1
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BenDavid E, Yang C, Zhou Y, Pfaller CK, Samuel CE, Ma D. Host WD repeat-containing protein 5 inhibits protein kinase R-mediated integrated stress response during measles virus infection. J Virol 2024; 98:e0102024. [PMID: 39194235 PMCID: PMC11406981 DOI: 10.1128/jvi.01020-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 07/09/2024] [Indexed: 08/29/2024] Open
Abstract
Some negative-sense RNA viruses, including measles virus (MeV), share the characteristic that during their infection cycle, cytoplasmic inclusion bodies (IBs) are formed where components of the viral replication machinery are concentrated. As a foci of viral replication, how IBs act to enhance the efficiency of infection by affecting virus-host interactions remains an important topic of investigation. We previously established that upon MeV infection, the epigenetic host protein, WD repeat-containing protein 5 (WDR5), translocates to cytoplasmic viral IBs and facilitates MeV replication. We now show that WDR5 is recruited to IBs by forming a complex with IB-associated MeV phosphoprotein via a conserved binding motif located on the surface of WDR5. Furthermore, we provide evidence that WDR5 promotes viral replication by suppressing a major innate immune response pathway, the double-stranded RNA-mediated activation of protein kinase R and integrated stress response. IMPORTANCE MeV is a pathogen that remains a global concern, with an estimated 9 million measles cases and 128,000 measles deaths in 2022 according to the World Health Organization. A large population of the world still has inadequate access to the effective vaccine against the exceptionally transmissible MeV. Measles disease is characterized by a high morbidity in children and in immunocompromised individuals. An important area of research for negative-sense RNA viruses, including MeV, is the characterization of the complex interactome between virus and host occurring at cytoplasmic IBs where viral replication occurs. Despite the progress made in understanding IB structures, little is known regarding the virus-host interactions within IBs and the role of these interactions in promoting viral replication and antagonizing host innate immunity. Herein we provide evidence suggesting a model by which MeV IBs utilize the host protein WDR5 to suppress the protein kinase R-integrated stress response pathway.
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Affiliation(s)
- Ethan BenDavid
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Chuyuan Yang
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Yuqin Zhou
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Christian K Pfaller
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
| | - Dzwokai Ma
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
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2
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Meyer CT, Smith BN, Wang J, Teuscher KB, Grieb BC, Howard GC, Silver AJ, Lorey SL, Stott GM, Moore WJ, Lee T, Savona MR, Weissmiller AM, Liu Q, Quaranta V, Fesik SW, Tansey WP. Expanded profiling of WD repeat domain 5 inhibitors reveals actionable strategies for the treatment of hematologic malignancies. Proc Natl Acad Sci U S A 2024; 121:e2408889121. [PMID: 39167600 PMCID: PMC11363251 DOI: 10.1073/pnas.2408889121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024] Open
Abstract
WD40 Repeat Domain 5 (WDR5) is a highly conserved nuclear protein that recruits MYC oncoprotein transcription factors to chromatin to stimulate ribosomal protein gene expression. WDR5 is tethered to chromatin via an arginine-binding cavity known as the "WIN" site. Multiple pharmacological inhibitors of the WDR5-interaction site of WDR5 (WINi) have been described, including those with picomolar affinity and oral bioavailability in mice. Thus far, however, WINi have only been shown to be effective against a number of rare cancer types retaining wild-type p53. To explore the full potential of WINi for cancer therapy, we systematically profiled WINi across a panel of cancer cells, alone and in combination with other agents. We report that WINi are unexpectedly active against cells derived from both solid and blood-borne cancers, including those with mutant p53. Among hematologic malignancies, we find that WINi are effective as a single agent against leukemia and diffuse large B cell lymphoma xenograft models, and can be combined with the approved drug venetoclax to suppress disseminated acute myeloid leukemia in vivo. These studies reveal actionable strategies for the application of WINi to treat blood-borne cancers and forecast expanded utility of WINi against other cancer types.
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Affiliation(s)
- Christian T. Meyer
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO80309
- Duet BioSystems, Nashville, TN37212
| | - Brianna N. Smith
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN37232
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN37232
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN37232
| | - Kevin B. Teuscher
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37240
| | - Brian C. Grieb
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | - Gregory C. Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37240
| | - Alexander J. Silver
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | - Shelly L. Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37240
| | - Gordon M. Stott
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD21701-4907
| | - William J. Moore
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD21702-1201
| | - Taekyu Lee
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37240
| | - Michael R. Savona
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | | | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN37232
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN37232
| | - Vito Quaranta
- Duet BioSystems, Nashville, TN37212
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37240
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37240
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN37240
- Department of Chemistry, Vanderbilt University, Nashville, TN37240
| | - William P. Tansey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37240
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37240
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3
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Wolf E, Herasymenko O, Kutera M, Lento C, Arrowsmith C, Ackloo S, Wilson D. Quantitative Hydrogen-Deuterium Exchange Mass Spectrometry for Simultaneous Structural Characterization and Affinity Indexing of Single Target Drug Candidate Libraries. Anal Chem 2024; 96:13015-13024. [PMID: 39074309 PMCID: PMC11326436 DOI: 10.1021/acs.analchem.4c01001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Hydrogen-deuterium eXchange mass spectrometry (HDX-MS) is increasingly used in drug development to locate binding sites and to identify allosteric effects in drug/target interactions. However, the potential of this technique to quantitatively analyze drug candidate libraries remains largely unexplored. Here, a collection of 13 WDR5-targeting small molecules with surface plasmon resonance (SPR) dissociation coefficients (KD) ranging from 20 nM to ∼116 μM were characterized using differential HDX-MS (ΔHDX-MS). Conventional qualitative analysis of the ΔHDX-MS data set revealed the binding interfaces for all compounds and allosteric effects where present. We then demonstrated that ΔHDX-MS signal-to-noise (S/N) not only can rank library-relative affinity but also can accurately predict KD from a calibration curve constructed from high-quality SPR data. Three methods for S/N calculation are explored, each suitable for libraries with different characteristics. Our results demonstrate the potential for ΔHDX-MS use in drug candidate library affinity validation and/or determination while simultaneously characterizing structure.
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Affiliation(s)
- Esther Wolf
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada
| | | | - Maria Kutera
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Derek Wilson
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada
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4
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Mayse L, Wang Y, Ahmad M, Movileanu L. Real-Time Measurement of a Weak Interaction of a Transcription Factor Motif with a Protein Hub at Single-Molecule Precision. ACS NANO 2024; 18:20468-20481. [PMID: 39049818 PMCID: PMC11308778 DOI: 10.1021/acsnano.4c04857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Transcription factors often interact with other protein cofactors, regulating gene expression. Direct detection of these brief events using existing technologies remains challenging due to their transient nature. In addition, intrinsically disordered domains, intranuclear location, and lack of cofactor-dependent active sites of transcription factors further complicate the quantitative analysis of these critical processes. Here, we create a genetically encoded label-free sensor to identify the interaction between a motif of the MYC transcription factor, a primary cancer driver, and WDR5, a chromatin-associated protein hub. Using an engineered nanopore equipped with this motif, WDR5 is probed through reversible captures and releases in a one-by-one and time-resolved fashion. Our single-molecule kinetic measurements indicate a weak-affinity interaction arising from a relatively slow complex association and a fast dissociation of WDR5 from the tethered motif. Further, we validate this subtle interaction by determinations in an ensemble using single nanodisc-wrapped nanopores immobilized on a biolayer interferometry sensor. This study also provides the proof-of-concept for a sensor that reveals unique recognition signatures of different protein binding sites. Our foundational work may be further developed to produce sensing elements for analytical proteomics and cancer nanomedicine.
