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Targeting cancer addiction for SALL4 by shifting its transcriptome with a pharmacologic peptide. (PNAS, Jul 2018)

Liu BH1, Jobichen C1,2, Chia CSB3, Chan THM1, Tang JP1, Chung TXY1, Li J1, Poulsen A3,4, Hung AW3, Koh-Stenta X3, Tan YS5, Verma CS2,5,6, Tan HK1,7, Wu CS1, Li F1, Hill J3, Joy J3, Yang H1, Chai L8, Sivaraman J9, Tenen DG10,11.

Author information
1 Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore.
2 Department of Biological Sciences, National University of Singapore, 117543 Singapore.
3 Experimental Therapeutics Centre, Agency for Science, Technology and Research, 138669 Singapore.
4 Department of Chemistry, National University of Singapore, 117543 Singapore.
5 Bioinformatics Institute, Agency for Science, Technology and Research, 138671 Singapore.
6 School of Biological Sciences, Nanyang Technological University, 637551 Singapore.
7 National University of Singapore, Graduate School for Integrative Sciences and Engineering, 117456 Singapore.
8 Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
9 Department of Biological Sciences, National University of Singapore, 117543 Singapore
10 Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
11 Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115.

Abstract
Sal-like 4 (SALL4) is a nuclear factor central to the maintenance of stem cell pluripotency and is a key component in hepatocellular carcinoma, a malignancy with no effective treatment. In cancer cells, SALL4 associates with nucleosome remodeling deacetylase (NuRD) to silence tumor-suppressor genes, such as PTEN. Here, we determined the crystal structure of an amino-terminal peptide of SALL4(1-12) complexed to RBBp4, the chaperone subunit of NuRD, at 2.7 Å, and subsequent design of a potent therapeutic SALL4 peptide (FFW) capable of antagonizing the SALL4-NURD interaction using systematic truncation and amino acid substitution studies. FFW peptide disruption of the SALL4-NuRD complex resulted in unidirectional up-regulation of transcripts, turning SALL4 from a dual transcription repressor-activator mode to singular transcription activator mode. We demonstrate that FFW has a target affinity of 23 nM, and displays significant antitumor effects, inhibiting tumor growth by 85% in xenograft mouse models. Using transcriptome and survival analysis, we discovered that the peptide inhibits the transcription-repressor function of SALL4 and causes massive up-regulation of transcripts that are beneficial to patient survival. This study supports the SALL4-NuRD complex as a drug target and FFW as a viable drug candidate, showcasing an effective strategy to accurately target oncogenes previously considered undruggable.

KEYWORDS: HCC; RBBp4/NuRD; SALL4; peptidomimetic; structural guided design

PMID: 29976840