Recent Publications

All publications

Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia

Eric Wang, Sydney X. Lu, Alessandro Pastore, Xufeng Chen, Jochen Imig, Stanley Chun-Wei Lee, Kathryn Hockemeyer, Yohana E. Ghebrechristos, Akihide Yoshimi, Daichi Inoue, Michelle Ki, Hana Cho, Lillian Bitner, Andreas Kloetgen, Kuan-Ting Lin, Taisuke Uehara, Takashi Owa, Raoul Tibes, Adrian R. Krainer, Omar Abdel-Wahab, Iannis Aifantis

Cancer Cell Volume 35, Issue 3, p337-534

RNA-binding proteins (RBPs) are essential modulators of transcription and translation frequently dysregulated in cancer. We systematically interrogated RBP dependencies in human cancers using a comprehensive CRISPR/Cas9 domain-focused screen targeting RNA-binding domains of 490 classical RBPs. This uncovered a network of physically interacting RBPs upregulated in acute myeloid leukemia (AML) and crucial for maintaining RNA splicing and AML survival. Genetic or pharmacologic targeting of one key member of this network, RBM39, repressed cassette exon inclusion and promoted intron retention within mRNAs encoding HOXA9 targets as well as in other RBPs preferentially required in AML. The effects of RBM39 loss on splicing further resulted in preferential lethality of spliceosomal mutant AML, providing a strategy for treatment of AML bearing RBP splicing mutations.


The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification

Mona Abed, Erik Verschueren, Hanna Budayeva, Peter Liu, Donald S. Kirkpatrick, Rohit Reja, Sarah K. Kummerfeld, Joshua D. Webster, Sarah Gierke, Mike Reichelt, Keith R. Anderson, Robert J. Newman, Merone Roose-Girma, Zora Modrusan, Hazal Pektas, Emin Maltepe, Kim Newton, Vishva M. Dixit

PLoS ONE 14(4): e0214110

Peg10 (paternally expressed gene 10) is an imprinted gene that is essential for placental development. It is thought to derive from a Ty3-gyspy LTR (long terminal repeat) retrotran- sposon and retains Gag and Pol-like domains. Here we show that the Gag domain of PEG10 can promote vesicle budding similar to the HIV p24 Gag protein. Expressed in a subset of mouse endocrine organs in addition to the placenta, PEG10 was identified as a substrate of the deubiquitinating enzyme USP9X. Consistent with PEG10 having a critical role in placental development, PEG10-deficient trophoblast stem cells (TSCs) exhibited impaired differentiation into placental lineages. PEG10 expressed in wild-type, differentiat- ing TSCs was bound to many cellular RNAs including Hbegf (Heparin-binding EGF-like growth factor), which is known to play an important role in placentation. Expression of Hbegf was reduced in PEG10-deficient TSCs suggesting that PEG10 might bind to and stabilize RNAs that are critical for normal placental development.

eCLIP

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).

Van Nostrand EL, Pratt GA, Shishkin, Gelboin-Burkhart C, Fang MY, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW

Nat Methods. 2016 Jun;13(6):508-14

As RNA-binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNA molecules, binding site identification by UV crosslinking and immunoprecipitation (CLIP) of ribonucleoprotein complexes is critical to understanding RBP function. However, current CLIP protocols are technically demanding and yield low-complexity libraries with high experimental failure rates. We have developed an enhanced CLIP (eCLIP) protocol that decreases requisite amplification by ∼1,000-fold, decreasing discarded PCR duplicate reads by ∼60% while maintaining single-nucleotide binding resolution. By simplifying the generation of paired IgG and size-matched input controls, eCLIP improves specificity in the discovery of authentic binding sites. We generated 102 eCLIP experiments for 73 diverse RBPs in HepG2 and K562 cells (available at https://www.encodeproject.org), demonstrating that eCLIP enables large-scale and robust profiling, with amplification and sample requirements similar to those of ChIP-seq. eCLIP enables integrative analysis of diverse RBPs to reveal factor-specific profiles, common artifacts for CLIP and RNA-centric perspectives on RBP activity.

Eclipse clients

Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia

Eric Wang, Sydney X. Lu, Alessandro Pastore, Xufeng Chen, Jochen Imig, Stanley Chun-Wei Lee, Kathryn Hockemeyer, Yohana E. Ghebrechristos, Akihide Yoshimi, Daichi Inoue, Michelle Ki, Hana Cho, Lillian Bitner, Andreas Kloetgen, Kuan-Ting Lin, Taisuke Uehara, Takashi Owa, Raoul Tibes, Adrian R. Krainer, Omar Abdel-Wahab, Iannis Aifantis

Cancer Cell Volume 35, Issue 3, p337-534

RNA-binding proteins (RBPs) are essential modulators of transcription and translation frequently dysregulated in cancer. We systematically interrogated RBP dependencies in human cancers using a comprehensive CRISPR/Cas9 domain-focused screen targeting RNA-binding domains of 490 classical RBPs. This uncovered a network of physically interacting RBPs upregulated in acute myeloid leukemia (AML) and crucial for maintaining RNA splicing and AML survival. Genetic or pharmacologic targeting of one key member of this network, RBM39, repressed cassette exon inclusion and promoted intron retention within mRNAs encoding HOXA9 targets as well as in other RBPs preferentially required in AML. The effects of RBM39 loss on splicing further resulted in preferential lethality of spliceosomal mutant AML, providing a strategy for treatment of AML bearing RBP splicing mutations.


The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification

Mona Abed, Erik Verschueren, Hanna Budayeva, Peter Liu, Donald S. Kirkpatrick, Rohit Reja, Sarah K. Kummerfeld, Joshua D. Webster, Sarah Gierke, Mike Reichelt, Keith R. Anderson, Robert J. Newman, Merone Roose-Girma, Zora Modrusan, Hazal Pektas, Emin Maltepe, Kim Newton, Vishva M. Dixit

PLoS ONE 14(4): e0214110

Peg10 (paternally expressed gene 10) is an imprinted gene that is essential for placental development. It is thought to derive from a Ty3-gyspy LTR (long terminal repeat) retrotran- sposon and retains Gag and Pol-like domains. Here we show that the Gag domain of PEG10 can promote vesicle budding similar to the HIV p24 Gag protein. Expressed in a subset of mouse endocrine organs in addition to the placenta, PEG10 was identified as a substrate of the deubiquitinating enzyme USP9X. Consistent with PEG10 having a critical role in placental development, PEG10-deficient trophoblast stem cells (TSCs) exhibited impaired differentiation into placental lineages. PEG10 expressed in wild-type, differentiat- ing TSCs was bound to many cellular RNAs including Hbegf (Heparin-binding EGF-like growth factor), which is known to play an important role in placentation. Expression of Hbegf was reduced in PEG10-deficient TSCs suggesting that PEG10 might bind to and stabilize RNAs that are critical for normal placental development.