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

Overview

Journal J Clin Invest

Specialty General Medicine

Date 2023 Mar 1

PMID 36856111

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

Affiliations

Soon will be listed here.

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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