Abstract
Long noncoding RNAs (lncRNAs) are widely dysregulated in cancer, yet their functional roles in cellular disease hallmarks remain unclear. Here we employ pooled CRISPR deletion to perturb all 831 lncRNAs in KRAS-mutant non-small cell lung cancer (NSCLC), and measure their contribution to proliferation, chemoresistance and migration across two cell backgrounds. Integrative analysis of this data outperforms conventional “dropout” screens in identifying cancer genes, while prioritising disease-relevant lncRNAs with pleiotropic and background-independent roles. Altogether 60 high-confidence oncogenic lncRNAs are active in NSCLC, the majority identified here for the first time, and which tend to be amplified and overexpressed in tumours. A follow-up antisense oligonucleotide (ASO) screen shortlisted two candidates, Cancer Hallmarks in Lung LncRNA (CHiLL 1&2), whose knockdown consistently suppressed cancer hallmarks in a variety of 2D and 3D tumour models. Molecular phenotyping reveals that CHiLL 1&2 control cellular-level phenotypes via distinct transcriptional networks converging on common oncogenic pathways. In summary, this work reveals a multi-dimensional functional lncRNA landscape underlying NSCLC that contains potential therapeutic vulnerabilities.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Abbreviations
- ASO
- Antisense oligonucleotide
- CRISPR
- Clustered regularly interspaced short palindromic repeats
- CHiLL
- Cancer Hallmark in Lung LncRNA
- DECKO
- Dual excision CRISPR knock-out
- FDR
- False Discovery Rate
- FISH
- Fluorescence in situ hybridisation
- FPKM
- Fragments per kilobase of exon per million mapped fragments
- KEGG
- Kyoto Encyclopedia of Genes and Genomes
- KO
- Knock-Out
- KRAS
- Kirsten rat sarcoma virus
- LNA
- Locked Nucleic Acid
- LncRNA
- Long non-coding RNA
- MOI
- Multiplicity of infection
- NGS
- Next-Generation Sequencing
- NSCLC
- Non small cell lung cancer
- ORF
- Open Reading Frame
- PCR
- Polymerase Chain Reaction
- pgRNA
- paired guide RNAs
- qPCR
- quantitative Polymerase Chain Reaction
- RNA-seq
- RNA-sequencing
- RRA
- Robust Rank Aggregation
- TCGA
- The Cancer Genome Atlas
- TFBS
- Transcription factor binding sites
- TPM
- Transcripts per million
- TPP
- Target prioritisation pipeline
- TSS
- Transcriptional Start Site