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Affiliation(s)
- Lauren
A. Mayse
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
| | - Yazheng Wang
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
| | - Mohammad Ahmad
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
| | - Liviu Movileanu
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, 114 Life Sciences Complex, Syracuse, New York 13244, United States
- The
BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
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5
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Bailey JK, Ma D, Clegg DO. Initial Characterization of WDR5B Reveals a Role in the Proliferation of Retinal Pigment Epithelial Cells. Cells 2024; 13:1189. [PMID: 39056772 PMCID: PMC11275010 DOI: 10.3390/cells13141189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
The chromatin-associated protein WDR5 has been widely studied due to its role in histone modification and its potential as a pharmacological target for the treatment of cancer. In humans, the protein with highest sequence homology to WDR5 is encoded by the retrogene WDR5B, which remains unexplored. Here, we used CRISPR-Cas9 genome editing to generate WDR5B knockout and WDR5B-FLAG knock-in cell lines for further characterization. In contrast to WDR5, WDR5B exhibits low expression in pluripotent cells and is upregulated upon neural differentiation. Loss or shRNA depletion of WDR5B impairs cell growth and increases the fraction of non-viable cells in proliferating retinal pigment epithelial (RPE) cultures. CUT&RUN chromatin profiling in RPE and neural progenitors indicates minimal WDR5B enrichment at established WDR5 binding sites. These results suggest that WDR5 and WDR5B exhibit several divergent biological properties despite sharing a high degree of sequence homology.
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Affiliation(s)
- Jeffrey K. Bailey
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Dzwokai Ma
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
| | - Dennis O. Clegg
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, CA 93106, USA
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6
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Yang Y, Xu L, Zhang S, Yao L, Ding Y, Li W, Chen X. Structural studies of WDR5 in complex with MBD3C WIN motif reveal a unique binding mode. J Biol Chem 2024; 300:107468. [PMID: 38876301 PMCID: PMC11261779 DOI: 10.1016/j.jbc.2024.107468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex plays a pivotal role in chromatin regulation and transcriptional repression. In mice, methyl-CpG binding domain 3 isoform C (MBD3C) interacts specifically with the histone H3 binding protein WD repeat-containing protein 5 (WDR5) and forms the WDR5-MBD3C/Norde complex. Despite the functional significance of this interaction on embryonic stem cell gene regulation, the molecular mechanism underlying MBD3C recognition by WDR5 remains elusive. Here, we determined the crystal structure of WDR5 in complex with the peptide (residues 40-51) derived from the MBD3C protein at a resolution of 1.9 Å. Structural analysis revealed that MBD3C utilizes a unique binding mode to interact with WDR5, wherein MBD3C Arg43 and Phe47 are involved in recognizing the WDR5-interacting (WIN) site and Tyr191-related B site on the small surface of WDR5, respectively. Notably, the binding induces a ∼91° rotation of WDR5 Tyr191, generating the hydrophobic B site. Furthermore, mutation experiments combined with isothermal titration calorimetry (ITC) assays confirmed the importance of both Arg43 and Phe47 in mediating WDR5 binding affinity. By determining structures of various peptides bound to WDR5, we demonstrated that the WDR5 WIN site and B site can be concurrently recognized by WIN motif peptides containing ''Arg-Cies/Ser-Arg-Val-Phe'' consensus sequence. Overall, this study reveals the structural basis for the formation of the WDR5-MBD3C subcomplex and provides new insights into the recognition mode of WDR5 for the WIN motif. Moreover, these findings shed light on structural-based designs of WDR5-targeted anti-cancer small molecule inhibitors or peptide-mimic drugs.
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Affiliation(s)
- Yang Yang
- School of Life Sciences, Anhui University, Hefei, Anhui, China.
| | - Li Xu
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, Beijing, China.
| | - Shuting Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Liangrui Yao
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Yuqing Ding
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Wenwen Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xuemin Chen
- School of Life Sciences, Anhui University, Hefei, Anhui, China.
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7
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Qin Y, Dong X, Lu M, Jing L, Chen Q, Guan F, Xiang Z, Huang J, Yang C, He X, Qu J, Yang Z. PARP1 interacts with WDR5 to enhance target gene recognition and facilitate tumorigenesis. Cancer Lett 2024; 593:216952. [PMID: 38750719 DOI: 10.1016/j.canlet.2024.216952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/18/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024]
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) is a nuclear protein that attaches negatively charged poly (ADP-ribose) (PAR) to itself and other target proteins. While its function in DNA damage repair is well established, its role in target chromatin recognition and regulation of gene expression remains to be better understood. This study showed that PARP1 interacts with SET1/MLL complexes by binding directly to WDR5. Notably, although PARP1 does not modulate WDR5 PARylation or the global level of H3K4 methylation, it exerts locus-specific effects on WDR5 binding and H3K4 methylation. Interestingly, PARP1 and WDR5 show extensive co-localization on chromatin, with WDR5 facilitating the recognition and expression of target genes regulated by PARP1. Furthermore, we demonstrated that inhibition of the WDR5 Win site impedes the interaction between PARP1 and WDR5, thereby inhibiting PARP1 from binding to target genes. Finally, the combined inhibition of the WDR5 Win site and PARP shows a profound inhibitory effect on the proliferation of cancer cells. These findings illuminate intricate mechanisms underlying chromatin recognition, gene transcription, and tumorigenesis, shedding light on previously unrecognized roles of PARP1 and WDR5 in these processes.
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Affiliation(s)
- Yali Qin
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaochuan Dong
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Manman Lu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lingyun Jing
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qingchuan Chen
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fei Guan
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhengkai Xiang
- Department of Thoracic Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
| | - Jiaojuan Huang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chengxuan Yang
- Department of Galactophore, Xinxiang First People's Hospital, Xinxiang, 453000, China
| | - Ximiao He
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jing Qu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Zhenhua Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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8
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Huang X, Zhang C, Shang X, Chen Y, Xiao Q, Wei Z, Wang G, Zhen X, Xu G, Min J, Shen S, Liu Y. The NTE domain of PTENα/β promotes cancer progression by interacting with WDR5 via its SSSRRSS motif. Cell Death Dis 2024; 15:335. [PMID: 38744853 PMCID: PMC11094138 DOI: 10.1038/s41419-024-06714-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024]
Abstract
PTENα/β, two variants of PTEN, play a key role in promoting tumor growth by interacting with WDR5 through their N-terminal extensions (NTEs). This interaction facilitates the recruitment of the SET1/MLL methyltransferase complex, resulting in histone H3K4 trimethylation and upregulation of oncogenes such as NOTCH3, which in turn promotes tumor growth. However, the molecular mechanism underlying this interaction has remained elusive. In this study, we determined the first crystal structure of PTENα-NTE in complex with WDR5, which reveals that PTENα utilizes a unique binding motif of a sequence SSSRRSS found in the NTE domain of PTENα/β to specifically bind to the WIN site of WDR5. Disruption of this interaction significantly impedes cell proliferation and tumor growth, highlighting the potential of the WIN site inhibitors of WDR5 as a way of therapeutic intervention of the PTENα/β associated cancers. These findings not only shed light on the important role of the PTENα/β-WDR5 interaction in carcinogenesis, but also present a promising avenue for developing cancer treatments that target this pathway.
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Affiliation(s)
- Xiaolei Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Cheng Zhang
- Institute of Aging & Tissue Regeneration, Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), 200127, Shanghai, China
| | - Xinci Shang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Yichang Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Qin Xiao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Zhengguo Wei
- School of Biology and Basic Medical Science, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Guanghui Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Xuechu Zhen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, 430079, Wuhan, Hubei, China
| | - Shaoming Shen
- Institute of Aging & Tissue Regeneration, Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), 200127, Shanghai, China.
| | - Yanli Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China.
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9
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Howard GC, Wang J, Rose KL, Jones C, Patel P, Tsui T, Florian AC, Vlach L, Lorey SL, Grieb BC, Smith BN, Slota MJ, Reynolds EM, Goswami S, Savona MR, Mason FM, Lee T, Fesik S, Liu Q, Tansey WP. Ribosome subunit attrition and activation of the p53-MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition. eLife 2024; 12:RP90683. [PMID: 38682900 PMCID: PMC11057873 DOI: 10.7554/elife.90683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
The chromatin-associated protein WD Repeat Domain 5 (WDR5) is a promising target for cancer drug discovery, with most efforts blocking an arginine-binding cavity on the protein called the 'WIN' site that tethers WDR5 to chromatin. WIN site inhibitors (WINi) are active against multiple cancer cell types in vitro, the most notable of which are those derived from MLL-rearranged (MLLr) leukemias. Peptidomimetic WINi were originally proposed to inhibit MLLr cells via dysregulation of genes connected to hematopoietic stem cell expansion. Our discovery and interrogation of small-molecule WINi, however, revealed that they act in MLLr cell lines to suppress ribosome protein gene (RPG) transcription, induce nucleolar stress, and activate p53. Because there is no precedent for an anticancer strategy that specifically targets RPG expression, we took an integrated multi-omics approach to further interrogate the mechanism of action of WINi in human MLLr cancer cells. We show that WINi induce depletion of the stock of ribosomes, accompanied by a broad yet modest translational choke and changes in alternative mRNA splicing that inactivate the p53 antagonist MDM4. We also show that WINi are synergistic with agents including venetoclax and BET-bromodomain inhibitors. Together, these studies reinforce the concept that WINi are a novel type of ribosome-directed anticancer therapy and provide a resource to support their clinical implementation in MLLr leukemias and other malignancies.
