1
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Takahashi M, Chong HB, Zhang S, Yang TY, Lazarov MJ, Harry S, Maynard M, Hilbert B, White RD, Murrey HE, Tsou CC, Vordermark K, Assaad J, Gohar M, Dürr BR, Richter M, Patel H, Kryukov G, Brooijmans N, Alghali ASO, Rubio K, Villanueva A, Zhang J, Ge M, Makram F, Griesshaber H, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Popoola G, Rachmin I, Khandelwal N, Neil JR, Tien PC, Chen N, Hosp T, van den Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen MQ, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Kastanos J, Oh E, Fisher DE, Maheswaran S, Haber DA, Boland GM, Sade-Feldman M, Jenkins RW, Hata AN, Bardeesy NM, Suvà ML, Martin BR, Liau BB, Ott CJ, Rivera MN, Lawrence MS, Bar-Peled L. DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. Cell 2024; 187:2536-2556.e30. [PMID: 38653237 DOI: 10.1016/j.cell.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/15/2024] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
Abstract
Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors for a wide range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed "DrugMap," an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NF-κB1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NF-κB1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription-factor activity.
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Affiliation(s)
- Mariko Takahashi
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA.
| | - Harrison B Chong
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Siwen Zhang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Tzu-Yi Yang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Matthew J Lazarov
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Stefan Harry
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | | | | | | | | | | | - Kira Vordermark
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Jonathan Assaad
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Magdy Gohar
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Benedikt R Dürr
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Marianne Richter
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Himani Patel
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | | | | | | | - Karla Rubio
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Antonio Villanueva
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Junbing Zhang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Maolin Ge
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Farah Makram
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Hanna Griesshaber
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Drew Harrison
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Ann-Sophie Koglin
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Samuel Ojeda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Barbara Karakyriakou
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Alexander Healy
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - George Popoola
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Inbal Rachmin
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Neha Khandelwal
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | | | - Pei-Chieh Tien
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Nicholas Chen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Tobias Hosp
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Sanne van den Ouweland
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Toshiro Hara
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lillian Bussema
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rui Dong
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lei Shi
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Martin Q Rasmussen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Ana Carolina Domingues
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Aleigha Lawless
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacy Fang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Satoshi Yoda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Linh Phuong Nguyen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Sarah Marie Reeves
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Farrah Nicole Wakefield
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Adam Acker
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Sarah Elizabeth Clark
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Taronish Dubash
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - John Kastanos
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Eugene Oh
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - David E Fisher
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shyamala Maheswaran
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Daniel A Haber
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Genevieve M Boland
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Surgery, Harvard Medical School, Boston, MA 02114, USA
| | - Moshe Sade-Feldman
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Russell W Jenkins
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Aaron N Hata
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Nabeel M Bardeesy
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Mario L Suvà
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | | | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher J Ott
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Miguel N Rivera
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Michael S Lawrence
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA.
| | - Liron Bar-Peled
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA.
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2
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Kumar Tiwari P, Reddy Doda S, Vannam R, Hudlikar M, Harrison DA, Ojeda S, Rai S, Koglin AS, Nguyen Gilbert A, Ott CJ. Exploration of bromodomain ligand-linker conjugation sites for efficient CBP/p300 heterobifunctional degrader activity. Bioorg Med Chem Lett 2024; 102:129676. [PMID: 38408512 DOI: 10.1016/j.bmcl.2024.129676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024]
Abstract
Synthesis of proteolysis targeting chimeras (PROTACs) involves conjugation of an E3 ligase binding ligand to a ligand targeting a protein of interest via a rigid or flexible chemical linker. The choice of linker conjugation site on these ligands can be informed by structural analysis of ligand-target binding modes, the feasibility of synthetic procedures to access specific sites, and computational modeling of predicted ternary complex formations. Small molecules that target bromodomains - epigenetic readers of lysine acetylation - typically offer several potential options for linker conjugation sites. Here we describe how varying the linker attachment site (exit vector) on a CBP/p300 bromodomain ligand along with linker length affects PROTAC degradation activity and ternary complex formation. Using kinetic live cell assays of endogenous CBP and p300 protein abundance and bead-based proximity assays for ternary complexes, we describe the structure-activity relationships of a diverse library of CBP/p300 degraders (dCBPs).
