1
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Ptakova A, Zimova L, Barvik I, Bon RS, Vlachova V. Functional determinants of lysophospholipid- and voltage-dependent regulation of TRPC5 channel. Cell Mol Life Sci 2024; 81:374. [PMID: 39210039 PMCID: PMC11362415 DOI: 10.1007/s00018-024-05417-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/30/2024] [Accepted: 08/17/2024] [Indexed: 09/04/2024]
Abstract
Lysophosphatidylcholine (LPC) is a bioactive lipid present at high concentrations in inflamed and injured tissues where it contributes to the initiation and maintenance of pain. One of its important molecular effectors is the transient receptor potential canonical 5 (TRPC5), but the explicit mechanism of the activation is unknown. Using electrophysiology, mutagenesis and molecular dynamics simulations, we show that LPC-induced activation of TRPC5 is modulated by xanthine ligands and depolarizing voltage, and involves conserved residues within the lateral fenestration of the pore domain. Replacement of W577 with alanine (W577A) rendered the channel insensitive to strong depolarizing voltage, but LPC still activated this mutant at highly depolarizing potentials. Substitution of G606 located directly opposite position 577 with tryptophan rescued the sensitivity of W577A to depolarization. Molecular simulations showed that depolarization widens the lower gate of the channel and this conformational change is prevented by the W577A mutation or removal of resident lipids. We propose a gating scheme in which depolarizing voltage and lipid-pore helix interactions act together to promote TRPC5 channel opening.
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Affiliation(s)
- Alexandra Ptakova
- Department of Cellular Neurophysiology, Institute of Physiology, Czech Academy of Sciences, Videnska 1083, 142 20, Prague 4, Czech Republic
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lucie Zimova
- Department of Cellular Neurophysiology, Institute of Physiology, Czech Academy of Sciences, Videnska 1083, 142 20, Prague 4, Czech Republic
| | - Ivan Barvik
- Division of Biomolecular Physics, Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Robin S Bon
- Leeds Institute of Cardiovascular and Metabolic Medicine (LICAMM) and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Viktorie Vlachova
- Department of Cellular Neurophysiology, Institute of Physiology, Czech Academy of Sciences, Videnska 1083, 142 20, Prague 4, Czech Republic.
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2
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Chen YF, Rahman A, Sax JL, Atala Pleshinger MJ, Friedrich RM, Adams DJ. C646 degrades Exportin-1 to modulate p300 chromatin occupancy and function. Cell Chem Biol 2024; 31:1363-1372.e8. [PMID: 38917791 PMCID: PMC11268802 DOI: 10.1016/j.chembiol.2024.05.016] [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: 11/10/2023] [Revised: 03/13/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024]
Abstract
Molecular glues can induce proximity between a target protein and ubiquitin ligases to induce target degradation, but strategies for their discovery remain limited. We screened 3,200 bioactive small molecules and identified that C646 requires neddylation-dependent protein degradation to induce cytotoxicity. Although the histone acetyltransferase p300 is the canonical target of C646, we provide extensive evidence that C646 directly targets and degrades Exportin-1 (XPO1). Multiple cellular phenotypes induced by C646 were abrogated in cells expressing the known XPO1C528S drug-resistance allele. While XPO1 catalyzes nuclear-to-cytoplasmic transport of many cargo proteins, it also directly binds chromatin. We demonstrate that p300 and XPO1 co-occupy hundreds of chromatin loci. Degrading XPO1 using C646 or the known XPO1 modulator S109 diminishes the chromatin occupancy of both XPO1 and p300, enabling direct targeting of XPO1 to phenocopy p300 inhibition. This work highlights the utility of drug-resistant alleles and further validates XPO1 as a targetable regulator of chromatin state.