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Affiliation(s)
- Gregory Caleb Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical CenterNashvilleUnited States
- Center for Quantitative Sciences, Vanderbilt University Medical CenterNashvilleUnited States
| | - Kristie L Rose
- Mass Spectrometry Research Center, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
| | - Camden Jones
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Purvi Patel
- Mass Spectrometry Research Center, Vanderbilt University School of MedicineNashvilleUnited States
| | - Tina Tsui
- Mass Spectrometry Research Center, Vanderbilt University School of MedicineNashvilleUnited States
| | - Andrea C Florian
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Logan Vlach
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Brian C Grieb
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Brianna N Smith
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Macey J Slota
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Elizabeth M Reynolds
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Soumita Goswami
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Michael R Savona
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Frank M Mason
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Taekyu Lee
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
| | - Stephen Fesik
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Pharmacology, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical CenterNashvilleUnited States
- Center for Quantitative Sciences, Vanderbilt University Medical CenterNashvilleUnited States
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
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10
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Streeter SA, Williams AG, Evans JR, Wang J, Guarnaccia AD, Florian AC, Al-Tobasei R, Liu Q, Tansey WP, Weissmiller AM. Mitotic gene regulation by the N-MYC-WDR5-PDPK1 nexus. BMC Genomics 2024; 25:360. [PMID: 38605297 PMCID: PMC11007937 DOI: 10.1186/s12864-024-10282-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 04/03/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND During mitosis the cell depends on proper attachment and segregation of replicated chromosomes to generate two identical progeny. In cancers defined by overexpression or dysregulation of the MYC oncogene this process becomes impaired, leading to genomic instability and tumor evolution. Recently it was discovered that the chromatin regulator WDR5-a critical MYC cofactor-regulates expression of genes needed in mitosis through a direct interaction with the master kinase PDPK1. However, whether PDPK1 and WDR5 contribute to similar mitotic gene regulation in MYC-overexpressing cancers remains unclear. Therefore, to characterize the influence of WDR5 and PDPK1 on mitotic gene expression in cells with high MYC levels, we performed a comparative transcriptomic analysis in neuroblastoma cell lines defined by MYCN-amplification, which results in high cellular levels of the N-MYC protein. RESULTS Using RNA-seq analysis, we identify the genes regulated by N-MYC and PDPK1 in multiple engineered CHP-134 neuroblastoma cell lines and compare them to previously published gene expression data collected in CHP-134 cells following inhibition of WDR5. We find that as expected N-MYC regulates a multitude of genes, including those related to mitosis, but that PDPK1 regulates specific sets of genes involved in development, signaling, and mitosis. Analysis of N-MYC- and PDPK1-regulated genes reveals a small group of commonly controlled genes associated with spindle pole formation and chromosome segregation, which overlap with genes that are also regulated by WDR5. We also find that N-MYC physically interacts with PDPK1 through the WDR5-PDPK1 interaction suggesting regulation of mitotic gene expression may be achieved through a N-MYC-WDR5-PDPK1 nexus. CONCLUSIONS Overall, we identify a small group of genes highly enriched within functional gene categories related to mitotic processes that are commonly regulated by N-MYC, WDR5, and PDPK1 and suggest that a tripartite interaction between the three regulators may be responsible for setting the level of mitotic gene regulation in N-MYC amplified cell lines. This study provides a foundation for future studies to determine the exact mechanism by which N-MYC, WDR5, and PDPK1 converge on cell cycle related processes.
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Affiliation(s)
- Sarah A Streeter
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Alexandria G Williams
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - James R Evans
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Jing Wang
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Alissa D Guarnaccia
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
- Department of Discovery Oncology, Genentech Inc, South San Francisco, CA, 94080, USA
| | - Andrea C Florian
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
- Department of Biology, Belmont University, Nashville, TN, 37212, USA
| | - Rafet Al-Tobasei
- Department of Computer Science, Middle Tennessee State University, Murfreesboro, TN, 32132, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - April M Weissmiller
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
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11
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Ahmad M, Imran A, Movileanu L. Overlapping characteristics of weak interactions of two transcriptional regulators with WDR5. Int J Biol Macromol 2024; 258:128969. [PMID: 38158065 PMCID: PMC10922662 DOI: 10.1016/j.ijbiomac.2023.128969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
The WD40 repeat protein 5 (WDR5) is a nuclear hub that critically influences gene expression by interacting with transcriptional regulators. Utilizing the WDR5 binding motif (WBM) site, WDR5 interacts with the myelocytomatosis (MYC), an oncoprotein transcription factor, and the retinoblastoma-binding protein 5 (RbBP5), a scaffolding element of an epigenetic complex. Given the clinical significance of these protein-protein interactions (PPIs), there is a pressing necessity for a quantitative assessment of these processes. Here, we use biolayer interferometry (BLI) to examine interactions of WDR5 with consensus peptide ligands of MYC and RbBP5. We found that both interactions exhibit relatively weak affinities arising from a fast dissociation process. Remarkably, live-cell imaging identified distinctive WDR5 localizations in the absence and presence of full-length binding partners. Although WDR5 tends to accumulate within nucleoli, WBM-mediated interactions with MYC and RbBP5 require their localization outside nucleoli. We utilize fluorescence resonance energy transfer (FRET) microscopy to confirm these weak interactions through a low FRET efficiency of the MYC-WDR5 and RbBP5-WDR5 complexes in living cells. In addition, we evaluate the impact of peptide and small-molecule inhibitors on these interactions. These outcomes form a fundamental basis for further developments to clarify the multitasking role of the WBM binding site of WDR5.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA; Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY 13244, USA; The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA.
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12
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Qin S, Feng L, Zhao Q, Yan Z, Lyu X, Li K, Mu B, Chen Y, Lu W, Wang C, Suo Y, Yue J, Cui M, Li Y, Zhao Y, Duan Z, Zhu J, Lu X. Discovery and Optimization of WDR5 Inhibitors via Cascade Deoxyribonucleic Acid-Encoded Library Selection Approach. J Med Chem 2024; 67:1079-1092. [PMID: 38166388 DOI: 10.1021/acs.jmedchem.3c01463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
The DNA-encoded library (DEL) is a powerful hit generation tool for chemical biology and drug discovery; however, the optimization of DEL hits remained a daunting challenge for the medicinal chemistry community. In this study, hit compounds targeting the WIN binding domain of WDR5 were discovered by the initial three-cycle linear DEL selection, and their potency was further enhanced by a cascade DEL selection from the focused DEL designed based on the original first run DEL hits. As expected, these new compounds from the second run of focused DEL were more potent WDR5 inhibitors in the protein binding assay confirmed by the off-DNA synthesis. Interestingly, selected inhibitors exhibited good antiproliferative activity in two human acute leukemia cell lines. Taken together, this new cascade DEL selection strategy may have tremendous potential for finding high-affinity leads against WDR5 and provide opportunities to explore and optimize inhibitors for other targets.