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Affiliation(s)
- Praveen Kumar Tiwari
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Sai Reddy Doda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Raghu Vannam
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Manish Hudlikar
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Drew A Harrison
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Samuel Ojeda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sumit Rai
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ann-Sophie Koglin
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | | | - Christopher J Ott
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA.
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3
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Bakaric A, Cironi L, Praz V, Sanalkumar R, Broye LC, Favre-Bulle K, Letovanec I, Digklia A, Renella R, Stamenkovic I, Ott CJ, Nakamura T, Antonescu CR, Rivera MN, Riggi N. CIC-DUX4 Chromatin Profiling Reveals New Epigenetic Dependencies and Actionable Therapeutic Targets in CIC-Rearranged Sarcomas. Cancers (Basel) 2024; 16:457. [PMID: 38275898 PMCID: PMC10814785 DOI: 10.3390/cancers16020457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
CIC-DUX4-rearranged sarcoma (CDS) is a rare and aggressive soft tissue tumor that occurs most frequently in young adults. The key oncogenic driver of this disease is the expression of the CIC-DUX4 fusion protein as a result of chromosomal rearrangements. CIC-DUX4 displays chromatin binding properties, and is therefore believed to function as an aberrant transcription factor. However, the chromatin remodeling events induced by CIC-DUX4 are not well understood, limiting our ability to identify new mechanism-based therapeutic strategies for these patients. Here, we generated a genome-wide profile of CIC-DUX4 DNA occupancy and associated chromatin states in human CDS cell models and primary tumors. Combining chromatin profiling, proximity ligation assays, as well as genetic and pharmacological perturbations, we show that CIC-DUX4 operates as a potent transcriptional activator at its binding sites. This property is in contrast with the repressive function of the wild-type CIC protein, and is mainly mediated through the direct interaction of CIC-DUX4 with the acetyltransferase p300. In keeping with this, we show p300 to be essential for CDS tumor cell proliferation; additionally, we find its pharmacological inhibition to significantly impact tumor growth in vitro and in vivo. Taken together, our study elucidates the mechanisms underpinning CIC-DUX4-mediated transcriptional regulation.
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Affiliation(s)
- Arnaud Bakaric
- Clinical Pathology Service, Department of Diagnostics, Geneva University Hospital, 1205 Geneva, Switzerland
| | - Luisa Cironi
- Pediatric Hematology-Oncology Research Laboratory, Woman-Mother-Child Department, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Viviane Praz
- Platform Genomics Technologies, Center for Integrative Genomics, Faculty of Biology and Medicine, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Rajendran Sanalkumar
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
- Department of Cell and Tissue Genomics, Genentech. Inc., South San Francisco, CA 94103, USA
| | - Liliane C. Broye
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
| | - Kerria Favre-Bulle
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
| | - Igor Letovanec
- Department of Histopathology, Central Institute, Valais Hospital, 1951 Sion, Switzerland
| | - Antonia Digklia
- Department of Oncology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Raffaele Renella
- Pediatric Hematology-Oncology Research Laboratory, Woman-Mother-Child Department, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Ivan Stamenkovic
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
| | - Christopher J. Ott
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; (C.J.O.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Takuro Nakamura
- Institute of Medical Science, Tokyo Medical University, Tokyo 160-0023, Japan
| | - Cristina R. Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Miguel N. Rivera
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; (C.J.O.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicolò Riggi
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
- Department of Cell and Tissue Genomics, Genentech. Inc., South San Francisco, CA 94103, USA
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4
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Bishop TR, Subramanian C, Bilotta EM, Garnar-Wortzel L, Ramos AR, Zhang Y, Asiaban JN, Ott CJ, Rock CO, Erb MA. Acetyl-CoA biosynthesis drives resistance to histone acetyltransferase inhibition. Nat Chem Biol 2023; 19:1215-1222. [PMID: 37127754 PMCID: PMC10538425 DOI: 10.1038/s41589-023-01320-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Histone acetyltransferases (HATs) are implicated as both oncogene and nononcogene dependencies in diverse human cancers. Acetyl-CoA-competitive HAT inhibitors have emerged as potential cancer therapeutics and the first clinical trial for this class of drugs is ongoing (NCT04606446). Despite these developments, the potential mechanisms of therapeutic response and evolved drug resistance remain poorly understood. Having discovered that multiple regulators of de novo coenzyme A (CoA) biosynthesis can modulate sensitivity to CBP/p300 HAT inhibition (PANK3, PANK4 and SLC5A6), we determined that elevated acetyl-CoA concentrations can outcompete drug-target engagement to elicit acquired drug resistance. This not only affects structurally diverse CBP/p300 HAT inhibitors, but also agents related to an investigational KAT6A/B HAT inhibitor that is currently in Phase 1 clinical trials. Altogether, this work uncovers CoA metabolism as an unexpected liability of anticancer HAT inhibitors and will therefore buoy future efforts to optimize the efficacy of this new form of targeted therapy.
