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Florian AC, Woodley CM, Wang J, Grieb BC, Slota MJ, Guerrazzi K, Hsu CY, Matlock B, Flaherty D, Lorey S, Fesik SW, Howard G, Liu Q, Weissmiller A, Tansey W. Synergistic action of WDR5 and HDM2 inhibitors in SMARCB1-deficient cancer cells. NAR Cancer 2022; 4:zcac007. [PMID: 35252869 PMCID: PMC8892060 DOI: 10.1093/narcan/zcac007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/14/2022] Open
Abstract
Rhabdoid tumors (RT) are rare and deadly pediatric cancers driven by loss of SMARCB1, which encodes the SNF5 component of the SWI/SNF chromatin remodeler. Loss of SMARCB1 is associated with a complex set of phenotypic changes including vulnerability to inhibitors of protein synthesis and of the p53 ubiquitin-ligase HDM2. Recently, we discovered small molecule inhibitors of the 'WIN' site of WDR5, which in MLL-rearranged leukemia cells decrease the expression of a set of genes linked to protein synthesis, inducing a translational choke and causing p53-dependent inhibition of proliferation. Here, we characterize how WIN site inhibitors act in RT cells. As in leukemia cells, WIN site inhibition in RT cells causes the comprehensive displacement of WDR5 from chromatin, resulting in a decrease in protein synthesis gene expression. Unlike leukemia cells, however, the growth response of RT cells to WIN site blockade is independent of p53. Exploiting this observation, we demonstrate that WIN site inhibitor synergizes with an HDM2 antagonist to induce p53 and block RT cell proliferation in vitro. These data reveal a p53-independent action of WIN site inhibitors and forecast that future strategies to treat RT could be based on dual WDR5/HDM2 inhibition.
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Affiliation(s)
- Andrea C Florian
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Chase M Woodley
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Brian C Grieb
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Macey J Slota
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kiana Guerrazzi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Chih-Yuan Hsu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Brittany K Matlock
- Vanderbilt University Medical Center Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - David K Flaherty
- Vanderbilt University Medical Center Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Stephen W Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Gregory C Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - April M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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Phi JH, Sun CH, Lee SH, Lee S, Park I, Choi SA, Park SH, Lee JY, Wang KC, Kim SK, Yun H, Park CK. NPM1 as a potential therapeutic target for atypical teratoid/rhabdoid tumors. BMC Cancer 2019; 19:848. [PMID: 31462227 PMCID: PMC6714307 DOI: 10.1186/s12885-019-6044-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 08/16/2019] [Indexed: 01/10/2023] Open
Abstract
Background Atypical teratoid/rhabdoid tumors (AT/RTs) are highly malignant brain tumors with inactivation of the SMARCB1 gene, which play a critical role in genomic transcriptional control. In this study, we analyzed the genomic and transcriptomic profiles of human AT/RTs to discover new druggable targets. Methods Multiplanar sequencing analyses, including whole exome sequencing (WES), single nucleotide polymorphism (SNP) arrays, array comparative genomic hybridization (aCGH), and whole transcriptome sequencing (RNA-Seq), were performed on 4 AT/RT tissues. Validation of a druggable target was conducted using AT/RT cell lines. Results WES revealed that the AT/RT genome is extremely stable except for the inactivation of SMARCB1. However, we identified 897 significantly upregulated genes and 523 significantly downregulated genes identified using RNA-Seq, indicating that the transcriptional profiles of the AT/RT tissues changed substantially. Gene set enrichment assays revealed genes related to the canonical pathways of cancers, and nucleophosmin (NPM1) was the most significantly upregulated gene in the AT/RT samples. An NPM1 inhibitor (NSC348884) effectively suppressed the viability of 7 AT/RT cell lines. Network analyses showed that genes associated with NPM1 are mainly involved in cell cycle regulation. Upon treatment with an NPM1 inhibitor, cell cycle arrest at G1 phase was observed in AT/RT cells. Conclusions We propose that NPM1 is a novel therapeutic target for AT/RTs. Electronic supplementary material The online version of this article (10.1186/s12885-019-6044-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ji Hoon Phi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Choong-Hyun Sun
- Genome opinion Co., Ltd. 7, Yeonmujang 5ga-gil, Seongdong-gu, Seoul, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seungmook Lee
- Graduated, Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Inho Park
- SD Genomics, Seoul, Republic of Korea
| | - Seung Ah Choi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ji Yeoun Lee
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea.,Department of Anatomy, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyu-Chang Wang
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea. .,Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea.
| | - Hongseok Yun
- Center for Precision Medicine, Seoul National University Hospital, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea.