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Affiliation(s)
- Shaozhao Qin
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Lijian Feng
- Etern BioPharma (Shanghai) Co., Ltd. F2-B13, No. 80, 1505 Lane, Zuchongzhi Road, Shanghai 201203, China
| | - Qingyi Zhao
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Ziqin Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Xilin Lyu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Kaige Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Baiyang Mu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Yujie Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Weiwei Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Chao Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yanrui Suo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jinfeng Yue
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Mengqing Cui
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Yingjie Li
- Etern BioPharma (Shanghai) Co., Ltd. F2-B13, No. 80, 1505 Lane, Zuchongzhi Road, Shanghai 201203, China
| | - Yujun Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhiqiang Duan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Jidong Zhu
- Etern BioPharma (Shanghai) Co., Ltd. F2-B13, No. 80, 1505 Lane, Zuchongzhi Road, Shanghai 201203, China
| | - Xiaojie Lu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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13
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Howard GC, Wang J, Rose KL, Jones C, Patel P, Tsui T, Florian AC, Vlach L, Lorey SL, Grieb BC, Smith BN, Slota MJ, Reynolds EM, Goswami S, Savona MR, Mason FM, Lee T, Fesik SW, Liu Q, Tansey WP. Ribosome subunit attrition and activation of the p53-MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.26.550648. [PMID: 37546802 PMCID: PMC10402127 DOI: 10.1101/2023.07.26.550648] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The chromatin-associated protein WD Repeat Domain 5 (WDR5) is a promising target for cancer drug discovery, with most efforts blocking an arginine-binding cavity on the protein called the "WIN" site that tethers WDR5 to chromatin. WIN site inhibitors (WINi) are active against multiple cancer cell types in vitro, the most notable of which are those derived from MLL-rearranged (MLLr) leukemias. Peptidomimetic WINi were originally proposed to inhibit MLLr cells via dysregulation of genes connected to hematopoietic stem cell expansion. Our discovery and interrogation of small molecule WIN site inhibitors, however, revealed that they act in MLLr cell lines to suppress ribosome protein gene (RPG) transcription, induce nucleolar stress, and activate p53. Because there is no precedent for an anti-cancer strategy that specifically targets RPG expression, we took an integrated multi-omics approach to further interrogate the mechanism of action of WINi in MLLr cancer cells. We show that WINi induce depletion of the stock of ribosomes, accompanied by a broad yet modest translational choke and changes in alternative mRNA splicing that inactivate the p53 antagonist MDM4. We also show that WINi are synergistic with agents including venetoclax and BET-bromodomain inhibitors. Together, these studies reinforce the concept that WINi are a novel type of ribosome-directed anti-cancer therapy and provide a resource to support their clinical implementation in MLLr leukemias and other malignancies.
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Affiliation(s)
- Gregory C. Howard
- 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
| | - Kristie Lindsey Rose
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Camden Jones
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Purvi Patel
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tina Tsui
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrea C. Florian
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Current address: Department of Biology, Belmont University, Nashville, TN 37212, USA
| | - Logan Vlach
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shelly L. Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 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
| | - Brianna N. Smith
- 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
- Current address: Department of Urology, University of California San Francisco, San Francisco CA 94143, USA
| | - Elizabeth M. Reynolds
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Soumita Goswami
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Michael R. Savona
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Frank M. Mason
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Taekyu Lee
- Department of Biochemistry, 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, 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
| | - 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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14
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Schröder M, Renatus M, Liang X, Meili F, Zoller T, Ferrand S, Gauter F, Li X, Sigoillot F, Gleim S, Stachyra TM, Thomas JR, Begue D, Khoshouei M, Lefeuvre P, Andraos-Rey R, Chung B, Ma R, Pinch B, Hofmann A, Schirle M, Schmiedeberg N, Imbach P, Gorses D, Calkins K, Bauer-Probst B, Maschlej M, Niederst M, Maher R, Henault M, Alford J, Ahrne E, Tordella L, Hollingworth G, Thomä NH, Vulpetti A, Radimerski T, Holzer P, Carbonneau S, Thoma CR. DCAF1-based PROTACs with activity against clinically validated targets overcoming intrinsic- and acquired-degrader resistance. Nat Commun 2024; 15:275. [PMID: 38177131 PMCID: PMC10766610 DOI: 10.1038/s41467-023-44237-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
Targeted protein degradation (TPD) mediates protein level through small molecule induced redirection of E3 ligases to ubiquitinate neo-substrates and mark them for proteasomal degradation. TPD has recently emerged as a key modality in drug discovery. So far only a few ligases have been utilized for TPD. Interestingly, the workhorse ligase CRBN has been observed to be downregulated in settings of resistance to immunomodulatory inhibitory drugs (IMiDs). Here we show that the essential E3 ligase receptor DCAF1 can be harnessed for TPD utilizing a selective, non-covalent DCAF1 binder. We confirm that this binder can be functionalized into an efficient DCAF1-BRD9 PROTAC. Chemical and genetic rescue experiments validate specific degradation via the CRL4DCAF1 E3 ligase. Additionally, a dasatinib-based DCAF1 PROTAC successfully degrades cytosolic and membrane-bound tyrosine kinases. A potent and selective DCAF1-BTK-PROTAC (DBt-10) degrades BTK in cells with acquired resistance to CRBN-BTK-PROTACs while the DCAF1-BRD9 PROTAC (DBr-1) provides an alternative strategy to tackle intrinsic resistance to VHL-degrader, highlighting DCAF1-PROTACS as a promising strategy to overcome ligase mediated resistance in clinical settings.
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Affiliation(s)
- Martin Schröder
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Basel, Switzerland
- Ridgeline Discovery, Basel, Switzerland
| | - Xiaoyou Liang
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Fabian Meili
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Thomas Zoller
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Francois Gauter
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Xiaoyan Li
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Scott Gleim
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Jason R Thomas
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Damien Begue
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Peggy Lefeuvre
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - BoYee Chung
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Renate Ma
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Benika Pinch
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Andreas Hofmann
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Patricia Imbach
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Delphine Gorses
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Keith Calkins
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Matt Niederst
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Rob Maher
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Martin Henault
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John Alford
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Erik Ahrne
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Luca Tordella
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Anna Vulpetti
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Thomas Radimerski
- Novartis Institutes for BioMedical Research, Basel, Switzerland
- Ridgeline Discovery, Basel, Switzerland
| | - Philipp Holzer
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Seth Carbonneau
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Claudio R Thoma
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
- Ridgeline Discovery, Basel, Switzerland.
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15
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Weissmiller AM, Fesik SW, Tansey WP. WD Repeat Domain 5 Inhibitors for Cancer Therapy: Not What You Think. J Clin Med 2024; 13:274. [PMID: 38202281 PMCID: PMC10779565 DOI: 10.3390/jcm13010274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
WDR5 is a conserved nuclear protein that scaffolds the assembly of epigenetic regulatory complexes and moonlights in functions ranging from recruiting MYC oncoproteins to chromatin to facilitating the integrity of mitosis. It is also a high-value target for anti-cancer therapies, with small molecule WDR5 inhibitors and degraders undergoing extensive preclinical assessment. WDR5 inhibitors were originally conceived as epigenetic modulators, proposed to inhibit cancer cells by reversing oncogenic patterns of histone H3 lysine 4 methylation-a notion that persists to this day. This premise, however, does not withstand contemporary inspection and establishes expectations for the mechanisms and utility of WDR5 inhibitors that can likely never be met. Here, we highlight salient misconceptions regarding WDR5 inhibitors as epigenetic modulators and provide a unified model for their action as a ribosome-directed anti-cancer therapy that helps focus understanding of when and how the tumor-inhibiting properties of these agents can best be understood and exploited.
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Affiliation(s)
- April M. Weissmiller
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 32132, 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, Nashville, TN 37232, USA
| | - William P. Tansey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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16
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Cai L, Liu B, Cao Y, Sun T, Li Y. Unveiling the molecular structure and role of RBBP4/7: implications for epigenetic regulation and cancer research. Front Mol Biosci 2023; 10:1276612. [PMID: 38028543 PMCID: PMC10679446 DOI: 10.3389/fmolb.2023.1276612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Retinoblastoma-binding protein (RBBP) family is a class of proteins that can interact with tumor suppressor retinoblastoma protein (pRb). RBBP4 and RBBP7 are the only pair of homologous proteins in this family, serving as scaffold proteins whose main function is to offer a platform to indirectly connect two proteins. This characteristic allows them to extensively participate in the binding of various proteins and epigenetic complexes, indirectly influencing the function of effector proteins. As a result, they are often highlighted in organism activities involving active epigenetic modifications, such as embryonic development and cancer activation. In this review, we summarize the structural characteristics of RBBP4/7, the complexes they are involved in, their roles in embryonic development and cancer, as well as potential future research directions, which we hope to inspire the field of epigenetic research in the future.