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Affiliation(s)
- Timothy R Bishop
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Eric M Bilotta
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Anissa R Ramos
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Yuxiang Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Joshua N Asiaban
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher J Ott
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Erb
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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5
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Isozaki H, Sakhtemani R, Abbasi A, Nikpour N, Stanzione M, Oh S, Langenbucher A, Monroe S, Su W, Cabanos HF, Siddiqui FM, Phan N, Jalili P, Timonina D, Bilton S, Gomez-Caraballo M, Archibald HL, Nangia V, Dionne K, Riley A, Lawlor M, Banwait MK, Cobb RG, Zou L, Dyson NJ, Ott CJ, Benes C, Getz G, Chan CS, Shaw AT, Gainor JF, Lin JJ, Sequist LV, Piotrowska Z, Yeap BY, Engelman JA, Lee JJK, Maruvka YE, Buisson R, Lawrence MS, Hata AN. Therapy-induced APOBEC3A drives evolution of persistent cancer cells. Nature 2023; 620:393-401. [PMID: 37407818 PMCID: PMC10804446 DOI: 10.1038/s41586-023-06303-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/08/2023] [Indexed: 07/07/2023]
Abstract
Acquired drug resistance to anticancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified1-4, the underlying molecular mechanisms shaping tumour evolution during treatment are incompletely understood. Genomic profiling of patient tumours has implicated apolipoprotein B messenger RNA editing catalytic polypeptide-like (APOBEC) cytidine deaminases in tumour evolution; however, their role during therapy and the development of acquired drug resistance is undefined. Here we report that lung cancer targeted therapies commonly used in the clinic can induce cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug-tolerant cancer cells persisting during therapy. Therapy-induced A3A promotes the formation of double-strand DNA breaks, increasing genomic instability in drug-tolerant persisters. Deletion of A3A reduces APOBEC mutations and structural variations in persister cells and delays the development of drug resistance. APOBEC mutational signatures are enriched in tumours from patients with lung cancer who progressed after extended responses to targeted therapies. This study shows that induction of A3A in response to targeted therapies drives evolution of drug-tolerant persister cells, suggesting that suppression of A3A expression or activity may represent a potential therapeutic strategy in the prevention or delay of acquired resistance to lung cancer targeted therapy.
