Expression Analysis Of Adamantinomatous Craniopharyngioma Suggests Two Subtypes Associated With Ctnnb1 Mutational Frequency And Highlights Potential Therapeutic Targets

Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA We conducted RNA-sequencing analysis of Adamantinomatous Craniopharnygioma (ACP), including Laser capture micro-dissection (LCM) of individual cellular compartments, to characterise both disease heterogeneity and targetable deregulated molecular pathways. RNA sequencing was performed on 18 samples of ACP (17 pediatric, 1 adult) and six control samples (three fetal pituitaries, three non-functioning pituitary adenomas). LCM and RNA sequencing were performed on a subset of cases selecting nuclear β catenin accumulating clusters, and paired non-cluster tumour tissue (palisading epithelium). Mouse ACP models indicate that these clusters initiate tumorigenesis in a non-cell autonomous manner. Consensus clustering analysis revealed two subgroups of human ACP, one associated with a high CTNNB1 mutational frequency (u003e30%), a relatively high tumour content and fibrous reactive tissue (Group H) and another with a lower mutation frequency (u003c30%) and glial reactive tissue (Group L). The meta-gene signature of Group H defined by non-negative matrix factorization included secreted factors, such as Sonic Hedgehog (SHH) and Fibroblast Growth Factors (FGFs) 3, 4 and 19, Keratins and Matrix Metalloproteinases and was enriched for genes related to odontogenesis. Weighted gene co-expression network analysis independently showed correlation of expression of such genes with mutational frequency. Glial markers and neural differentiation genes were up-regulated in Group L tumors. Differential expression showed up-regulation in ACPs of potential therapeutic targets including SHH (32x), EGFR (8.9x) and TNF (10x). Similarly, differential expression analysis of LCM dissected nuclear β catenin accumulating clusters identified up-regulation of SHH, FGFs and other secreted factors including as WNTs and BMPs. Analysis of the SHH pathway found that SHH is over expressed in clusters (9x) whilst its downstream targets Ptch1 (1.7x), Gli1 (2.1x), Gli3 (2.9x) are over expressed in palisading epithelium, indicating the presence of paracrine signaling. These findings were independently confirmed by in situ hybridisation in human samples and the mouse model. Clustering of murine expression data with those genes differentially expressed in the human clusters revealed murine and human clusters group together, suggesting they are similar structures functionally and biologically. Together, these results suggest that a subset of cells, carrying CTNNB1 mutations and showing nuclear β-catenin accumulation, express secreted pro-oncogenic factors and the response may be observed in neighboring cell types. Targeting such signalling offers an attractive therapeutic opportunity, for which the results suggest the mouse model is well placed for testing. The clinical significance of the two putative ACP subgroups remains to be determined. Citation Format: John R. Apps, Nital Jani, Gabriela Carreno, Jose M. Gonzalez-Meljem, Kyoko Tossell, Thomas J. Stone, Mark A. Ungless, Hywel J. Williams, Thomas S. Jacques, Juan-Pedro Martinez-Barbera. Expression analysis of adamantinomatous craniopharyngioma suggests two subtypes associated with CTNNB1 mutational frequency and highlights potential therapeutic targets. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1804.