Abstract
Synthetic lethality and collateral lethality are two well-validated conceptual strategies for identifying therapeutic targets in cancers with tumour-suppressor gene deletions1,2,3. Here, we explore an approach to identify potential synthetic-lethal interactions by screening mutually exclusive deletion patterns in cancer genomes. We sought to identify ‘synthetic-essential’ genes: those that are occasionally deleted in some cancers but are almost always retained in the context of a specific tumour-suppressor deficiency. We also posited that such synthetic-essential genes would be therapeutic targets in cancers that harbour specific tumour-suppressor deficiencies. In addition to known synthetic-lethal interactions, this approach uncovered the chromatin helicase DNA-binding factor CHD1 as a putative synthetic-essential gene in PTEN-deficient cancers. In PTEN-deficient prostate and breast cancers, CHD1 depletion profoundly and specifically suppressed cell proliferation, cell survival and tumorigenic potential. Mechanistically, functional PTEN stimulates the GSK3β-mediated phosphorylation of CHD1 degron domains, which promotes CHD1 degradation via the β-TrCP-mediated ubiquitination–proteasome pathway. Conversely, PTEN deficiency results in stabilization of CHD1, which in turn engages the trimethyl lysine-4 histone H3 modification to activate transcription of the pro-tumorigenic TNF–NF-κB gene network. This study identifies a novel PTEN pathway in cancer and provides a framework for the discovery of ‘trackable’ targets in cancers that harbour specific tumour-suppressor deficiencies.
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Acknowledgements
We thank S. W. Hayward for the BPH1 cell line; P. Shepherd for the PDX models, Y. Chen for Flag-tagged β-TrCP plasmid; T. Gutschner for CRISPR X330-Cherry vector; Y. L. Deribe for the HA-tagged PTEN plasmid; S. Jiang and K. Zhao for assistance in maintenance of mouse colonies; Q. E. Chang for assistance in IHC slides scanning; and the MD Anderson Sequencing and Microarray Facility (SMF) and Flow Cytometry and Cellular Imaging Core Facility. This work was supported in part by the Odyssey Program and Theodore N. Law Endowment For Scientific Achievement at The University of Texas MDACC 600649-80-116647-21 (D.Z.); DOD Prostate Cancer Research Program (PCRP) Idea Development Award–New Investigator Option W81XWH-14-1-0576 (X. Lu); NIH Pathway to Independence (PI) Award (K99/R00)-NCI: 1K99CA194289 (G.W.); DOD PCRP W81XWH-14-1-0429 (P.Dey.); CPRIT research training award RP140106-DC (D.C.); NIH grants P01 CA117969 (R.A.D.) and R01 CA084628 (R.A.D.).
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Contributions
D.Z., Y.A.W. and R.A.D. conceived the original hypothesis of synthetic essentiality. D.Z. designed and performed cell-line-derived xenograft-model and signalling-pathway experiments. X.Lu and X.S. performed the patient-derived xenograft-model experiments and siRNA treatment. G.W. performed microarray and GSEA analyses. Z.L. performed ChIP–seq experiments, and M.T. performed ChIP–seq data analysis. W.L. reviewed and scored human tissue sections. P.T. and W.L. provided the human prostate cancer tissue sections. J.L., J.Z. and J.R.C. performed TCGA data analyses. X.Li., S.S., J.R.C., P.Den. and P.C. provided technical support. N.M.N. provided the PDX model. Y.A.W., X. Lu, G.W., Z.L., D.C. and P.Dey provided intellectual contributions throughout the project. D.Z., Y.A.W., D.J.S. and R.A.D. wrote the paper.
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Reviewer Information Nature thanks W. Wei and the other anonymous reviewer(s) for their contribution to the peer review of this work.
Extended data figures and tables
Extended Data Figure 1 Mutually exclusive deletion patterns in prostate cancer genome.
a–d, Genetic alterations of BRCA1–PARP1 (a), PTEN–PARP1, and PTEN–PLK4 (b), CHD1–PTEN (c), and PTEN–CHD homologues (d) in prostate cancer databases. The gene alteration percentages are shown.
Extended Data Figure 2 Inhibiting CHD1 suppresses tumour growth of PTEN-null prostate cancer.