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Affiliation(s)
- Hideko Isozaki
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Ramin Sakhtemani
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ammal Abbasi
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Naveed Nikpour
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Sunwoo Oh
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA, USA
| | | | - Susanna Monroe
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Wenjia Su
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Heidie Frisco Cabanos
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Nicole Phan
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Pégah Jalili
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Daria Timonina
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Samantha Bilton
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | | | - Varuna Nangia
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Kristin Dionne
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Amanda Riley
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Matthew Lawlor
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Rosemary G Cobb
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Christopher J Ott
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cyril Benes
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Gad Getz
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Chang S Chan
- Department of Medicine, Rutgers Robert Wood Johnson Medical School and Center for Systems and Computational Biology, Rutgers Cancer Institute, New Brunswick, NJ, USA
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica J Lin
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Zofia Piotrowska
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Beow Y Yeap
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jeffrey A Engelman
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jake June-Koo Lee
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yosef E Maruvka
- Faculty of Biotechnology and Food Engineering, Lorey Loki Center for Life Science and Engineering, Technion, Haifa, Israel
| | - Rémi Buisson
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA, USA
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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6
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Zhang Y, Remillard D, Onubogu U, Karakyriakou B, Asiaban JN, Ramos AR, Bowland K, Bishop TR, Barta PA, Nance S, Durbin AD, Ott CJ, Janiszewska M, Cravatt BF, Erb MA. Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities. Nat Struct Mol Biol 2023; 30:1160-1171. [PMID: 37488358 PMCID: PMC10529074 DOI: 10.1038/s41594-023-01041-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/22/2023] [Indexed: 07/26/2023]
Abstract
Transcriptional co-regulators have been widely pursued as targets for disrupting oncogenic gene regulatory programs. However, many proteins in this target class are universally essential for cell survival, which limits their therapeutic window. Here we unveil a genetic interaction between histone deacetylase 1 (HDAC1) and HDAC2, wherein each paralog is synthetically lethal with hemizygous deletion of the other. This collateral synthetic lethality is caused by recurrent chromosomal deletions that occur in diverse solid and hematological malignancies, including neuroblastoma and multiple myeloma. Using genetic disruption or dTAG-mediated degradation, we show that targeting HDAC2 suppresses the growth of HDAC1-deficient neuroblastoma in vitro and in vivo. Mechanistically, we find that targeted degradation of HDAC2 in these cells prompts the degradation of several members of the nucleosome remodeling and deacetylase (NuRD) complex, leading to diminished chromatin accessibility at HDAC2-NuRD-bound sites of the genome and impaired control of enhancer-associated transcription. Furthermore, we reveal that several of the degraded NuRD complex subunits are dependencies in neuroblastoma and multiple myeloma, providing motivation to develop paralog-selective HDAC1 or HDAC2 degraders that could leverage HDAC1/2 synthetic lethality to target NuRD vulnerabilities. Altogether, we identify HDAC1/2 collateral synthetic lethality as a potential therapeutic target and reveal an unexplored mechanism for targeting NuRD-associated cancer dependencies.
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Affiliation(s)
- Yuxiang Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - David Remillard
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Ugoma Onubogu
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | | | - Joshua N Asiaban
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Anissa R Ramos
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Kirsten Bowland
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Timothy R Bishop
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Paige A Barta
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Stephanie Nance
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adam D Durbin
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher J Ott
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Michalina Janiszewska
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Michael A Erb
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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7
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de Matos Simoes R, Shirasaki R, Downey-Kopyscinski SL, Matthews GM, Barwick BG, Gupta VA, Dupéré-Richer D, Yamano S, Hu Y, Sheffer M, Dhimolea E, Dashevsky O, Gandolfi S, Ishiguro K, Meyers RM, Bryan JG, Dharia NV, Hengeveld PJ, Brüggenthies JB, Tang H, Aguirre AJ, Sievers QL, Ebert BL, Glassner BJ, Ott CJ, Bradner JE, Kwiatkowski NP, Auclair D, Levy J, Keats JJ, Groen RWJ, Gray NS, Culhane AC, McFarland JM, Dempster JM, Licht JD, Boise LH, Hahn WC, Vazquez F, Tsherniak A, Mitsiades CS. Genome-scale functional genomics identify genes preferentially essential for multiple myeloma cells compared to other neoplasias. Nat Cancer 2023; 4:754-773. [PMID: 37237081 PMCID: PMC10918623 DOI: 10.1038/s43018-023-00550-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/29/2023] [Indexed: 05/28/2023]
Abstract
Clinical progress in multiple myeloma (MM), an incurable plasma cell (PC) neoplasia, has been driven by therapies that have limited applications beyond MM/PC neoplasias and do not target specific oncogenic mutations in MM. Instead, these agents target pathways critical for PC biology yet largely dispensable for malignant or normal cells of most other lineages. Here we systematically characterized the lineage-preferential molecular dependencies of MM through genome-scale clustered regularly interspaced short palindromic repeats (CRISPR) studies in 19 MM versus hundreds of non-MM lines and identified 116 genes whose disruption more significantly affects MM cell fitness compared with other malignancies. These genes, some known, others not previously linked to MM, encode transcription factors, chromatin modifiers, endoplasmic reticulum components, metabolic regulators or signaling molecules. Most of these genes are not among the top amplified, overexpressed or mutated in MM. Functional genomics approaches thus define new therapeutic targets in MM not readily identifiable by standard genomic, transcriptional or epigenetic profiling analyses.
