesis of the majority of these tumors. The introduction of imatinib mesylate, a selective tyrosine kinase inhibitor, has dramatically improved the outcome for GIST patients. However, half of the advanced patients treated with imatinib eventually progress and acquire resistance within two years of treatment, underscoring the need to get better insight into the resistance mechanisms. In this context we examined the miRNA and mRNA expression profiles in primary (imatinib-naïve) and imatinib resistant GIST samples.

Material and Methods: Fifty-three frozen GIST samples derived from various anatomical sites (small intestine, stomach, colon) harboring a KIT mutation including exon 9 (n=11), exon 11 (n=41) and exon 17 (n=1), were analyzed. Total RNA was isolated from imatinib naïve (IM-n; n=33) and resistant (IM-r; n=20) tumors. The resistant tumors bearing secondary mutations in exon 13 (n=3), exon 17 (n=6) or no secondary mutations (n=11). The miRNA expression profiles were determined using LNA™ oligonucleotide arrays (Exiqon) capable of detecting 725 human miRNAs. Furthermore, from a subset of samples (IM-n; n=14; IM-r; n=15) the mRNA expression profile was established using Affymetrix U133A oligonucleotide arrays. Using the mRNA expression data and the Biocarta and KEGG databases, global testing identified a number of biochemical pathways containing genes that are differentially expressed between the primary and progressive tumors.

Results: Thirty-five differentially expressed miRNAs (P<0.009, FDR<20%) between IM-n and IM-r GIST samples were identified. MiR-30c, miR-181a and miR-144 were among the most significantly different, with p values of 0.006, 0.006 and 0.003, respectively. Analysis of the mRNA data has revealed the up-regulation of genes (P <0002, FDR<30%) involved in cell cycle, DNA replication and cancer related pathways (i.e. proliferation, genomic instability, resistance to chemotherapy, evading apoptosis, etc.) in IM-r samples. To further elucidate the possible involvement of the deregulated miRNAs in the regulation of the indicated genes, the most significantly differentially expressed genes were correlated to miRNA expression. Negative correlations indicate miRNA mediated gene regulation, and were further examined in target prediction programs.

Conclusion: A molecular comparison between primary, IM-n and IM-r GIST samples revealed significant differentially expressed miRNAs and mRNAs. Bioinformatic analyses provided insight into biochemical pathways, and their putative regulation by miRNAs, that may contribute to imatinib resistance as observed in GIST patients.

Citation Format: Azadeh Amirnasr, Caroline M. Gits, Patricia F. Kuijk, Marcel Smid, Maria Debiec-Rychter, Stefan Sleijfer, Erik A. Wiemer. Molecular comparison of imatinib-naïve and resistant gastrointestinal stromal tumors: Differentially expressed microRNAs and mRNAs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4345.

Abstract 4433: Deregulated microRNAs in NF1 derived malignant peripheral nerve sheath tumors (MPNST) and their role in carcinogenesis

Background and aim: MPNSTs are rare and highly aggressive soft tissue sarcomas that can occur spontaneously (sporadic MPNST) or from pre-existing plexiform neurofibromas in neurofibromatosis type 1 (NF1) patients. MPNSTs are usually diagnosed relatively late, metastasize easily, are resistant to therapeutic intervention and frequently fatal for the patient. Diagnostic biomarkers that detect early malignant transformation in the NF1 setting as well identification of putative targets for treatment are urgently needed. In this context we investigated the miRNA expression profiles in NF1-derived MPNST. Materials and

Methods: Total RNA was isolated from sections of formalin fixed paraffin embedded (FFPE) tumor samples. miRNA expression was determined using a RT-PCR platform (TaqMan® Low Density Array Human MicroRNA Cards; Applied Biosystems). The expression of selected miRNAs was transiently modulated in neurofibroma and MPNST cell lines by transfection with miRNA mimics (Dharmacon) or LNA™ based anti-miRs (Exiqon) and effects on cell proliferation, invasion/migration and Wnt/β-catenin signaling were studied.

Results: In order to identify miRNAs that are specifically deregulated in MPNST we analyzed miRNA expression in a unique set paired tumor samples (n=9) of plexiform neurofibroma and MPNST which were derived from the same NF1 patient. At least 90 miRNAs were found to be differentially expressed (FDR <10%; p<0.025) between neurofibromas and MPNST; the vast majority (82/90) of miRNAs being downregulated in MPNST. Interestingly, and in contrast to reports in the literature, sporadic MPNST samples (n=10) could be easily discriminated from NF1-derived MPNST by their miRNA expression profiles. On the basis of their statistical significance, fold difference and expression level, we selected miRNAs to examine their role in MPNST pathogenesis. MiRNA levels were modulated in MPNST (ST88-14, sNF96.2, 90-8TL) and neurofibroma (Hs53.T) cell lines using miRNA mimics for let-7b, miR-16, miR-26a, miR-29a, miR-139-5p, miR-146a and antisense inhibitors for miR-889, miR-135b. The effects of miRNA expression levels on cellular proliferation, invasion and migration were determined. As Wnt/β-catenin signaling is considered a cancer related driver pathway in MPNST we also investigated whether differentially expressed miRNAs could regulate this pathway focusing on miRNA previously linked to Wnt regulation or predicted to target Wnt signaling components. Using TOP/FOP luciferase reporter assays we analyzed the effects of miR-135b, miR-30a, miR-139-5p and miR-146a.

Conclusion: miRNAs specifically deregulated in MPNST may fulfil key oncogenic roles and may be used as biomarker or for therapeutic purposes.

Citation Format: Azadeh Amirnasr, Patricia F. van Kuijk, Robert M. Verdijk, Walter Taal, Stefan Sleijfer, Erik A. C. Wiemer. Deregulated microRNAs in NF1 derived malignant peripheral nerve sheath tumors (MPNST) and their role in carcinogenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4433. doi:10.1158/1538-7445.AM2017-4433