a, Representative images of PTEN staining (scores 0–2). b, The negative correlation between CHD1 and PTEN staining in human prostate cancer samples was analysed by two-tailed Pearson’s correlation coefficient. c, The correlation between CHD1 staining and Gleason grade in human prostate cancer samples was analysed by two-tailed Pearson correlation coefficient. d, e, Representative CHD1 staining and immunoblots of lysates of prostate tissues of wild-type and prostate-specific Pten-deleted mice (Ptenpc−/−). AP, anterior prostate; DLP, dorsal lateral prostate; VP, ventral prostate. pAKT indicates phosphorylation of AKT at Ser473. f, Immunoblots of lysates generated from CHD1-knockout and control LNCaP cells. Cell proliferation was determined by counting cell numbers in triplicate wells. g, CHD1-knockout and control LNCaP cells were stained with annexin V, phycoerythrin (PE) and DAPI; cell apoptosis was detected by flow cytometry. h–j, Immunoblots of lysates and colony formation assays generated from CHD1-knockdown and control LNCaP cells, PtenSmad4 3132 cells (a mouse prostate cancer cell line generated from the Pten Smad4 co-deletion prostate cancer mouse model) or PtenCap8 cells (a mouse prostate cancer cell line generated from the Pten-deletion prostate cancer mouse model). k, Representative migration images of CHD1-knockdown and control PC-3 cells determined by transwell assay. l, Weight of subcutaneous tumours derived from CHD1-knockdown and control PC-3 cells (n = 10 for both control and shCHD1 #2 groups; n = 8 for shCHD1 #4 group). m, Growth of subcutaneous tumours derived from CHD1-knockdown and control LNCaP cells (n = 10 for both control and shCHD1 #2 groups; n = 8 for shCHD1 #4 group). n, Representative images and quantification of CHD1 and caspase-3 staining in subcutaneous tumour tissues generated by CHD1-knockdown and control PC-3 cells (n = 4). o, Mice bearing patient-derived xenografts (PDX) were treated with siRNA targeting CHD1 at three time points (40 μg per tumour per week). Fold changes of tumour volume are shown (siCtrl group n = 6; siCHD1 group n = 7). p, Representative images and quantification of CHD1-stained xenograft tumour tissues generated in o (n = 4). PTEN status of the PDX tumour. Error bars indicate s.d. (f, l, m, n, p), P values were determined by two-tailed t-test. Scale bars, 50 μm (a, d, n), 100 μm (p). Representative data of triplicate experiments are shown.
Extended Data Figure 3 Targeting CHD1 has minimal impact on tumour growth of PTEN-intact prostate cancer.
a, Immunoblots of lysates and colony-formation assays generated from CHD1-knockdown and control 22Rv1 cells, followed by measurement of subcutaneous tumour growth in vivo (control group n = 8; shCHD1 group n = 7). b, Immunoblots of lysates and colony formation assays generated from CHD1-knockdown and control RWPE-2 cells. c, Immunoblots of lysates and colony formation assays generated from CHD1-knockdown wild-type or PTEN-knockout DU145 cells. d, Weights of subcutaneous tumours derived from CHD1-knockdown DU145 cells (n = 5 for the PTEN-knockout shCHD1 group; other group n = 6). e, CHD1 mRNA levels were detected by qPCR in PC-3 cells overexpressing PTEN. f, Immunoblot time courses of CHD1 protein in control PC-3 (GFP) and PTEN-overexpressing (HA–PTEN) cells treated with 50 μg ml−1 cycloheximide (CHX). C-Myc was used as the positive control, LDH-A as the negative control. g, Immunoblot time courses of CHD1 protein in LNCaP and 22Rv1 cells treated with cycloheximide. h, Immunoblot of CHD1 protein in PTEN-intact and -deficient cell lines. Error bars in a and d indicate s.d. P values were determined by two-tailed t-test. N.S., not significant.
Extended Data Figure 4 PTEN–AKT–GSK3β pathway promotes CHD1 degradation through β-TrCP-mediated ubiquitination–proteasome pathway.
a, HA-tagged ubiquitin (HA–Ub) was transfected into 293T cells for 40 h, followed by 6 h of MG132 treatment and immunoprecipitation (IP) of endogenous CHD1. CHD1 and HA were detected by immunoblot. b, Conservation of two β-TrCP binding motifs in vertebrates. c, d, Immunoblots of CHD1 in BPH1 cells overexpressing Flag-tagged β-TrCP or knockdown of β-TrCP (Yap as positive control). e, HA–Ub and siBTRC (targeting β-TrCP) were transfected into 293T cells for 48 h, followed by 8-h of treatment with MG132 treatment (10 μM) and detection of ubiquitin-bound CHD1 by immunoblot. f, V5-tagged wild-type (WT) or two β-TrCP binding motif mutants (DSGXXS ≥ DAGXXA) of CHD1 were introduced into BPH1 cells, followed by CHX treatment over a time course, and V5-tagged CHD1 was detected by immunoblot. g, h, V5-tagged wild type or the two β-TrCP-binding-motif mutants of CHD1 were introduced into BPH1 cells, followed by V5-immunoprecipitation and detection of ubiquitination and β-TrCP binding by immunoblot. i, Schematic diagram of GSK3β substrate consensus sequences in β-TrCP binding motifs of CHD1. j, Endogenous CHD1 was immunoprecipitated, followed by immunoblot using GSK3β antibody. k, LNCaP cells overexpressing PTEN were treated with 2 μM CHIR for 24 h, and CHD1 protein levels were detected by immunoblot. β-actin was used as a loading control. Representative data of triplicate experiments are shown.