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Affiliation(s)
- Ricardo de Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Ryosuke Shirasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Sondra L Downey-Kopyscinski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Geoffrey M Matthews
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Benjamin G Barwick
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Vikas A Gupta
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | | | - Shizuka Yamano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yiguo Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Sara Gandolfi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Kazuya Ishiguro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Robin M Meyers
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jordan G Bryan
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Neekesh V Dharia
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul J Hengeveld
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Johanna B Brüggenthies
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Huihui Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Quinlan L Sievers
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Brian J Glassner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Nicholas P Kwiatkowski
- Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Joan Levy
- Multiple Myeloma Research Foundation, Norwalk, CT, USA
| | | | - Richard W J Groen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Nathanael S Gray
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aedin C Culhane
- Department of Data Sciences, Dana-Farber Cancer Institute & Harvard School of Public Health, Boston, MA, USA
- Limerick Digital Cancer Research Center, Health Research Institute, School of Medicine, University of Limerick, Limerick, Ireland
| | - James M McFarland
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Joshua M Dempster
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jonathan D Licht
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Francisca Vazquez
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
| | - Aviad Tsherniak
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Ludwig Center at Harvard, Boston, MA, USA.
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8
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Marsh GP, Goggins S, Bosnakovski D, Kyba M, Ojeda S, Harrison DA, Ott CJ, Maple HJ. Abstract 3841: Development of p300-targeting PROTAC degraders with enhanced selectivity and onset of degradation. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
CREB-binding protein (CBP, CREBBP, KAT3A) and E1A-binding protein (EP300, p300, KAT3B) are paralogous multi-domain proteins that act as chromatin regulators and transcriptional co-activators. They contain a histone acetyltransferase (HAT) domain that catalyzes the histone H3, lysine 27 acetylation (H3K27ac) mark at regulatory elements such as enhancers and promoters. Transcription factors associate with stretches of H3K27ac marks (known as ‘super-enhancer’ elements) and result in gene transcription that ultimately establishes cell identity and fate. They are implicated in cancer pathology, and small molecule inhibition of the bromodomain (BRD) or HAT domain of CBP/p300 are considered promising therapeutic strategies for a number of cancer types.
CBP and p300 are highly homologous but have distinct roles that have to date been hard to delineate, since small molecule inhibitors developed to date are unable to selectively target each protein independently. Additionally, small molecule inhibitors that target individual domains are unable to entirely abrogate the full functionality of CBP/p300. A bromodomain-recruiting dual CBP/p300 PROTAC Degrader ‘dCBP1’ was therefore recently developed to provide a chemical tool to explore the phenotypic consequences of CBP/p300 chemical knockdown. A further study demonstrated that it is possible to degrade p300 with some selectivity by converting a CBP/p300 dual HAT-domain inhibitor into a PROTAC, called ‘JQAD1’.
We have used a different HAT-domain recruiting ligand to develop novel PROTACs that elicit proteasome-mediated degradation of p300 with significantly enhanced selectivity over CBP, compared with JQAD1. We additionally demonstrate a faster onset of degradation for lead PROTAC molecules and present data exploring the consequences of selective p300 degradation in CIC-DIX4 sarcoma.
Citation Format: Graham P. Marsh, Sean Goggins, Darko Bosnakovski, Michael Kyba, Samuel Ojeda, Drew A. Harrison, Christopher J. Ott, Hannah J. Maple. Development of p300-targeting PROTAC degraders with enhanced selectivity and onset of degradation. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3841.