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Affiliation(s)
- Yi Fan Chen
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Atikur Rahman
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Joel L Sax
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Matthew J Atala Pleshinger
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ryan M Friedrich
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Drew J Adams
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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3
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Waterbury AL, Kwok HS, Lee C, Narducci DN, Freedy AM, Su C, Raval S, Reiter AH, Hawkins W, Lee K, Li J, Hoenig SM, Vinyard ME, Cole PA, Hansen AS, Carr SA, Papanastasiou M, Liau BB. An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing. Mol Cell 2024; 84:2238-2254.e11. [PMID: 38870936 PMCID: PMC11193646 DOI: 10.1016/j.molcel.2024.05.017] [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: 09/12/2023] [Revised: 03/21/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
Transcriptional coregulators and transcription factors (TFs) contain intrinsically disordered regions (IDRs) that are critical for their association and function in gene regulation. More recently, IDRs have been shown to promote multivalent protein-protein interactions between coregulators and TFs to drive their association into condensates. By contrast, here we demonstrate how the IDR of the corepressor LSD1 excludes TF association, acting as a dynamic conformational switch that tunes repression of active cis-regulatory elements. Hydrogen-deuterium exchange shows that the LSD1 IDR interconverts between transient open and closed conformational states, the latter of which inhibits partitioning of the protein's structured domains with TF condensates. This autoinhibitory switch controls leukemic differentiation by modulating repression of active cis-regulatory elements bound by LSD1 and master hematopoietic TFs. Together, these studies unveil alternative mechanisms by which disordered regions and their dynamic crosstalk with structured regions can shape coregulator-TF interactions to control cis-regulatory landscapes and cell fate.
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Affiliation(s)
- Amanda L Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Hui Si Kwok
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ceejay Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Domenic N Narducci
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Allyson M Freedy
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Cindy Su
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Shaunak Raval
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Andrew H Reiter
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - William Hawkins
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jiaming Li
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Samuel M Hoenig
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Anders S Hansen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Steven A Carr
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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4
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Chen YF, Ghazala M, Friedrich RM, Cordova BA, Petroze FN, Srinivasan R, Allan KC, Yan DF, Sax JL, Carr K, Tomchuck SL, Fedorov Y, Huang AY, Desai AB, Adams DJ. Targeting the chromatin binding of exportin-1 disrupts NFAT and T cell activation. Nat Chem Biol 2024:10.1038/s41589-024-01586-5. [PMID: 38528120 DOI: 10.1038/s41589-024-01586-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 02/22/2024] [Indexed: 03/27/2024]
Abstract
Exportin-1 (XPO1/CRM1) plays a central role in the nuclear-to-cytoplasmic transport of hundreds of proteins and contributes to other cellular processes, such as centrosome duplication. Small molecules targeting XPO1 induce cytotoxicity, and selinexor was approved by the Food and Drug Administration in 2019 as a cancer chemotherapy for relapsed multiple myeloma. Here, we describe a cell-type-dependent chromatin-binding function for XPO1 that is essential for the chromatin occupancy of NFAT transcription factors and thus the appropriate activation of T cells. Additionally, we establish a class of XPO1-targeting small molecules capable of disrupting the chromatin binding of XPO1 without perturbing nuclear export or inducing cytotoxicity. This work defines a broad transcription regulatory role for XPO1 that is essential for T cell activation as well as a new class of XPO1 modulators to enable therapeutic targeting of XPO1 beyond oncology including in T cell-driven autoimmune disorders.
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Affiliation(s)
- Yi Fan Chen
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Maryam Ghazala
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ryan M Friedrich
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Brittany A Cordova
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Frederick N Petroze
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ramya Srinivasan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kevin C Allan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - David F Yan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Joel L Sax
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kelley Carr
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Suzanne L Tomchuck
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yuriy Fedorov
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Alex Y Huang
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Amar B Desai
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Drew J Adams
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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5
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Zhan J, Li Z, Lin C, Wang D, Yu L, Xiao X. The role of circRNAs in regulation of drug resistance in ovarian cancer. Front Genet 2023; 14:1320185. [PMID: 38152652 PMCID: PMC10751324 DOI: 10.3389/fgene.2023.1320185] [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: 10/11/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
Ovarian cancer is one of the female reproductive system tumors. Chemotherapy is used for advanced ovarian cancer patients; however, drug resistance is a pivotal cause of chemotherapeutic failure. Hence, it is critical to explore the molecular mechanisms of drug resistance of ovarian cancer cells and to ameliorate chemoresistance. Noncoding RNAs (ncRNAs) have been identified to critically participate in drug sensitivity in a variety of human cancers, including ovarian cancer. Among ncRNAs, circRNAs sponge miRNAs and prevent miRNAs from regulation of their target mRNAs. CircRNAs can interact with DNA or proteins to modulate gene expression. In this review, we briefly describe the biological functions of circRNAs in the development and progression of ovarian cancer. Moreover, we discuss the underneath regulatory molecular mechanisms of circRNAs on governing drug resistance in ovarian cancer. Furthermore, we mention the novel strategies to overcome drug resistance via targeting circRNAs in ovarian cancer. Due to that circRNAs play a key role in modulation of drug resistance in ovarian cancer, targeting circRNAs could be a novel approach for attenuation of chemoresistance in ovarian cancer.
