Recent technological advancements such as CRISPR/Cas-based systems enable multiplexed, high-throughput screening for new therapeutic targets in cancer. While numerous functional screens have been performed on protein-coding genes to date, long non-coding RNAs (lncRNAs) represent an emerging class of potential oncogenes and tumor suppressors, with only a handful of large-scale screens performed thus far. Here, we review in detail currently available screening approaches to identify new lncRNA drivers of tumorigenesis and tumor progression. We discuss the various approaches of genomic and transcriptional targeting using CRISPR/Cas9, as well as methods to post-transcriptionally target lncRNAs via RNA interference (RNAi), antisense oligonucleotides (ASOs) and CRISPR/Cas13. We discuss potential advantages, caveats and future applications of each method to provide an overview and guide on investigating lncRNAs as new therapeutic targets in cancer.

Triple negative breast cancer (TNBC) lacks targeted therapies. Recently, our laboratory and other groups described long non-coding RNAs (lncRNAs) as new drivers of TNBC progression, which represent an exciting new avenue for targeted treatments. LncRNAs are the most versatile and diverse class of non-coding RNAs with roles in the progression of TNBC development, including cell proliferation, differentiation, apoptosis, metastasis and drug resistance. LncRNAs have greater tissue-specific expression compared to proteins and can be targeted using nucleotide sequence-specific RNA therapeutics, leading to reduced systemic toxicities when used as a cancer target. Using a combined approach of computational analysis of patient data and CRISPR functional screening, we identified hundreds of lncRNAs as novel drivers of TNBC. We prioritized one lncRNA target (lncTNBC3) with high translational potential. LncTNBC3 knockdown lead to reduced TNBC cell proliferation in two different loss-of-function models. To gain initial insights into the mechanism via which lncTNBC3 functions, RNA sequencing was carried out on knockdown cells, revealing that lncTNBC3 impacts cell cycle and DNA repair pathways. Cell cycle analysis confirmed an increase in G2/M cell cycle arrest upon lncTNBC3 knockdown. In conclusion, we have identified a promising novel lncRNA target with a role in TNBC growth. Citation Format: Megan O'Malley, Zohaib Rana, Debina Sarkar, Jolyn Chia, Sarah Diermeier. Identification of lncRNAs as potential novel therapeutic targets in triple negative breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3961.