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea.
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Darr J, Klochendler A, Isaac S, Geiger T, Geiger T, Eden A. Phosphoproteomic analysis reveals Smarcb1 dependent EGFR signaling in Malignant Rhabdoid tumor cells. Mol Cancer 2015; 14:167. [PMID: 26370283 PMCID: PMC4570560 DOI: 10.1186/s12943-015-0439-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/31/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The SWI/SNF ATP dependent chromatin remodeling complex is a multi-subunit complex, conserved in eukaryotic evolution that facilitates nucleosomal re-positioning relative to the DNA sequence. In recent years the SWI/SNF complex has emerged to play a role in cancer development as various sub-units of the complex are found to be mutated in a variety of tumors. One core-subunit of the complex, which has been well established as a tumor suppressor gene is SMARCB1 (SNF5/INI1/BAF47). Mutation and inactivation of SMARCB1 have been identified as the underlying mechanism leading to Malignant Rhabdoid Tumors (MRT) and Atypical Teratoid/Rhabdoid Tumors (AT/RT), two highly aggressive forms of pediatric neoplasms. METHODS We present a phosphoproteomic study of Smarcb1 dependent changes in signaling networks. The SILAC (Stable Isotopic Labeling of Amino Acids in Cell Culture) protocol was used to quantify in an unbiased manner any changes in the phosphoproteomic profile of Smarcb1 deficient murine rhabdoid tumor cell lines following Smarcb1 stable re-expression and under different serum conditions. RESULTS This study illustrates broad changes in the regulation of multiple biological networks including cell cycle progression, chromatin remodeling, cytoskeletal regulation and focal adhesion. Specifically, we identify Smarcb1 dependent changes in phosphorylation and expression of the EGF receptor, demonstrate downstream signaling and show that inhibition of EGFR signaling specifically hinders the proliferation of Smarcb1 deficient cells. CONCLUSIONS These results support recent findings regarding the effectivity of EGFR inhibitors in hindering the proliferation of human MRT cells and demonstrate that activation of EGFR signaling in Rhabdoid tumors is SMARCB1 dependent.
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Affiliation(s)
- Jonatan Darr
- Department of Cell and Developmental Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Agnes Klochendler
- Department of Cell and Developmental Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Sara Isaac
- Department of Cell and Developmental Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Tami Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Amir Eden
- Department of Cell and Developmental Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Wang X, Haswell JR, Roberts CWM. Molecular pathways: SWI/SNF (BAF) complexes are frequently mutated in cancer--mechanisms and potential therapeutic insights. Clin Cancer Res 2013; 20:21-7. [PMID: 24122795 DOI: 10.1158/1078-0432.ccr-13-0280] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
SWI/SNF chromatin remodeling complexes are pleomorphic multisubunit cellular machines that utilize the energy of ATP hydrolysis to modulate chromatin structure. The complexes interact with transcription factors at promoters and enhancers to modulate gene expression and contribute to lineage specification, differentiation, and development. Initial clues to a role in tumor suppression for SWI/SNF complexes came over a decade ago when the gene encoding the SMARCB1/SNF5 core subunit was found specifically inactivated in nearly all pediatric rhabdoid tumors. In the last three years, cancer-genome sequencing efforts have revealed an unexpectedly high mutation rate of SWI/SNF subunit genes, which are collectively mutated in 20% of all human cancers and approach the frequency of p53 mutations. Here, we provide a background on these newly recognized tumor suppressor complexes, discuss mechanisms implicated in the tumor suppressor activity, and highlight findings that may lead to potential therapeutic targets for SWI/SNF-mutant cancers.
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Affiliation(s)
- Xiaofeng Wang
- Authors' Affiliations: Department of Pediatric Oncology, Dana-Farber Cancer Institute; Division of Hematology/Oncology, Children's Hospital Boston; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
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