Abstract P6-08-12: DSCAM-AS1, a breast cancer specific and Estrogen receptor α-dependent long noncoding RNA, is a key component of the pathway controlling cell growth and migration
Authors: De Bortoli M , Miano V , Ferrero G , Annaratone L , Coscujuela L , Castellano I , Cordero F , Sapino A 
Published: March 2017

We previously reported that the long noncoding RNA (lncRNA) DSCAM-AS1 is one of the most interesting functional molecules in the Estrogen Receptor alpha (ERα) pathway in breast cancer cells, among a set of lncRNAs showing dependency on ERα in MCF7 cells (Miano et al., Oncotarget Jan 19, 2016. DOI: 10.18632/oncotarget.6420). Importantly, these lncRNAs were identified as dependent on ERα expression in absence of hormones, and DSCAM-AS1 was the most representative of them, presenting a clear ERα ChIP-Seq signal on the DSCAM-AS1 promoter and responding sharply to ERα silencing, but not to estradiol treatment. This behavior was shared with some other, but not all, ERα-dependent lncRNAs. We showed also that DSCAM-AS1 expression was strongly related to the luminal B &gt; A tumor subtype and strongly related to ER+, in all datasets examined. Together with other lncRNAs we identified, they constituted a sharp luminal-specific gene signature. All this was confirmed more recently by another group (Niknafs et al., Nat. Comm. Sept 26, 2016. DOI: 10.1038/ncomms12791), also showing that DSCAM-AS1 may be related to endocrine resistance in breast cancer.

We report here that DSCAM-AS1 silencing in MCF7 cells evokes a response very similar to what we observed by knocking down ERα (Caizzi et al., PNAS 2009. DOI: 10.1073/pnas.1315445111), i.e. growth arrest, morphological changes and cell death. Noteworthy, ERα expression was not altered by DSCAM-AS1 silencing, thus indicating that DSCAM-AS1 is downstream ERα. Thus, we were interested in evaluating the overall transcriptional response to DSCAM-AS1 silencing. LNA-mediated DSCAM-AS1 down-regulation led to changes in the expression level of 436 protein-coding genes, as determined by RNA-seq and the following sample validation by qRT-PCR. Data analysis by means of IPA and EnrichR indicated that DSCAM-AS1 silencing regulated genes of cell growth and proliferation, cell signaling, cell death and survival and cellular movement. On the other side, there was also a clear stress response with involvement of the interferon signaling pathway. As in the case of ERα silencing, the overall picture is that DSCAM-AS1 may have a function in the maintenance of the luminal epithelial phenotype in breast cancer cells. Interestingly, genes related to cell movement were actually activated by DSCAM-AS1 knock-down and, in this respect, our result may be somehow contrasting with those shown by Niknafs et al. (above) who reported that stable DCAM-AS1 silencing by shRNA led to decreased migration and invasiveness. Differences in RNA-mediated long-term downregulation versus shorter term, LNA-mediated downregulation may account for discrepancies, but the matter clearly deserves more investigation.

Finally, we present further data on the association of DSCAM-AS1 with ERα in breast tumors and clinical data. We suggest that its high level of expression, tissue-of-origin specificity and breast tumor phenotype specificity make DSCAM-AS1 an extremely interesting novel biomarker of luminal breast cancer.We previously reported that the long noncoding RNA (lncRNA) DSCAM-AS1 is one of the most interesting functional molecules in the Estrogen Receptor alpha (ERα) pathway in breast cancer cells, among a set of lncRNAs showing dependency on ERα in MCF7 cells (Miano et al., Oncotarget Jan 19, 2016. DOI: 10.18632/oncotarget.6420). Importantly, these lncRNAs were identified as dependent on ERα expression in absence of hormones, and DSCAM-AS1 was the most representative of them, presenting a clear ERα ChIP-Seq signal on the DSCAM-AS1 promoter and responding sharply to ERα silencing, but not to estradiol treatment. This behavior was shared with some other, but not all, ERα-dependent lncRNAs. We showed also that DSCAM-AS1 expression was strongly related to the luminal B &gt; A tumor subtype and strongly related to ER+, in all datasets examined. Together with other lncRNAs we identified, they constituted a sharp luminal-specific gene signature. All this was confirmed more recently by another group (Niknafs et al., Nat. Comm. Sept 26, 2016. DOI: 10.1038/ncomms12791), also showing that DSCAM-AS1 may be related to endocrine resistance in breast cancer.

We report here that DSCAM-AS1 silencing in MCF7 cells evokes a response very similar to what we observed by knocking down ERα (Caizzi et al., PNAS 2009. DOI: 10.1073/pnas.1315445111), i.e. growth arrest, morphological changes and cell death. Noteworthy, ERα expression was not altered by DSCAM-AS1 silencing, thus indicating that DSCAM-AS1 is downstream ERα. Thus, we were interested in evaluating the overall transcriptional response to DSCAM-AS1 silencing. LNA-mediated DSCAM-AS1 down-regulation led to changes in the expression level of 436 protein-coding genes, as determined by RNA-seq and the following sample validation by qRT-PCR. Data analysis by means of IPA and EnrichR indicated that DSCAM-AS1 silencing regulated genes of cell growth and proliferation, cell signaling, cell death and survival and cellular movement. On the other side, there was also a clear stress response with involvement of the interferon signaling pathway. As in the case of ERα silencing, the overall picture is that DSCAM-AS1 may have a function in the maintenance of the luminal epithelial phenotype in breast cancer cells. Interestingly, genes related to cell movement were actually activated by DSCAM-AS1 knock-down and, in this respect, our result may be somehow contrasting with those shown by Niknafs et al. (above) who reported that stable DCAM-AS1 silencing by shRNA led to decreased migration and invasiveness. Differences in RNA-mediated long-term downregulation versus shorter term, LNA-mediated downregulation may account for discrepancies, but the matter clearly deserves more investigation.

Finally, we present further data on the association of DSCAM-AS1 with ERα in breast tumors and clinical data. We suggest that its high level of expression, tissue-of-origin specificity and breast tumor phenotype specificity make DSCAM-AS1 an extremely interesting novel biomarker of luminal breast cancer.

Citation Format: De Bortoli M, Miano V, Ferrero G, Annaratone L, Coscujuela L, Castellano I, Cordero F, Sapino A. DSCAM-AS1, a breast cancer specific and Estrogen receptor α-dependent long noncoding RNA, is a key component of the pathway controlling cell growth and migration [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-08-12.