Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing

Abstract

Alternative RNA splicing plays an important role in cancer. To determine which factors involved in RNA processing are essential in prostate cancer, we performed a genome-wide CRISPR/Cas9 knockout screen to identify the genes that are required for prostate cancer growth. Functional annotation defined a set of essential spliceosome and RNA binding protein (RBP) genes, including most notably heterogeneous nuclear ribonucleoprotein L (HNRNPL). We defined the HNRNPL-bound RNA landscape by RNA immunoprecipitation coupled with next-generation sequencing and linked these RBP-RNA interactions to changes in RNA processing. HNRNPL directly regulates the alternative splicing of a set of RNAs, including those encoding the androgen receptor, the key lineage-specific prostate cancer oncogene. HNRNPL also regulates circular RNA formation via back splicing. Importantly, both HNRNPL and its RNA targets are aberrantly expressed in human prostate tumors, supporting their clinical relevance. Collectively, our data reveal HNRNPL and its RNA clients as players in prostate cancer growth and potential therapeutic targets.CRISPR screen | HNRNPL | prostate cancer | RNA binding protein | alternative splicing P rostate cancer is among the most prevalent adult malignancies in developed countries. The principal treatment for prostate cancer once it is no longer amenable to surgery or radiation treatment is androgen deprivation therapy, which targets androgen or androgen receptor (AR) signaling. However, resistance to androgen deprivation therapy often develops and leads to a state termed "castration-resistant prostate cancer," which still lacks an effective cure (1-3). Therefore, significant efforts have been devoted to better understand the mechanism of oncogenesis and to develop additional effective therapeutics targeting pivotal oncogenes, cancer-related signal transduction pathways, and epigenetic regulators (4, 5).Alternative RNA splicing is a fundamental cellular process by which a single gene can give rise to multiple different transcripts and proteins. This process is tightly regulated by core spliceosomes and other splicing factors, such as the serine/ arginine-rich family of proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) (6, 7). Multiple studies indicate that deregulation of alternative splicing is implicated in cancer progression and that the splicing machinery may be targeted therapeutically (8-10). In addition to RNA splicing, the physical interactions between RNAs and RNA binding proteins (RBPs) underlie multiple RNA processing steps, such as capping, polyadenylation, transport, localization, modification, and translation, thereby regulating many aspects of RNA fate (11).Which RBPs and their related RNA processing steps are functionally important, especially in prostate cancer, remains elusive.The recent implementation of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease Cas9 genome editing system has proved effective in high-throughput lossof-function screens (12)(13)(14)...

hnRNP L‐dependent protection of normal mRNAs from NMD subverts quality control in B cell lymphoma

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The Long Noncoding RNA Cancer Susceptibility 9 and RNA Binding Protein Heterogeneous Nuclear Ribonucleoprotein L Form a Complex and Coregulate Genes Linked to AKT Signaling

“…). HNRNPL is mainly localized in the nucleus and participates in transcription, splicing, and processing of RNA . However, HNRNPL has cytoplasmic functions as well, including the regulation of vascular endothelial growth factor A translation …”

“…Importantly, we establish the CASC9 and HNRNPL interaction in HCC cells by the RAP and RIP methods. The interacting protein HNRNPL is a multifunctional RBP and involved in splicing, RNA stability, regulation of translation, and transcription . HNRNPL itself is an oncogenic protein and interacts with lncRNAs in different cancer types .…”

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