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Affiliation(s)
| | - Sean Goggins
- 1Bio-Techne Corporation, Bristol, United Kingdom
| | | | | | - Samuel Ojeda
- 3Massachusetts General Hospital Cancer Center, Boston, MA
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9
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Gill T, Wang H, Bandaru R, Lawlor M, Lu C, Nieman LT, Tao J, Zhang Y, Anderson DG, Ting DT, Chen X, Bradner JE, Ott CJ. Selective targeting of MYC mRNA by stabilized antisense oligonucleotides. Oncogene 2021; 40:6527-6539. [PMID: 34650218 PMCID: PMC8627489 DOI: 10.1038/s41388-021-02053-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 09/07/2021] [Accepted: 09/30/2021] [Indexed: 12/30/2022]
Abstract
MYC is a prolific proto-oncogene driving the malignant behaviors of numerous common cancers, yet potent and selective cell-permeable inhibitors of MYC remain elusive. In order to ultimately realize the goal of therapeutic MYC inhibition in cancer, we have initiated discovery chemistry efforts aimed at inhibiting MYC translation. Here we describe a series of conformationally stabilized synthetic antisense oligonucleotides designed to target MYC mRNA (MYCASOs). To support bioactivity, we designed and synthesized this focused library of MYCASOs incorporating locked nucleic acid (LNA) bases at the 5'- and 3'-ends, a phosphorothioate backbone, and internal DNA bases. Treatment of MYC-expressing cancer cells with MYCASOs leads to a potent decrease in MYC mRNA and protein levels. Cleaved MYC mRNA in MYCASO-treated cells is detected with a sensitive 5' Rapid Amplification of cDNA Ends (RACE) assay. MYCASO treatment of cancer cell lines leads to significant inhibition of cellular proliferation while specifically perturbing MYC-driven gene expression signatures. In a MYC-induced model of hepatocellular carcinoma, MYCASO treatment decreases MYC protein levels within tumors, decreases tumor burden, and improves overall survival. MYCASOs represent a new chemical tool for in vitro and in vivo modulation of MYC activity, and promising therapeutic agents for MYC-addicted tumors.
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Affiliation(s)
- Taylor Gill
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Haichuan Wang
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, CA, 94143, USA
| | - Raj Bandaru
- ENZON Pharmaceuticals, Cranford, NJ, 07016, USA
| | - Matthew Lawlor
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
| | - Chenyue Lu
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
| | - Linda T Nieman
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
| | - Junyan Tao
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, CA, 94143, USA
| | | | - Daniel G Anderson
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - David T Ting
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, CA, 94143, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA.
| | - Christopher J Ott
- Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA.
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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10
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Kong W, Dimitri A, Wang W, Jung IY, Ott CJ, Fasolino M, Wang Y, Kulikovskaya I, Gupta M, Yoder T, DeNizio JE, Everett JK, Williams EF, Xu J, Scholler J, Reich TJ, Bhoj VG, Haines KM, Maus MV, Melenhorst JJ, Young RM, Jadlowsky JK, Marcucci KT, Bradner JE, Levine BL, Porter DL, Bushman FD, Kohli RM, June CH, Davis MM, Lacey SF, Vahedi G, Fraietta JA. BET bromodomain protein inhibition reverses chimeric antigen receptor extinction and reinvigorates exhausted T cells in chronic lymphocytic leukemia. J Clin Invest 2021; 131:e145459. [PMID: 34396987 DOI: 10.1172/jci145459] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 07/06/2021] [Indexed: 12/17/2022] Open
Abstract
Chimeric antigen receptor (CAR) T cells have induced remarkable antitumor responses in B cell malignancies. Some patients do not respond because of T cell deficiencies that hamper the expansion, persistence, and effector function of these cells. We used longitudinal immune profiling to identify phenotypic and pharmacodynamic changes in CD19-directed CAR T cells in patients with chronic lymphocytic leukemia (CLL). CAR expression maintenance was also investigated because this can affect response durability. CAR T cell failure was accompanied by preexisting T cell-intrinsic defects or dysfunction acquired after infusion. In a small subset of patients, CAR silencing was observed coincident with leukemia relapse. Using a small molecule inhibitor, we demonstrated that the bromodomain and extra-terminal (BET) family of chromatin adapters plays a role in downregulating CAR expression. BET protein blockade also ameliorated CAR T cell exhaustion as manifested by inhibitory receptor reduction, enhanced metabolic fitness, increased proliferative capacity, and enriched transcriptomic signatures of T cell reinvigoration. BET inhibition decreased levels of the TET2 methylcytosine dioxygenase, and forced expression of the TET2 catalytic domain eliminated the potency-enhancing effects of BET protein targeting in CAR T cells, providing a mechanism linking BET proteins and T cell dysfunction. Thus, modulating BET epigenetic readers may improve the efficacy of cell-based immunotherapies.
