Identification and characterization of long non-coding RNAs as targets of mammary tumor cell proliferation and migration

Sarah D Diermeier; Kung-Chi Chang; Susan M Freier; Junyan Song; Alexander Krasnitz; Frank Rigo; C. Frank Bennett; David Spector

doi:10.1101/036418

bioRxiv · 10.1101/036418

Identification and characterization of long non-coding RNAs as targets of mammary tumor cell proliferation and migration

Sarah D Diermeier·Kung-Chi Chang·Susan M Freier·Junyan Song·Alexander Krasnitz·Frank Rigo·C. Frank Bennett·David Spector

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Abstract

Recent genome-wide studies revealed that as much as 80% of the human genome can be transcribed whereas only 2% of this RNA is translated into proteins. Non-coding transcripts can be subdivided into several groups, with long non-coding RNAs (lncRNAs) representing the largest and most diverse class. With breast cancer being the most frequent malignancy in women worldwide, we set out to investigate the potential of lncRNAs as novel therapeutic targets. By performing RNA-Seq on tumor sections and mammary organoids from MMTV-PyMT and MMTV-Neu-NDL mice, modeling the luminal B and HER2/neu-amplified subtypes of human breast cancer respectively, we generated a comprehensive catalog of differentially expressed lncRNAs. We identified several hundred potentially oncogenic lncRNAs that were over-expressed in a subtype-specific manner as well as numerous lncRNAs up-regulated in both models. Among these lncRNA we defined a subset of 30 previously uncharacterized lncRNAs as Mammary Tumor Associated RNAs (MaTARs) and we identified human orthologs. We functionally validated the role of these MaTARs by antisense oligonucleotide (ASO) mediated knockdown in primary mammary tumor cells and 3D ex vivo organoids. Upon independent knockdown of 15 MaTARs, we observed significantly reduced cell proliferation, invasion and/or collective cell migration in a cancer-specific context. Thus, MaTARs are likely key drivers of mammary tumor progression and/or metastasis and represent promising new therapeutic targets.

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Sarah D Diermeier, Kung-Chi Chang, Susan M Freier, Junyan Song, Alexander Krasnitz, Frank Rigo, C. Frank Bennett, David Spector. 2016-01-11. Identification and characterization of long non-coding RNAs as targets of mammary tumor cell proliferation and migration. https://doi.org/10.1101/036418

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