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Affiliation(s)
- Lize Cai
- The First Affiliated Hospital of Soochow University, Suzhou University, Suzhou, China
| | - Bin Liu
- Department of Neurosurgery, Qinghai Provincial People’s Hospital, Xining, China
| | - Yufei Cao
- The First Affiliated Hospital of Soochow University, Suzhou University, Suzhou, China
| | - Ting Sun
- The First Affiliated Hospital of Soochow University, Suzhou University, Suzhou, China
| | - Yanyan Li
- The First Affiliated Hospital of Soochow University, Suzhou University, Suzhou, China
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17
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Chen Y, Su H, Zhao J, Na Z, Jiang K, Bacchiocchi A, Loh KH, Halaban R, Wang Z, Cao X, Slavoff SA. Unannotated microprotein EMBOW regulates the interactome and chromatin and mitotic functions of WDR5. Cell Rep 2023; 42:113145. [PMID: 37725512 PMCID: PMC10629662 DOI: 10.1016/j.celrep.2023.113145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 07/20/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023] Open
Abstract
The conserved WD40-repeat protein WDR5 interacts with multiple proteins both inside and outside the nucleus. However, it is currently unclear whether and how the distribution of WDR5 between complexes is regulated. Here, we show that an unannotated microprotein EMBOW (endogenous microprotein binder of WDR5) dually encoded in the human SCRIB gene interacts with WDR5 and regulates its binding to multiple interaction partners, including KMT2A and KIF2A. EMBOW is cell cycle regulated, with two expression maxima at late G1 phase and G2/M phase. Loss of EMBOW decreases WDR5 interaction with KIF2A, aberrantly shortens mitotic spindle length, prolongs G2/M phase, and delays cell proliferation. In contrast, loss of EMBOW increases WDR5 interaction with KMT2A, leading to WDR5 binding to off-target genes, erroneously increasing H3K4me3 levels, and activating transcription of these genes. Together, these results implicate EMBOW as a regulator of WDR5 that regulates its interactions and prevents its off-target binding in multiple contexts.
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Affiliation(s)
- Yanran Chen
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Brain Functional Genomics, Ministry of Education and Shanghai, School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Haomiao Su
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Jianing Zhao
- Frontier Innovation Center, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200433, China; Shanghai Fifth People's Hospital, Fudan University, Shanghai 200433, China
| | - Zhenkun Na
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Kevin Jiang
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Antonella Bacchiocchi
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ken H Loh
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Zhentian Wang
- Frontier Innovation Center, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200433, China; Shanghai Fifth People's Hospital, Fudan University, Shanghai 200433, China
| | - Xiongwen Cao
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Brain Functional Genomics, Ministry of Education and Shanghai, School of Life Sciences, East China Normal University, Shanghai 200062, China.
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA.
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18
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Bumpous LA, Moe KC, Wang J, Carver LA, Williams AG, Romer AS, Scobee JD, Maxwell JN, Jones CA, Chung DH, Tansey WP, Liu Q, Weissmiller AM. WDR5 facilitates recruitment of N-MYC to conserved WDR5 gene targets in neuroblastoma cell lines. Oncogenesis 2023; 12:32. [PMID: 37336886 PMCID: PMC10279693 DOI: 10.1038/s41389-023-00477-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/11/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023] Open
Abstract
Collectively, the MYC family of oncoprotein transcription factors is overexpressed in more than half of all malignancies. The ability of MYC proteins to access chromatin is fundamental to their role in promoting oncogenic gene expression programs in cancer and this function depends on MYC-cofactor interactions. One such cofactor is the chromatin regulator WDR5, which in models of Burkitt lymphoma facilitates recruitment of the c-MYC protein to chromatin at genes associated with protein synthesis, allowing for tumor progression and maintenance. However, beyond Burkitt lymphoma, it is unknown whether these observations extend to other cancers or MYC family members, and whether WDR5 can be deemed as a "universal" MYC recruiter. Here, we focus on N-MYC amplified neuroblastoma to determine the extent of colocalization between N-MYC and WDR5 on chromatin while also demonstrating that like c-MYC, WDR5 can facilitate the recruitment of N-MYC to conserved WDR5-bound genes. We conclude based on this analysis that N-MYC and WDR5 colocalize invariantly across cell lines at predicted sites of facilitated recruitment associated with protein synthesis genes. Surprisingly, we also identify N-MYC-WDR5 cobound genes that are associated with DNA repair and cell cycle processes. Dissection of chromatin binding characteristics for N-MYC and WDR5 at all cobound genes reveals that sites of facilitated recruitment are inherently different than most N-MYC-WDR5 cobound sites. Our data reveals that WDR5 acts as a universal MYC recruiter at a small cohort of previously identified genes and highlights novel biological functions that may be coregulated by N-MYC and WDR5 to sustain the neuroblastoma state.
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Affiliation(s)
- Leigh A Bumpous
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Kylie C Moe
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Jing Wang
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37240, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37240, USA
| | - Logan A Carver
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Alexandria G Williams
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Alexander S Romer
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Jesse D Scobee
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Jack N Maxwell
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Cheyenne A Jones
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Dai H Chung
- Department of Pediatric Surgery, University of Texas Southwestern Medical Center and Children's Health, Dallas, TX, 75234, USA
| | - William P Tansey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37240, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37240, USA
| | - April M Weissmiller
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
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19
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Mocciaro E, Giambruno R, Micheloni S, Cernilogar FM, Andolfo A, Consonni C, Pannese M, Ferri G, Runfola V, Schotta G, Gabellini D. WDR5 is required for DUX4 expression and its pathological effects in FSHD muscular dystrophy. Nucleic Acids Res 2023; 51:5144-5161. [PMID: 37021550 PMCID: PMC10250208 DOI: 10.1093/nar/gkad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is one of the most prevalent neuromuscular disorders. The disease is linked to copy number reduction and/or epigenetic alterations of the D4Z4 macrosatellite on chromosome 4q35 and associated with aberrant gain of expression of the transcription factor DUX4, which triggers a pro-apoptotic transcriptional program leading to muscle wasting. As today, no cure or therapeutic option is available to FSHD patients. Given its centrality in FSHD, blocking DUX4 expression with small molecule drugs is an attractive option. We previously showed that the long non protein-coding RNA DBE-T is required for aberrant DUX4 expression in FSHD. Using affinity purification followed by proteomics, here we identified the chromatin remodeling protein WDR5 as a novel DBE-T interactor and a key player required for the biological activity of the lncRNA. We found that WDR5 is required for the expression of DUX4 and its targets in primary FSHD muscle cells. Moreover, targeting WDR5 rescues both cell viability and myogenic differentiation of FSHD patient cells. Notably, comparable results were obtained by pharmacological inhibition of WDR5. Importantly, WDR5 targeting was safe to healthy donor muscle cells. Our results support a pivotal role of WDR5 in the activation of DUX4 expression identifying a druggable target for an innovative therapeutic approach for FSHD.