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Affiliation(s)
- Jun Zhan
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - Zhiyi Li
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - Changsheng Lin
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - Dingding Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - Lei Yu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - Xue Xiao
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China
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6
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Yang KB, Cameranesi M, Gowder M, Martinez C, Shamovsky Y, Epshtein V, Hao Z, Nguyen T, Nirenstein E, Shamovsky I, Rasouly A, Nudler E. High-resolution landscape of an antibiotic binding site. Nature 2023; 622:180-187. [PMID: 37648864 PMCID: PMC10550828 DOI: 10.1038/s41586-023-06495-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Antibiotic binding sites are located in important domains of essential enzymes and have been extensively studied in the context of resistance mutations; however, their study is limited by positive selection. Using multiplex genome engineering1 to overcome this constraint, we generate and characterize a collection of 760 single-residue mutants encompassing the entire rifampicin binding site of Escherichia coli RNA polymerase (RNAP). By genetically mapping drug-enzyme interactions, we identify an alpha helix where mutations considerably enhance or disrupt rifampicin binding. We find mutations in this region that prolong antibiotic binding, converting rifampicin from a bacteriostatic to bactericidal drug by inducing lethal DNA breaks. The latter are replication dependent, indicating that rifampicin kills by causing detrimental transcription-replication conflicts at promoters. We also identify additional binding site mutations that greatly increase the speed of RNAP.Fast RNAP depletes the cell of nucleotides, alters cell sensitivity to different antibiotics and provides a cold growth advantage. Finally, by mapping natural rpoB sequence diversity, we discover that functional rifampicin binding site mutations that alter RNAP properties or confer drug resistance occur frequently in nature.
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Affiliation(s)
- Kevin B Yang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Maria Cameranesi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Manjunath Gowder
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Criseyda Martinez
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Yosef Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Vitaliy Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Thao Nguyen
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Eric Nirenstein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Aviram Rasouly
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
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7
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Kwok HS, Freedy AM, Siegenfeld AP, Morriss JW, Waterbury AL, Kissler SM, Liau BB. Drug addiction unveils a repressive methylation ceiling in EZH2-mutant lymphoma. Nat Chem Biol 2023; 19:1105-1115. [PMID: 36973442 PMCID: PMC10522050 DOI: 10.1038/s41589-023-01299-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 02/23/2023] [Indexed: 03/29/2023]
Abstract
Drug addiction, a phenomenon where cancer cells paradoxically depend on continuous drug treatment for survival, has uncovered cell signaling mechanisms and cancer codependencies. Here we discover mutations that confer drug addiction to inhibitors of the transcriptional repressor polycomb repressive complex 2 (PRC2) in diffuse large B-cell lymphoma. Drug addiction is mediated by hypermorphic mutations in the CXC domain of the catalytic subunit EZH2, which maintain H3K27me3 levels even in the presence of PRC2 inhibitors. Discontinuation of inhibitor treatment leads to overspreading of H3K27me3, surpassing a repressive methylation ceiling compatible with lymphoma cell survival. Exploiting this vulnerability, we show that inhibition of SETD2 similarly induces the spread of H3K27me3 and blocks lymphoma growth. Collectively, our findings demonstrate that constraints on chromatin landscapes can yield biphasic dependencies in epigenetic signaling in cancer cells. More broadly, we highlight how approaches to identify drug addiction mutations can be leveraged to discover cancer vulnerabilities.
