Abstract A027: Genome-wide quantification of copy-number aberration impact on gene expression in ovarian high-grade serous carcinoma
Authors: Hautaniemi Sampsa , Jamalzadeh Sanaz , Dai Jun , Lavikka Kari , Li Yilin , Huhtinen Kaisa , Virtanen Anni , Oikkonen Jaana , Hietanen Sakari , Hynninen Johanna , Vähärautio Anna , Häkkinen Antti 
Published: March 2024

Abstract
Background: Copy-number alterations (CNAs) are a key hallmark of cancer and play a major role in chemotherapy resistance. Earlier studies aiming to identify genes with CNA-associated expression levels do not explicitly quantify the degree of CNA regulation on expression levels, leading to an overabundance of false positive discoveries. To overcome this, we propose a robust statistical method to quantify the impact of CNAs on gene expression levels, thereby addressing a longstanding unresolved issue of the relevance of CNA exerted regulation to expression levels at gene and pathway levels. Materials and methods: We used whole-genome sequencing (WGS) and RNA-seq data from 263 matched samples of 93 HGSC patients in the prospective, longitudinal and observational DECIDER clinical trial (ClinicalTrials.gov identifier: NCT04846933). To discover genes and pathways whose activity is regulated by CNAs, we developed copy-number regulation (CNR) analysis that is based on nonlinear monotonic Poisson regression model. The KRAS down-regulation and up-regulation experiments were done in KURAMOCHI and CAOV3 cell lines, respectively, using CRISPR technology. Results: The CNR analysis identified several pathways that are driven by genes whose expression levels are regulated by CNAs. These pathways were further divided into four classes based on the number of CNAs and the degree of regulation due to CNAs. Six pathways characterized by high CNAs and high CNA regulation were associated to survival. Interestingly, in three of them the pathway activity was driven by wild-type KRAS amplification (wtKRASamp). KRAS expression was significantly associated with poor overall survival in the DECIDER and TCGA cohorts, whereas KRAS amplification alone was not. To functionally test the effect of KRAS amplification on platinum response, we mimicked the modulation of KRAS CNAs by CRISPR perturbation in cell lines. Our findings demonstrate that KRAS plays a functional role in platinum resistance and suggest wtKRASamp induced chemoresistance as a putative cause for treatment resistance in patients with high KRAS expression. KRAS mutations were not detected in any patient in the DECIDER cohort. Conclusions: We have developed an approach that enables quantifying gene copy-number regulation, i.e., revealing CNAs that have a strong impact on gene expression values. This allows pinpointing the genes and pathways that are likely to be play crucial roles in cancer progression and therapy resistance, as abundant CNAs alone can lead to high levels of noise and manifests in passenger findings. Our approach also provides a means to identify the most important copy-number alterations contributing to pathway dysregulation. This enables elucidating the context for genes whose activity is highly influenced by CNAs. Importantly, our results underscore the role of wtKRASamp, which is amplified with high expression in 13% of the patients in the DECIDER cohort, in driving chemotherapy resistance in HGSC.
Citation Format: Sampsa Hautaniemi, Sanaz Jamalzadeh, Jun Dai, Kari Lavikka, Yilin Li, Kaisa Huhtinen, Anni Virtanen, Jaana Oikkonen, Sakari Hietanen, Johanna Hynninen, Anna Vähärautio, Antti Häkkinen. Genome-wide quantification of copy-number aberration impact on gene expression in ovarian high-grade serous carcinoma [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr A027.