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Affiliation(s)
- Emanuele Mocciaro
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Roberto Giambruno
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Stefano Micheloni
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Annapaola Andolfo
- ProMeFa, Proteomics and Metabolomics Facility, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Cristina Consonni
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Maria Pannese
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Giulia Ferri
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Valeria Runfola
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Davide Gabellini
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
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20
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Xiao M, Wu CH, Meek G, Kelly B, Castillo DB, Young LEA, Martire S, Dhungel S, McCauley E, Saha P, Dube AL, Gentry MS, Banaszynski LA, Sun RC, Kikani CK. PASK links cellular energy metabolism with a mitotic self-renewal network to establish differentiation competence. eLife 2023; 12:e81717. [PMID: 37052079 PMCID: PMC10162801 DOI: 10.7554/elife.81717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 04/11/2023] [Indexed: 04/14/2023] Open
Abstract
Quiescent stem cells are activated in response to a mechanical or chemical injury to their tissue niche. Activated cells rapidly generate a heterogeneous progenitor population that regenerates the damaged tissues. While the transcriptional cadence that generates heterogeneity is known, the metabolic pathways influencing the transcriptional machinery to establish a heterogeneous progenitor population remains unclear. Here, we describe a novel pathway downstream of mitochondrial glutamine metabolism that confers stem cell heterogeneity and establishes differentiation competence by countering post-mitotic self-renewal machinery. We discovered that mitochondrial glutamine metabolism induces CBP/EP300-dependent acetylation of stem cell-specific kinase, PAS domain-containing kinase (PASK), resulting in its release from cytoplasmic granules and subsequent nuclear migration. In the nucleus, PASK catalytically outcompetes mitotic WDR5-anaphase-promoting complex/cyclosome (APC/C) interaction resulting in the loss of post-mitotic Pax7 expression and exit from self-renewal. In concordance with these findings, genetic or pharmacological inhibition of PASK or glutamine metabolism upregulated Pax7 expression, reduced stem cell heterogeneity, and blocked myogenesis in vitro and muscle regeneration in mice. These results explain a mechanism whereby stem cells co-opt the proliferative functions of glutamine metabolism to generate transcriptional heterogeneity and establish differentiation competence by countering the mitotic self-renewal network via nuclear PASK.
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Affiliation(s)
- Michael Xiao
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD ProgramNew YorkUnited States
| | - Chia-Hua Wu
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
| | - Graham Meek
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
| | - Brian Kelly
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
| | - Dara Buendia Castillo
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
| | - Lyndsay EA Young
- Molecular and Cellular Biochemistry, College of Medicine, University of KentuckyLexingtonUnited States
| | - Sara Martire
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Children’s Medical Center Research Institute, Department of Obstetrics & Gynecology, Hamon Center for Regenerative Science and Medicine at the University of Texas Southwestern Medical CenterDallasUnited States
| | - Sajina Dhungel
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
| | - Elizabeth McCauley
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
| | - Purbita Saha
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Children’s Medical Center Research Institute, Department of Obstetrics & Gynecology, Hamon Center for Regenerative Science and Medicine at the University of Texas Southwestern Medical CenterDallasUnited States
| | - Altair L Dube
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Children’s Medical Center Research Institute, Department of Obstetrics & Gynecology, Hamon Center for Regenerative Science and Medicine at the University of Texas Southwestern Medical CenterDallasUnited States
| | - Matthew S Gentry
- Molecular and Cellular Biochemistry, College of Medicine, University of KentuckyLexingtonUnited States
| | - Laura A Banaszynski
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Children’s Medical Center Research Institute, Department of Obstetrics & Gynecology, Hamon Center for Regenerative Science and Medicine at the University of Texas Southwestern Medical CenterDallasUnited States
| | - Ramon C Sun
- Molecular and Cellular Biochemistry, College of Medicine, University of KentuckyLexingtonUnited States
- Department of Neuroscience, College of Medicine, University of KentuckyLexingtonUnited States
| | - Chintan K Kikani
- Department of Biology, College of Arts and Sciences, University of Kentucky, Thomas Hunt Morgan BuildingLexingtonUnited States
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21
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Mehta S, Buyanbat A, Orkin S, Nabet B. High-efficiency knock-in of degradable tags (dTAG) at endogenous loci in cell lines. Methods Enzymol 2023; 681:1-22. [PMID: 36764753 DOI: 10.1016/bs.mie.2022.08.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The dTAG system is a versatile strategy for tunable control of protein abundance and facilitates the time-resolved assessment of disease-associated protein function. A "co-opted" fusion-based degron peptide, the "dTAG" facilitates the study of endogenous protein function when knocked-in at the endogenous genetic loci of proteins of interest. We combine CRISPR/Cas9 mediated induction of double-strand breaks (DSB) with the delivery of a single-stranded DNA HDR-donor-template via crude preparations of recombinant adeno-associated virus (rAAV). Our approach to knock-in of large (1-2kb) DNA fragments via crude-rAAV mediated HDR donor delivery is rapid and inexpensive. It facilitates genetic modification of a variety of human as well as mouse cell lines at high efficiency and precision.
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Affiliation(s)
- Stuti Mehta
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, United States
| | - Altantsetseg Buyanbat
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, United States
| | - Stuart Orkin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, United States
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, United States.
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22
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Mitchell K, Sprowls SA, Arora S, Shakya S, Silver DJ, Goins CM, Wallace L, Roversi G, Schafer RE, Kay K, Miller TE, Lauko A, Bassett J, Kashyap A, D'Amato Kass J, Mulkearns-Hubert EE, Johnson S, Alvarado J, Rich JN, Holland EC, Paddison PJ, Patel AP, Stauffer SR, Hubert CG, Lathia JD. WDR5 represents a therapeutically exploitable target for cancer stem cells in glioblastoma. Genes Dev 2023; 37:86-102. [PMID: 36732025 PMCID: PMC10069451 DOI: 10.1101/gad.349803.122] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023]
Abstract
Glioblastomas (GBMs) are heterogeneous, treatment-resistant tumors driven by populations of cancer stem cells (CSCs). However, few molecular mechanisms critical for CSC population maintenance have been exploited for therapeutic development. We developed a spatially resolved loss-of-function screen in GBM patient-derived organoids to identify essential epigenetic regulators in the SOX2-enriched, therapy-resistant niche and identified WDR5 as indispensable for this population. WDR5 is a component of the WRAD complex, which promotes SET1 family-mediated Lys4 methylation of histone H3 (H3K4me), associated with positive regulation of transcription. In GBM CSCs, WDR5 inhibitors blocked WRAD complex assembly and reduced H3K4 trimethylation and expression of genes involved in CSC-relevant oncogenic pathways. H3K4me3 peaks lost with WDR5 inhibitor treatment occurred disproportionally on POU transcription factor motifs, including the POU5F1(OCT4)::SOX2 motif. Use of a SOX2/OCT4 reporter demonstrated that WDR5 inhibitor treatment diminished cells with high reporter activity. Furthermore, WDR5 inhibitor treatment and WDR5 knockdown altered the stem cell state, disrupting CSC in vitro growth and self-renewal, as well as in vivo tumor growth. These findings highlight the role of WDR5 and the WRAD complex in maintaining the CSC state and provide a rationale for therapeutic development of WDR5 inhibitors for GBM and other advanced cancers.
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Affiliation(s)
- Kelly Mitchell
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
| | - Samuel A Sprowls
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Sajina Shakya
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Daniel J Silver
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Christopher M Goins
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA;
| | - Lisa Wallace
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Gustavo Roversi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Rachel E Schafer
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Kristen Kay
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Adam Lauko
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Medical Scientist Training Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - John Bassett
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Anjali Kashyap
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Jonathan D'Amato Kass
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Erin E Mulkearns-Hubert
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Sadie Johnson
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Joseph Alvarado
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Jeremy N Rich
- University of Pittsburgh Medical Center Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Anoop P Patel
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, Washington 98195, USA
| | - Shaun R Stauffer
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Christopher G Hubert
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Justin D Lathia
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA;
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio 44106, USA
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23
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Yuan J, Peng H, Mo B, Yin C, Fang G, Li Y, Wang Y, Chen R, Wang Q. Inhibition of Wdr5 Attenuates Ang-II-Induced Fibroblast-to-Myofibroblast Transition in Cardiac Fibrosis by Regulating Mdm2/P53/P21 Pathway. Biomolecules 2022; 12:1574. [PMID: 36358925 PMCID: PMC9687631 DOI: 10.3390/biom12111574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 09/29/2023] Open
Abstract
Cardiac fibrosis is an important pathological process in many diseases. Wdr5 catalyzes the trimethylation of lysine K4 on histone H3. The effects of Wdr5 on the cardiac fibrosis phenotype and the activation or transformation of cardiac fibroblasts were investigated by Ang-II-infused mice by osmotic mini-pump and isolated primary neonatal rat cardiac fibroblasts. We found that the Wdr5 expression and histone H3K4me3 modification were significantly increased in Ang-II-infused mice. By stimulating primary neonatal rat cardiac fibroblasts with Ang II, we detected that the expression of Wdr5 and H3K4me3 modification were also significantly increased. Two Wdr5-specific inhibitors, and the lentivirus that transfected Sh-Wdr5, were used to treat primary mouse cardiac fibroblasts, which not only inhibited the histone methylation by Wdr5 but also significantly reduced the activation and migration ability of Ang-II-treated fibroblasts. To explore its mechanism, we found that the inhibition of Wdr5 increased the expression of P53, P21. Cut&Tag-qPCR showed that the inhibition of Wdr5 significantly reduced the enrichment of H3K4me3 in the Mdm2 promoter region. For in vivo experiments, we finally proved that the Wdr5 inhibitor OICR9429 significantly reduced Ang-II-induced cardiac fibrosis and increased the expression of P21 in cardiac fibroblasts. Inhibition of Wdr5 may mediate cardiac fibroblast cycle arrest through the Mdm2/P53/P21 pathway and alleviate cardiac fibrosis.