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Affiliation(s)
- Weimin Kong
- Department of Microbiology.,Center for Cellular Immunotherapies.,Abramson Cancer Center, and
| | - Alexander Dimitri
- Department of Microbiology.,Center for Cellular Immunotherapies.,Abramson Cancer Center, and
| | - Wenliang Wang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - In-Young Jung
- Department of Microbiology.,Center for Cellular Immunotherapies.,Abramson Cancer Center, and
| | - Christopher J Ott
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Maria Fasolino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yan Wang
- Center for Cellular Immunotherapies
| | | | | | | | - Jamie E DeNizio
- Department of Medicine and.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Erik F Williams
- Department of Microbiology.,Center for Cellular Immunotherapies.,Abramson Cancer Center, and
| | - Jun Xu
- Center for Cellular Immunotherapies
| | | | | | - Vijay G Bhoj
- Center for Cellular Immunotherapies.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Marcela V Maus
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts, USA
| | - J Joseph Melenhorst
- Center for Cellular Immunotherapies.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - James E Bradner
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Bruce L Levine
- Center for Cellular Immunotherapies.,Abramson Cancer Center, and.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David L Porter
- Abramson Cancer Center, and.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Rahul M Kohli
- Department of Medicine and.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carl H June
- Center for Cellular Immunotherapies.,Abramson Cancer Center, and.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Megan M Davis
- Center for Cellular Immunotherapies.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Simon F Lacey
- Center for Cellular Immunotherapies.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Golnaz Vahedi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joseph A Fraietta
- Department of Microbiology.,Center for Cellular Immunotherapies.,Abramson Cancer Center, and.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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11
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Willers H, Pan X, Borgeaud N, Korovina I, Koi L, Egan R, Greninger P, Rosenkranz A, Kung J, Liss AS, Parsels LA, Morgan MA, Lawrence TS, Lin SH, Hong TS, Yeap BY, Wirth L, Hata AN, Ott CJ, Benes CH, Baumann M, Krause M. Screening and Validation of Molecular Targeted Radiosensitizers. Int J Radiat Oncol Biol Phys 2021; 111:e63-e74. [PMID: 34343607 DOI: 10.1016/j.ijrobp.2021.07.1694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/18/2021] [Indexed: 11/16/2022]
Abstract
The development of molecular targeted drugs with radiation and chemotherapy are critically important for improving the outcomes of patients with hard-to-treat, potentially curable cancers. However, too many preclinical studies have not translated into successful radiation oncology trials. Major contributing factors to this insufficiency include poor reproducibility of preclinical data, inadequate preclinical modeling of inter-tumoral genomic heterogeneity that influences treatment sensitivity in the clinic, and a reliance on tumor growth delay instead of local control (TCD50) endpoints. There exists an urgent need to overcome these barriers to facilitate successful clinical translation of targeted radiosensitizers. To this end, we have employed 3D cell culture assays to better model tumor behavior in vivo. Examples of successful prediction of in vivo effects with these 3D assays include radiosensitization of head and neck cancers by inhibiting epidermal growth factor receptor or focal adhesion kinase signaling, and radioresistance associated with oncogenic mutation of KRAS. To address the issue of tumor heterogeneity we leveraged institutional resources that allow high-throughput 3D screening of radiation combinations with small molecule inhibitors across genomically characterized cell lines from lung, head and neck, and pancreatic cancers. This high-throughput screen is expected to uncover genomic biomarkers that will inform the successful clinical translation of targeted agents from the NCI CTEP portfolio and other sources. Screening "hits" need to be subjected to refinement studies that include clonogenic assays, addition of disease-specific chemotherapeutics, target/biomarker validation, and integration of patient-derived tumor models. The chemoradiosensitizing activities of the most promising drugs should be confirmed in TCD50 assays in xenograft models with/without relevant biomarker and utilizing clinically relevant radiation fractionation. We predict that appropriately validated and biomarker-directed targeted therapies will have a higher likelihood than past efforts to be successfully incorporated into the standard management of hard-to-treat tumors.
