ᐊ P3-92
Open Readings 2023 • P3-93
P3-94 ᐅ

TRANSCRIPTOMIC AND MUTATIONAL ANALYSIS OF GYNEGOLOGIC CELL LINES AND TUMORS

Ieva Vaicekauskaitė1, 2, Daiva Dabkevičienė1, 2, Julija Šimienė1, 2, Diana Žilovič1, 2, Rūta Čiurlienė2, Sonata Jarmalaitė1, 2, Rasa Sabaliauskaitė2

1 Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania

2 National Cancer Institute, Vilnius, Lithuania

[email protected]

Ovarian cancer (OC) has the second highest rate of death among all gynecological cancers [1]. The high mortality rates are attributed to the lack of specific symptoms and appropriate screening biomarkers for OC. Chromatin remodeling complex gene ARID1A is the second most frequently mutated gene in gynecologic cancers, while NOTCH/WNT pathway is involved in both the development and cancerogenesis of gynecologic organs, thus ARID1A and NOTCH/WNT members could be useful as biomarkers in gynecologic malignancy diagnostic biomarkers [2].

In this pilot study two OC cell lines SKOV3 and A2780 as well 51 gynecologic tumors (32 high-grade serous OC (HGSOC), 9 other OC cases, 1 endometrial cancer, and 9 benign ovarian tumors) were investigated for NOTCH/WNT pathway as well as SWI/SNF chromatin remodeling complex gene ARID1A mRNA expression analysis using qPCR. ARID1A and NOTCH/WNT pathway gene CTNNB1, FBXW7, and PPP2R1A predicted mutations were analyzed using targeted NGS, while cell line mutations were analyzed using publicly available databases. Mutation pathogenicity prediction was conducted on VarSome [3] and VarCards [4] databases.

We detected significant NOTCH3 downregulation in HGSOC/clear-cell OC model cell culture SKOV3 when compared to endometrial type OC cell line A2780. Both cell lines had mutations in ARID1A mutations, while SKOV3 also had FBXW7 mutations. HGSOC tissue mRNA expression was significantly downregulated when compared to benign gynecologic tumors. Lower WNT gene CTNNB1 expression was significantly associated with tumor stage (p=0.02, Mann-Whitney test) while ARID1A expression a showed tendency positive correlation with good prognosis (HR:3.4, 95% CI: 1.1-10.2). In all 15 alterations were detected in 13 OC tissues. Of them, 10 ARID1A alterations were detected in 6 HGSOC and 6 other OC tissues. At least 50% of detected ARID1A mutations were predicted as pathogenic by in silico analysis.

In summary, ARID1A and NOTCH/WNT pathway mutational and transcriptional changes are abundant in OC tissues. Next, these promising biomarkers should be further analyzed in a non-invasive samples type in order to adapt their use as OC biomarkers.

[1] F. Bray, J. Ferlay, I. Soerjomataram et al., Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries, CA. Cancer J. Clin. 68, 394-424 (2018).

[2] Bocchicchio, S., Tesone, M. and Irusta, G., Convergence of Wnt and Notch signaling controls ovarian cancer cell survival, J. Cell. Physiol. 234, 22130–22143 (2019).

[3] C. Kopanos, V. Tsiolkas, A. Kouris et al., VarSome: the human genomic variant search engine, Bioinformatics 35, 1978-1980 (2018).

[4] J. Li, L. Shi, K. Zhang K et al., VarCards: An integrated genetic and clinical database for coding variants in the human genome, Nucleic. Acids. Res. 46, D1039–D1048 (2018)