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Affiliation(s)
- Jiali Yuan
- Department of Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, #1665 Kongjiang Road, Shanghai 200082, China
| | - Hong Peng
- Department of Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, #1665 Kongjiang Road, Shanghai 200082, China
| | - Binfeng Mo
- Department of Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, #1665 Kongjiang Road, Shanghai 200082, China
| | - Chengye Yin
- Department of Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, #1665 Kongjiang Road, Shanghai 200082, China
| | - Guojian Fang
- Department of Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, #1665 Kongjiang Road, Shanghai 200082, China
| | - Yingze Li
- Department of Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, #1665 Kongjiang Road, Shanghai 200082, China
| | - Yuepeng Wang
- Department of Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, #1665 Kongjiang Road, Shanghai 200082, China
| | - Renhua Chen
- Department of Cardiology, Quanzhou Hospital of Traditional Chinese Medicine, #388 SunJiang Road, Quanzhou 362000, China
| | - Qunshan Wang
- Department of Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, #1665 Kongjiang Road, Shanghai 200082, China
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24
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TRIB3 Modulates PPARγ-Mediated Growth Inhibition by Interfering with the MLL Complex in Breast Cancer Cells. Int J Mol Sci 2022; 23:ijms231810535. [PMID: 36142452 PMCID: PMC9503934 DOI: 10.3390/ijms231810535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/03/2022] Open
Abstract
Aberrant expression or activity of proteins are amongst the best understood mechanisms that can drive cancer initiation and progression, as well as therapy resistance. TRIB3, a member of the Tribbles family of pseudokinases, is often dysregulated in cancer and has been associated with breast cancer initiation and metastasis formation. However, the underlying mechanisms by which TRIB3 contributes to these events are unclear. In this study, we demonstrate that TRIB3 regulates the expression of PPARγ, a transcription factor that has gained attention as a potential drug target in breast cancer for its antiproliferative actions. Proteomics and phosphoproteomics analyses together with classical biochemical assays indicate that TRIB3 interferes with the MLL complex and reduces MLL-mediated H3K4 trimethylation of the PPARG locus, thereby reducing PPARγ mRNA expression. Consequently, the overexpression of TRIB3 blunts the antiproliferative effect of PPARγ ligands in breast cancer cells, while reduced TRIB3 expression gives the opposite effect. In conclusion, our data implicate TRIB3 in epigenetic gene regulation and suggest that expression levels of this pseudokinase may serve as a predictor of successful experimental treatments with PPARγ ligands in breast cancer.
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25
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Cai WL, Chen JFY, Chen H, Wingrove E, Kurley SJ, Chan LH, Zhang M, Arnal-Estape A, Zhao M, Balabaki A, Li W, Yu X, Krop ED, Dou Y, Liu Y, Jin J, Westbrook TF, Nguyen DX, Yan Q. Human WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation. eLife 2022; 11:e78163. [PMID: 36043466 PMCID: PMC9584608 DOI: 10.7554/elife.78163] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/24/2022] [Indexed: 12/26/2022] Open
Abstract
Metastatic breast cancer remains a major cause of cancer-related deaths in women, and there are few effective therapies against this advanced disease. Emerging evidence suggests that key steps of tumor progression and metastasis are controlled by reversible epigenetic mechanisms. Using an in vivo genetic screen, we identified WDR5 as an actionable epigenetic regulator that is required for metastatic progression in models of triple-negative breast cancer. We found that knockdown of WDR5 in breast cancer cells independently impaired their tumorigenic as well as metastatic capabilities. Mechanistically, WDR5 promotes cell growth by increasing ribosomal gene expression and translation efficiency in a KMT2-independent manner. Consistently, pharmacological inhibition or degradation of WDR5 impedes cellular translation rate and the clonogenic ability of breast cancer cells. Furthermore, a combination of WDR5 targeting with mTOR inhibitors leads to potent suppression of translation and proliferation of breast cancer cells. These results reveal novel therapeutic strategies to treat metastatic breast cancer.
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Affiliation(s)
- Wesley L Cai
- Hillman Cancer Center, University of Pittsburgh Medical CenterPittsburghUnited States
- Department of Pathology, Yale UniversityNew HavenUnited States
| | | | - Huacui Chen
- Department of Pathology, Yale UniversityNew HavenUnited States
| | - Emily Wingrove
- Department of Pathology, Yale UniversityNew HavenUnited States
| | - Sarah J Kurley
- Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | - Lok Hei Chan
- Department of Pathology, Yale UniversityNew HavenUnited States
| | - Meiling Zhang
- Department of Pathology, Yale UniversityNew HavenUnited States
| | - Anna Arnal-Estape
- Department of Pathology, Yale UniversityNew HavenUnited States
- Yale Cancer Center, Yale School of MedicineNew HavenUnited States
| | - Minghui Zhao
- Department of Pathology, Yale UniversityNew HavenUnited States
| | - Amer Balabaki
- Department of Pathology, Yale UniversityNew HavenUnited States
| | - Wenxue Li
- Yale Cancer Biology Institute, Department of Pharmacology, Yale UniversityWest HavenUnited States
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Ethan D Krop
- Department of Pathology, Yale UniversityNew HavenUnited States
- Department of Biosciences, Rice University,HoustonUnited States
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann ArborAnn ArborUnited States
- Department of Medicine, Department of Biochemistry and Molecular Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Yansheng Liu
- Yale Cancer Center, Yale School of MedicineNew HavenUnited States
- Yale Cancer Biology Institute, Department of Pharmacology, Yale UniversityWest HavenUnited States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Thomas F Westbrook
- Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | - Don X Nguyen
- Department of Pathology, Yale UniversityNew HavenUnited States
- Yale Cancer Center, Yale School of MedicineNew HavenUnited States
- Yale Stem Cell Center, Yale School of MedicineNew HavenUnited States
- Department of Internal Medicine (Section of Medical Oncology), Yale School of Medicine,New HavenUnited States
| | - Qin Yan
- Department of Pathology, Yale UniversityNew HavenUnited States
- Yale Cancer Center, Yale School of MedicineNew HavenUnited States
- Yale Stem Cell Center, Yale School of MedicineNew HavenUnited States
- Yale Center for Immuno-Oncology, Yale School of MedicineNew HavenUnited States
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26
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Imran A, Moyer BS, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Convergent Alterations of a Protein Hub Produce Divergent Effects within a Binding Site. ACS Chem Biol 2022; 17:1586-1597. [PMID: 35613319 PMCID: PMC9207812 DOI: 10.1021/acschembio.2c00273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Progress in tumor
sequencing and cancer databases has created an
enormous amount of information that scientists struggle to sift through.
