Abstract A1-27: Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) beyond SMARCA4 mutations: A comprehensive genomic analysis
Authors: Auguste Aurélie , Deloger Marc , Cyrta Joanna , Formal Audrey Le , Richon Catherine , Droin Nathalie , Brunn Beatrice , Caron Olivier , Devouassoux Mojgan , Lhomme Catherine , Pautier Patricia , Genestie Catherine , Leary Alexandra 
Published: November 2015

Abstract
Background: Small cell ovarian carcinoma of the hypercalcemic type (SCCOHT) is an extremely rare and aggressive tumor that affects mainly young women (median age = 24 years). Prognosis is poor as most patients die within 2 years of diagnosis. Until recently, the literature describing the genomic profile of SCCOHT was scarce. In the last few months, four groups have now confirmed that SMARCA4 mutations are a frequent event in SCCOHT.
Methods: We performed an integrated genomic analysis using WES, RNA-seq and CGH approaches to identify other recurrent genomic alteration and potential therapeutic targets. Candidate SNVs identified by WES were validated by Sanger and RNA-Seq. 8 frozen tumors were available, including 6 with matching normal control DNA. In addition 33 tumor samples were available as FFPE.
Results: Despite their high grade and aggressive clinical course, SCCOHT tumors display genomic stability, low mutation load (0.53mut.Mb) and few SCNAs. However when present, genomic alterations were recurrent. Integrated WES and CGH analysis revealed a frequent and unusual 19p CN LOH (in 5 of 6 tumors). Although overall mutation rate was low, the mutations that did occur were novel and recurrent in 50%-80% of SCCOHT. In addition to SMARCA4 mutation (M+), we validated 10 novel recurrent M+ (including ABCA7, ANKRD24, CACTIN, EMR1, FBN3, FUT5, GRIN3B, KANK3, KRI1 and PLK5) in 50%-80% of tumors at high allelic frequencies (mean=0.87). Similarly, when present, amplifications were recurrent, common to a third of tumors: such as the mitochondrial redox enzymes (SHMT2, NDUFA4L2) or the transmembrane transporter LRP1 were amplified (Log2&gt;2.3). No common fusion transcripts were identified.
Since SCCOHT often display initial chemosensitivity, but rapid progressions, we investigated the differential genomic profiles of treatment naive versus chemotherapy treated tumors to uncover candidate resistance genes. The only alteration significantly enriched in post treatment tumors were M+ in the putative efflux pump, ABCA7. These M+ could not be identified even at low allele fractions in treatment naive tumors, but were identified in all 3 treated tumors with a mean allelic frequency of 0.83.
In terms of therapeutic implications, modulating mitochondrial metabolism or targeting the membrane transporter LRP1 or the ABCA7 efflux pump could provide therapeutic venues in the future. However the most promising approaches for now may be targeting cell cycle checkpoint regulators or chromatin remodelling. M+ in the tumor suppressor PLK5 were confirmed in 79% of a cohort of 33 SCCOHT and many were predicted as damaging. Inactivation of PLK5 is associated with a loss of G2/M checkpoint regulation and cell harbouring PLK5 mutations were sensitive to PLK1 inhibitors. More interestingly, SMARCA4-M+ SCCOHT demonstrated complete loss of SMARCA4 expression as well as loss of the only other SWI/SNF catalytic subunit SMARCA2 suggesting that double SMARCA4/SMARCA2 negative SCCOHTs are characterized by a catalytically inactive SWI/SNF complex. This hypothesis was supported by changes in RNA expression levels in the main transcriptional targets for SWI/SNF (RHOA, RB and the E2F family). Importantly, the double SMARCA2/4 negative BIN-67 SCCOHT cell line displaying both a SMARCA4 M+ and loss of SMARCA2 expression was exquisitely sensitive to HDAC and MT inhibitors, while cell lines with either a SMARCB1-M+ or SMARCA4-M+ with retained SMARCA2 expression were not. These data make double SMARCA2/4 negative by IHC a potential predictive biomarker for histone modifying inhibitors in SCCOHT or potentially in other double SMARCA2/4 negative malignancies.
Conclusions: We present the 1st integrated genomic analysis of SCCOHT. SCCOHT demonstrate a remarkably homogeneous genomic profile and potentially actionable alterations. In particular, dual null SMARCA2/SMARCA4 SCCOHTs could be selected for clinical trials with EZH2, HDAC or MT inhibitors.
Citation Format: Aurélie Auguste, Marc Deloger, Joanna Cyrta, Audrey Le Formal, Catherine Richon, Nathalie Droin, Beatrice Brunn, Olivier Caron, Mojgan Devouassoux, Catherine Lhomme, Patricia Pautier, Catherine Genestie, Alexandra Leary. Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) beyond SMARCA4 mutations: A comprehensive genomic analysis. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-27.