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

Teng Fei; Yiwen Chen; Tengfei Xiao; Wei Li; Laura Cato; Peng Zhang; Maura B Cotter; Michaela Bowden; Rosina T Lis; Shuang G Zhao; Qiu Wu; Felix Y Feng; Massimo Loda; Housheng Hansen He; X Shirley Liu; Myles Brown

doi:10.1073/pnas.1617467114

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

Proc Natl Acad Sci U S A. 2017 Jun 27;114(26):E5207-E5215. doi: 10.1073/pnas.1617467114. Epub 2017 Jun 13.

Authors

Teng Fei^{1

2

3

4}, Yiwen Chen⁵, Tengfei Xiao^{2

3

4}, Wei Li⁴, Laura Cato^{2

3}, Peng Zhang⁵, Maura B Cotter^{6

7}, Michaela Bowden^{6

7}, Rosina T Lis^{6

7}, Shuang G Zhao^{8

9}, Qiu Wu¹⁰, Felix Y Feng^{8

9}, Massimo Loda^{6

7

11

12}, Housheng Hansen He^{13

14}, X Shirley Liu¹⁵, Myles Brown^{16

3}

Affiliations

¹ College of Life and Health Sciences, Northeastern University, Shenyang 110819, People's Republic of China; feiteng@mail.neu.edu.cn xsliu@jimmy.harvard.edu myles_brown@dfci.harvard.edu.
² Division of Molecular and Cellular Oncology, Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215.
³ Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215.
⁴ Department of Biostatistics and Computational Biology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215.
⁵ Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.
⁶ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215.
⁷ Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215.
⁸ Michigan Center for Translational Pathology, Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109.
⁹ Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109.
¹⁰ Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
¹¹ Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215.
¹² Broad Institute of Harvard and MIT, Cambridge, MA 02142.
¹³ Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada M5G1L7.
¹⁴ Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G1L7.
¹⁵ Department of Biostatistics and Computational Biology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215; feiteng@mail.neu.edu.cn xsliu@jimmy.harvard.edu myles_brown@dfci.harvard.edu.
¹⁶ Division of Molecular and Cellular Oncology, Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215; feiteng@mail.neu.edu.cn xsliu@jimmy.harvard.edu myles_brown@dfci.harvard.edu.

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.

Keywords: CRISPR screen; HNRNPL; RNA binding protein; alternative splicing; prostate cancer.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

CRISPR-Cas Systems*
Cell Line, Tumor
Gene Expression Regulation, Neoplastic*
Genome-Wide Association Study*
Humans
Male
Neoplasm Proteins / genetics
Neoplasm Proteins / metabolism*
Prostatic Neoplasms / genetics
Prostatic Neoplasms / metabolism*
Prostatic Neoplasms / pathology
RNA Splicing*
RNA, Neoplasm / biosynthesis*
RNA, Neoplasm / genetics
Ribonucleoproteins / genetics
Ribonucleoproteins / metabolism*

Substances

HNRNPL protein, human
Neoplasm Proteins
RNA, Neoplasm
Ribonucleoproteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding