Abstract 5057: microRNA profiling in combination with whole exome sequencing reveals insights into long-term recurrence patterns in chordoma
Authors: Ullmann Sarah R. , Karras Franziska , Schreier Julian , Körber-Ferl Kerstin , Ullmann David A. , Franke Sabine , Roessner Albert , Jechorek Dörthe 
Published: March 2024

Abstract
While few studies on miRNA profiling in primary chordomas have been published, there is no data on the miRNA landscape of long-term recurrences. Therefore, we performed a miRNA analysis and whole exome sequencing (WES) investigating four patients with multiple recurrences over seven to 16 years and eight patients with non-recurrent tumors (NRTs), conventional, sacral chordomas in order to compare both groups as well as the recurrence cases (RCs) to each other. Our aim was to find typical miRNA patterns distinguishing the recurrences from the NRTs. After histopathological classification, immunohistochemical and morphometric analysis, DNA and miRNA were extracted from formalin-fixed-paraffin-embedded tissue samples and analyzed by WES and Nanostring. The microRNA regulation patterns showed similarities within RCs differing from NRTs. In unsupervised clustering there is a tendency of recurrences clustering apart from the NRTs. The differential expression between cases developing recurrences and NRTs showed highly significant differences between both groups with 32 miRNAs upregulated in the RCs being downregulated in NRTs. The miRNA expression of long-term recurrences of each patient are quite homogenous differing only from their primary tumor. Comparing NRTs with primary tumors that would later develop long-term recurrences showed significant up-regulation of 5 miRNAs in the RCs. This suggests a pivotal molecular difference between singular and long-term recurring chordomas. Our WES analysis confirmed known and revealed possible new driver genes. Recurring tumors had a higher number of mutations classified as pathogenic as well as increased proliferation rates and pleomorphic changes. Recurrences displayed a change in mutational distribution, showing considerably more disturbances in embryonic signaling and our proposed driver genes. Intriguingly, our study found a progress in number of alterations throughout the recurrences most of all affecting chromatin regulation and the new drivers.
Less disruption of these pathways in primary cases than in recurrences implies their pivotal role not only in chordoma formation, but also in recurrence evolution. The miRNA alterations were correlated with the genomic differences. Validated affected genes of miRNAs deregulated primarily in the recurrences are involved in those pathways as well. As current targeted therapy options are only sporadically altered in few patients, the progress in number of pathogenic mutations throughout the recurrences as well as the drastic change in miRNA expression could present new research approaches for chordomas with long-term recurrences. Combined clinical and molecular studies of miRNA patterns and genetic alterations could expand the understanding of recurrence development leading to new therapeutic targets inhibiting or delaying recurrence formation.
Citation Format: Sarah R. Ullmann, Franziska Karras, Julian Schreier, Kerstin Körber-Ferl, David A. Ullmann, Sabine Franke, Albert Roessner, Dörthe Jechorek. microRNA profiling in combination with whole exome sequencing reveals insights into long-term recurrence patterns in chordoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5057.