CRISPR/Cas9 Screen Uncovers Functional Translation of Cryptic lncRNA-Encoded Open Reading Frames in Human Cancer

Authors

Caishang Zheng
Yanjun Wei
Peng Zhang
Longyong Xu
Zhenzhen Zhang
Kangyu Lin
Jiakai Hou
Xiangdong Lv
Yao Ding
Yulun Chiu
Antrix Jain
Nelufa Islam
Anna Malovannaya
Yun Wu
Feng Ding
Han Xu
Ming Sun
Xi Chen
Yiwen Chen

Publication Date

3-1-2023

Journal

Journal of Clinical Investigation

DOI

10.1172/JCI159940

PMID

36856111

PMCID

PMC9974104

PubMedCentral® Posted Date

3-1-2023

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

Humans, Female, RNA, Long Noncoding, Open Reading Frames, CRISPR-Cas Systems, Breast Neoplasms, Estrogens, Breast cancer, Noncoding RNAs, Translation, Genetics, Oncology

Abstract

Emerging evidence suggests that cryptic translation within long noncoding RNAs (lncRNAs) may produce novel proteins with important developmental/physiological functions. However, the role of this cryptic translation in complex diseases (e.g., cancer) remains elusive. Here, we applied an integrative strategy combining ribosome profiling and CRISPR/Cas9 screening with large-scale analysis of molecular/clinical data for breast cancer (BC) and identified estrogen receptor α-positive (ER+) BC dependency on the cryptic ORFs encoded by lncRNA genes that were upregulated in luminal tumors. We confirmed the in vivo tumor-promoting function of an unannotated protein, GATA3-interacting cryptic protein (GT3-INCP) encoded by LINC00992, the expression of which was associated with poor prognosis in luminal tumors. GTE-INCP was upregulated by estrogen/ER and regulated estrogen-dependent cell growth. Mechanistically, GT3-INCP interacted with GATA3, a master transcription factor key to mammary gland development/BC cell proliferation, and coregulated a gene expression program that involved many BC susceptibility/risk genes and impacted estrogen response/cell proliferation. GT3-INCP/GATA3 bound to common cis regulatory elements and upregulated the expression of the tumor-promoting and estrogen-regulated BC susceptibility/risk genes MYB and PDZK1. Our study indicates that cryptic lncRNA-encoded proteins can be an important integrated component of the master transcriptional regulatory network driving aberrant transcription in cancer, and suggests that the "hidden" lncRNA-encoded proteome might be a new space for therapeutic target discovery.

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