While several research groups have created computational methods to
analyze these databases, much work still remains in distinguishing
key implications of pathogenic mutations. Here, we describe an approach
to identify and evaluate somatic cancer mutations of WD40 repeat protein
5 (WDR5), a chromatin-associated protein hub. This multitasking protein
maintains the functional integrity of large multi-subunit enzymatic
complexes of the six human SET1 methyltransferases. Remarkably, the
somatic cancer mutations of WDR5 preferentially distribute within
and around an essential cavity, which hosts the WDR5 interaction (Win)
binding site. Hence, we assessed the real-time binding kinetics of
the interactions of key clustered WDR5 mutants with the Win motif
peptide ligands of the SET1 family members (SET1Win). Our
measurements highlight that this subset of mutants exhibits divergent
perturbations in the kinetics and strength of interactions not only
relative to those of the native WDR5 but also among various SET1Win ligands. These outcomes could form a fundamental basis
for future drug discovery and other developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Brandon S. Moyer
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
| | - Dan Kalina
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
- The BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
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27
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Mayse LA, Imran A, Larimi MG, Cosgrove MS, Wolfe AJ, Movileanu L. Disentangling the recognition complexity of a protein hub using a nanopore. Nat Commun 2022; 13:978. [PMID: 35190547 PMCID: PMC8861093 DOI: 10.1038/s41467-022-28465-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
WD40 repeat proteins are frequently involved in processing cell signaling and scaffolding large multi-subunit machineries. Despite their significance in physiological and disease-like conditions, their reversible interactions with other proteins remain modestly examined. Here, we show the development and validation of a protein nanopore for the detection and quantification of WD40 repeat protein 5 (WDR5), a chromatin-associated hub involved in epigenetic regulation of histone methylation. Our nanopore sensor is equipped with a 14-residue Win motif of mixed lineage leukemia 4 methyltransferase (MLL4Win), a WDR5 ligand. Our approach reveals a broad dynamic range of MLL4Win-WDR5 interactions and three distant subpopulations of binding events, representing three modes of protein recognition. The three binding events are confirmed as specific interactions using a weakly binding WDR5 derivative and various environmental contexts. These outcomes demonstrate the substantial sensitivity of our nanopore sensor, which can be utilized in protein analytics. Nanopores are powerful tools for sampling protein-peptide interactions. Here, the authors convert a protein-based nanopore into a sensitive biosensor to characterize the complex binding of WDR5 protein to a 14-residue ligand.
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28
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Siladi AJ, Wang J, Florian AC, Thomas LR, Creighton JH, Matlock BK, Flaherty DK, Lorey SL, Howard GC, Fesik SW, Weissmiller AM, Liu Q, Tansey WP. WIN site inhibition disrupts a subset of WDR5 function. Sci Rep 2022; 12:1848. [PMID: 35115608 PMCID: PMC8813994 DOI: 10.1038/s41598-022-05947-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/19/2022] [Indexed: 11/09/2022] Open
Abstract
WDR5 nucleates the assembly of histone-modifying complexes and acts outside this context in a range of chromatin-centric processes. WDR5 is also a prominent target for pharmacological inhibition in cancer. Small-molecule degraders of WDR5 have been described, but most drug discovery efforts center on blocking the WIN site of WDR5, an arginine binding cavity that engages MLL/SET enzymes that deposit histone H3 lysine 4 methylation (H3K4me). Therapeutic application of WIN site inhibitors is complicated by the disparate functions of WDR5, but is generally guided by two assumptions-that WIN site inhibitors disable all functions of WDR5, and that changes in H3K4me drive the transcriptional response of cancer cells to WIN site blockade. Here, we test these assumptions by comparing the impact of WIN site inhibition versus WDR5 degradation on H3K4me and transcriptional processes. We show that WIN site inhibition disables only a specific subset of WDR5 activity, and that H3K4me changes induced by WDR5 depletion do not explain accompanying transcriptional responses. These data recast WIN site inhibitors as selective loss-of-function agents, contradict H3K4me as a relevant mechanism of action for WDR5 inhibitors, and indicate distinct clinical applications of WIN site inhibitors and WDR5 degraders.
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Affiliation(s)
- Andrew J Siladi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue South, 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
| | - Andrea C Florian
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37232, USA
| | - Lance R Thomas
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37232, USA
- Oncocyte Corporation, 2 International Drive, Suite 510, Nashville, TN, 37217, USA
| | - Joy H Creighton
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37232, USA
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 32132, USA
| | - Brittany K Matlock
- Vanderbilt University Medical Center Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - David K Flaherty
- Vanderbilt University Medical Center Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37232, USA
| | - Gregory C Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue South, 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, Nashville, TN, 37232, USA
| | - April M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37232, USA
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 32132, 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
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37232, USA.
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
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29
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Guarnaccia AD, Weissmiller AM, Tansey WP. Gene-specific quantification of nascent transcription following targeted degradation of endogenous proteins in cultured cells. STAR Protoc 2021; 2:101000. [PMID: 34917979 PMCID: PMC8669106 DOI: 10.1016/j.xpro.2021.101000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome-wide nuclear run-ons are a powerful way to determine the impact of a perturbation such as transcription factor degradation on transcriptional patterns. But often investigators are interested in monitoring transcriptional effects at specific sets of genes, rather than the entire genome. Here we describe an approach that couples genome engineering to tag endogenous proteins for degradation with a streamlined nuclear run-on assay to yield gene-specific information on primary transcriptional changes elicited by factor depletion. For complete details on the use and execution of this protocol, please refer to Guarnaccia et al. (2021).
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Affiliation(s)
- Alissa D. Guarnaccia
- Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
- Department of Microchemistry, Proteomics, Lipidomics, and Next Generation Sequencing, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - April M. Weissmiller
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 32132, 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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30
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Zhou Y, Gao X, Yuan M, Yang B, He Q, Cao J. Targeting Myc Interacting Proteins as a Winding Path in Cancer Therapy. Front Pharmacol 2021; 12:748852. [PMID: 34658888 PMCID: PMC8511624 DOI: 10.3389/fphar.2021.748852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/10/2021] [Indexed: 12/26/2022] Open
Abstract
MYC, as a well-known oncogene, plays essential roles in promoting tumor occurrence, development, invasion and metastasis in many kinds of solid tumors and hematologic neoplasms. In tumors, the low expression and the short half-life of Myc are reversed, cause tumorigenesis. And proteins that directly interact with different Myc domains have exerted a significant impact in the process of Myc-driven carcinogenesis. Apart from affecting the transcription of Myc target genes, Myc interaction proteins also regulate the stability of Myc through acetylation, methylation, phosphorylation and other post-translational modifications, as well as competitive combination with Myc. In this review, we summarize a series of Myc interacting proteins and recent advances in the related inhibitors, hoping that can provide new opportunities for Myc-driven cancer treatment.
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Affiliation(s)
- Yihui Zhou
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaomeng Gao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Meng Yuan
- Cancer Center of Zhejiang University, Hangzhou, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Cancer Center of Zhejiang University, Hangzhou, China.,The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Cancer Center of Zhejiang University, Hangzhou, China.,The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
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31
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Imran A, Moyer BS, Canning AJ, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Kinetics of the multitasking high-affinity Win binding site of WDR5 in restricted and unrestricted conditions. Biochem J 2021; 478:2145-2161. [PMID: 34032265 PMCID: PMC8214142 DOI: 10.1042/bcj20210253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/05/2023]
Abstract
Recent advances in quantitative proteomics show that WD40 proteins play a pivotal role in numerous cellular networks. Yet, they have been fairly unexplored and their physical associations with other proteins are ambiguous. A quantitative understanding of these interactions has wide-ranging significance. WD40 repeat protein 5 (WDR5) interacts with all members of human SET1/MLL methyltransferases, which regulate methylation of the histone 3 lysine 4 (H3K4). Here, using real-time binding measurements in a high-throughput setting, we identified the kinetic fingerprint of transient associations between WDR5 and 14-residue WDR5 interaction (Win) motif peptides of each SET1 protein (SET1Win). Our results reveal that the high-affinity WDR5-SET1Win interactions feature slow association kinetics. This finding is likely due to the requirement of SET1Win to insert into the narrow WDR5 cavity, also named the Win binding site. Furthermore, our explorations indicate fairly slow dissociation kinetics. This conclusion is in accordance with the primary role of WDR5 in maintaining the functional integrity of a large multisubunit complex, which regulates the histone methylation. Because the Win binding site is considered a key therapeutic target, the immediate outcomes of this study could form the basis for accelerated developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Brandon S. Moyer
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
| | - Ashley J. Canning
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Dan Kalina
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- The BioInspired Institute, Syracuse University, Syracuse, New York, 13244, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
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