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Affiliation(s)
- Hui Si Kwok
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Allyson M Freedy
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Allison P Siegenfeld
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia W Morriss
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amanda L Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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8
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Lue NZ, Liau BB. Base editor screens for in situ mutational scanning at scale. Mol Cell 2023; 83:2167-2187. [PMID: 37390819 PMCID: PMC10330937 DOI: 10.1016/j.molcel.2023.06.009] [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: 04/21/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 07/02/2023]
Abstract
A fundamental challenge in biology is understanding the molecular details of protein function. How mutations alter protein activity, regulation, and response to drugs is of critical importance to human health. Recent years have seen the emergence of pooled base editor screens for in situ mutational scanning: the interrogation of protein sequence-function relationships by directly perturbing endogenous proteins in live cells. These studies have revealed the effects of disease-associated mutations, discovered novel drug resistance mechanisms, and generated biochemical insights into protein function. Here, we discuss how this "base editor scanning" approach has been applied to diverse biological questions, compare it with alternative techniques, and describe the emerging challenges that must be addressed to maximize its utility. Given its broad applicability toward profiling mutations across the proteome, base editor scanning promises to revolutionize the investigation of proteins in their native contexts.
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Affiliation(s)
- Nicholas Z Lue
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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9
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Mao Z, Kim JH, Lee J, Xiong H, Zhang F, Kim JS. Engineering of BODIPY-based theranostics for cancer therapy. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Ngan KCH, Hoenig SM, Kwok HS, Lue NZ, Gosavi PM, Tanner DA, Garcia EM, Lee C, Liau BB. Activity-based CRISPR scanning uncovers allostery in DNA methylation maintenance machinery. eLife 2023; 12:80640. [PMID: 36762644 PMCID: PMC9946446 DOI: 10.7554/elife.80640] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Allostery enables dynamic control of protein function. A paradigmatic example is the tightly orchestrated process of DNA methylation maintenance. Despite the fundamental importance of allosteric sites, their identification remains highly challenging. Here, we perform CRISPR scanning on the essential maintenance methylation machinery-DNMT1 and its partner UHRF1-with the activity-based inhibitor decitabine to uncover allosteric mechanisms regulating DNMT1. In contrast to non-covalent DNMT1 inhibition, activity-based selection implicates numerous regions outside the catalytic domain in DNMT1 function. Through computational analyses, we identify putative mutational hotspots in DNMT1 distal from the active site that encompass mutations spanning a multi-domain autoinhibitory interface and the uncharacterized BAH2 domain. We biochemically characterize these mutations as gain-of-function, exhibiting increased DNMT1 activity. Extrapolating our analysis to UHRF1, we discern putative gain-of-function mutations in multiple domains, including key residues across the autoinhibitory TTD-PBR interface. Collectively, our study highlights the utility of activity-based CRISPR scanning for nominating candidate allosteric sites, and more broadly, introduces new analytical tools that further refine the CRISPR scanning framework.
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Affiliation(s)
- Kevin Chun-Ho Ngan
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Samuel M Hoenig
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Hui Si Kwok
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Nicholas Z Lue
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Pallavi M Gosavi
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - David A Tanner
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Emma M Garcia
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Ceejay Lee
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
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11
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Boudreau MW, Hergenrother PJ. Evolution of 3-(4-hydroxyphenyl)indoline-2-one as a scaffold for potent and selective anticancer activity. RSC Med Chem 2022; 13:711-725. [PMID: 35814932 PMCID: PMC9215341 DOI: 10.1039/d2md00110a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
Development of targeted anticancer modalities has prompted a new era in cancer treatment that is notably different from the age of radical surgery and highly toxic chemotherapy. Behind each effective compound is a rich and complex history from first identification of chemical matter, detailed optimization, and mechanistic investigations, ultimately leading to exciting molecules for drug development. Herein we review the history and on-going journey of one such anticancer scaffold, the 3-(4-hydroxyphenyl)indoline-2-ones. With humble beginnings in 19th century Bavaria, we review this scaffold's synthetic history and anticancer optimization, including its recent demonstration of tumor eradication of drug-resistant, estrogen receptor-positive breast cancer. Compounds containing the 3-(4-hydroxyphenyl)indoline-2-one pharmacophore are emerging as intriguing candidates for the treatment of cancer.
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Affiliation(s)
- Matthew W Boudreau
- Dept. of Chemistry, Carl R. Woese Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Paul J Hergenrother
- Dept. of Chemistry, Carl R. Woese Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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Robinson SA, Banik SM. CRISPR-Suppressor Scanning Unsticks Molecular Glues. ACS CENTRAL SCIENCE 2022; 8:408-411. [PMID: 35505876 PMCID: PMC9052799 DOI: 10.1021/acscentsci.2c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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