CRISPR/Cas9 screen uncovers functional translation of cryptic lncRNA-encoded open reading frames in human cancer.
CRISPR/Cas9 screen uncovers functional translation of cryptic lncRNA-encoded open reading frames in human cancer.
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DOI：
10.1172/jci159940
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发表时间：
2023-03-01
影响因子：
15.9
通讯作者：
Chen, Yiwen
中科院分区：
文献类型：
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作者：
Zheng, Caishang;Wei, Yanjun;Zhang, Peng;Xu, Longyong;Zhang, Zhenzhen;Lin, Kangyu;Hou, Jiakai;Lv, Xiangdong;Ding, Yao;Chiu, Yulun;Jain, Antrix;Islam, Nelufa;Malovannaya, Anna;Wu, Yun;Ding, Feng;Xu, Han;Sun, Ming;Chen, Xi;Chen, Yiwen
新出现的证据表明，长链非编码RNA（lncRNA）内的隐蔽翻译可能产生具有重要发育/生理功能的新蛋白质。然而，这种神秘的翻译在复杂疾病中的作用（例如，癌症）仍然难以捉摸。在这里，我们应用了一种综合策略，将核糖体分析和CRISPR/Cas9筛选与乳腺癌（BC）的分子/临床数据的大规模分析相结合，并确定了雌激素受体α阳性（ER+）BC对由在管腔肿瘤中上调的lncRNA基因编码的隐蔽ORF的依赖性。我们证实了LINC 00992编码的一种未注释的蛋白GATA 3相互作用隐蔽蛋白（GT3-INCP）的体内肿瘤促进功能，其表达与管腔肿瘤的预后不良相关。GTE-INCP被雌激素/ER上调，并调节雌激素依赖性细胞生长。在机制上，GT3-INCP与GATA 3相互作用，GATA 3是乳腺发育/BC细胞增殖的关键主转录因子，并共同调节涉及许多BC易感性/风险基因并影响雌激素反应/细胞增殖的基因表达程序。GT3-INCP/GATA 3与共同的顺式调节元件结合，并上调肿瘤促进和雌激素调节的BC易感性/风险基因MYB和PDZK 1的表达。我们的研究表明，隐蔽的lncRNA编码的蛋白质可能是一个重要的组成部分的主转录调控网络驱动异常转录在癌症中，并建议“隐藏”的lncRNA编码的蛋白质组可能是一个新的空间，为治疗靶点的发现。
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.