Extended Data Figure 5 CHD1 collaborates with H3K4me3 to activate gene transcription.
a, Endogenous H3K4me3 was immunoprecipitated from BPH1 cells and CHD1 binding was detected by immunoblot. b, c, Immunoblots of H3K4me3 in CHD1-knockdown PC-3 cells or CHD1-knockout LNCaP cells. d, Heat maps showing the CHD1- and H3K4me3-binding features across gene promoters in shCHD1-treated versus control shRNA (Ctrl)-treated PC-3 cells (only CHD1/H3K4me3-overlap genes shown). Each panel represents 5 kb upstream and downstream of the transcription start site. e, Top ten hallmark pathways showing enrichment of CHD1-target genes identified by ChIP–seq. Fifty MSigDB hallmark pathways emerged following IPA core analysis. Graph displays category scores as –log10(P value) from Fisher’s exact test. f, Microarray analysis was performed in CHD1-knockdown and control PC-3 cells. Top ten hallmark pathways exhibiting enrichment of the downregulated genes in shCHD1 PC-3 cells (fold changes > 1.5). g, h, GSEA correlation of NF-κB signature with alternatively expressed genes in CHD1-knockout LNCaP cells (g) and wild-type and PTEN-knockout mouse prostate tissues (h). Normalized enrichment score (NES), nominal P-value and false discovery rate q value of correlation are shown. i, Heat map representation of 25 most downregulated NF-κB pathway genes in CHD1-knockdown PC-3 cells (from blue (low expression) to red (high expression)). j, Validation of CHD1-regulating genes in two individual CHD1-knockout LNCaP cells using qPCR. Data are mean ± s.d. of triplicate experiments.
Extended Data Figure 6 CHD1 activates gene transcription in NF-κB pathway.
a, Heat maps showing expression of downregulated TNF–NF-κB pathway genes in 498 TCGA prostate samples, with all samples sorted relative to CHD1 expression level (shown in top bar). Gene names, Pearson’s correlation coefficient between CHD1 and indicated genes and two-tailed P value are shown. b, Immunoblot of total and activated NF-κB p65 in control and CHD1-knockdown PC-3 cells. c, CHD1/H3K4me3-enriched profiles at indicated genes in CHD1-knockdown and control PC-3 cells. d, Colony-formation assays of CHD1-knockdown PC-3 cells rescued by addition of indicated recombinant proteins or PGE2 (prostaglandin E2), the metabolic product of PTGS2.
Extended Data Figure 7 CHD1 shows synthetic essentiality in PTEN-deficient breast cancer.
a, b, Schematic representations of the role of CHD1 in prostate cancer. In PTEN-intact prostate cells, GSK3β is activated by PTEN through inhibition of AKT and phosphorylates CHD1, which stimulates its degradation through the β-TrCP-mediated ubiquitination–proteasome pathway (a). However, in PTEN-deficient prostate cancer cells, accumulated CHD1 interacts with and maintains H3K4me3, followed by transcriptional activation of genes downstream of NF-κB, leading to disease progression (b). c, Mutual exclusivity of PTEN and CHD1 deletions also occurs in breast cancer and colon cancer. d, e, Immunoblots of lysates and colony-formation assays generated from CHD1-knockdown and control BT549 and MDA-MB-468 cells. f, Growth of subcutaneous tumours derived from CHD1-knockdown MDA-MB-468 cells (control group, n = 10; shCHD1 group, n = 8). Error bars indicate s.d., P values were determined by two-tailed t-test. g, h, Immunoblots of lysates and colony formation assays generated from CHD1-knockdown and control MDA-MB-231 and T47D cells. Representative data of triplicate experiments are shown.
Supplementary information
Supplementary Figures
This file contain the Western Blots for Figures 1d, 2a, c, 3 a, b, d, e, f, g, h, i. (PDF 3693 kb)
Supplementary Table 1
CHD1 and H3K4me3 ChIP-seq overlap TSS signal annotate. The CHD1/H3K4me3-enriched TSS regions across gene promoters in PC-3 cells (only CHD1 and H3K4me3 ChIP-seq overlap genes shown). (XLSX 498 kb)
Supplementary Table 2
CHD1 ChIP-seq signal annotate. The annotated CHD1 binding regions across gene promoters in PC-3 cells. (XLSX 916 kb)
Supplementary Table 3
Alternatively expressed genes in CHD1 knockdown PC-3 cells. Fold changes of down-regulated and up-regulated genes in shCHD1 (#2 and #4) vs. control PC-3 cells are shown (Fold change >1.5). P values are calculated by t test. (XLSX 1984 kb)
Supplementary Table 4
Alternatively expressed genes in CHD1 knockout LNCaP cells. Fold changes of down-regulated and up-regulated genes in CHD1 knockout vs. control LNCaP cells are shown (Fold change >1.5). P values are calculated by t test. (XLSX 4981 kb)
Supplementary Table 5
Real-time PCR primers. (XLSX 43 kb)
Supplementary Data
This zipped file contains 2 Supplementary Data files. (ZIP 382 kb)
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Zhao, D., Lu, X., Wang, G. et al. Synthetic essentiality of chromatin remodelling factor CHD1 in PTEN-deficient cancer. Nature 542, 484–488 (2017). https://doi.org/10.1038/nature21357
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DOI: https://doi.org/10.1038/nature21357
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