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Affiliation(s)
- Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Xiao Pan
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nathalie Borgeaud
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), partner site Dresden
| | - Irina Korovina
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), partner site Dresden; Helmholtz-Zentrum Dresden - Rossendorf, Institute of Radiooncology - OncoRay, Dresden, Germany
| | - Lydia Koi
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf, Institute of Radiooncology - OncoRay, Dresden, Germany
| | - Regina Egan
- Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | - Patricia Greninger
- Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | - Aliza Rosenkranz
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jong Kung
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andrew S Liss
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Leslie A Parsels
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan
| | - Meredith A Morgan
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan
| | - Theodore S Lawrence
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan
| | - Steven H Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Beow Y Yeap
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lori Wirth
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Aaron N Hata
- Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | - Christopher J Ott
- Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | - Cyril H Benes
- Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | - Michael Baumann
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Core center Heidelberg, Germany
| | - Mechthild Krause
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), partner site Dresden; Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf, Institute of Radiooncology - OncoRay, Dresden, Germany; National Center for Tumour Diseases (NCT), Partner site Dresden, Germany
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12
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Lazarian G, Yin S, Ten Hacken E, Sewastianik T, Uduman M, Font-Tello A, Gohil SH, Li S, Kim E, Joyal H, Billington L, Witten E, Zheng M, Huang T, Severgnini M, Lefebvre V, Rassenti LZ, Gutierrez C, Georgopoulos K, Ott CJ, Wang L, Kipps TJ, Burger JA, Livak KJ, Neuberg DS, Baran-Marszak F, Cymbalista F, Carrasco RD, Wu CJ. A hotspot mutation in transcription factor IKZF3 drives B cell neoplasia via transcriptional dysregulation. Cancer Cell 2021; 39:380-393.e8. [PMID: 33689703 PMCID: PMC8034546 DOI: 10.1016/j.ccell.2021.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/25/2020] [Accepted: 02/04/2021] [Indexed: 12/20/2022]
Abstract
Hotspot mutation of IKZF3 (IKZF3-L162R) has been identified as a putative driver of chronic lymphocytic leukemia (CLL), but its function remains unknown. Here, we demonstrate its driving role in CLL through a B cell-restricted conditional knockin mouse model. Mutant Ikzf3 alters DNA binding specificity and target selection, leading to hyperactivation of B cell receptor (BCR) signaling, overexpression of nuclear factor κB (NF-κB) target genes, and development of CLL-like disease in elderly mice with a penetrance of ~40%. Human CLL carrying either IKZF3 mutation or high IKZF3 expression was associated with overexpression of BCR/NF-κB pathway members and reduced sensitivity to BCR signaling inhibition by ibrutinib. Our results thus highlight IKZF3 oncogenic function in CLL via transcriptional dysregulation and demonstrate that this pro-survival function can be achieved by either somatic mutation or overexpression of this CLL driver. This emphasizes the need for combinatorial approaches to overcome IKZF3-mediated BCR inhibitor resistance.
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Affiliation(s)
- Gregory Lazarian
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; INSERM, U978, Université Paris 13, Bobigny, France; Laboratoire d'Hématologie, APHP Hôpital Avicenne, Bobigny, France
| | - Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Elisa Ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Tomasz Sewastianik
- Harvard Medical School, Boston, MA, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Mohamed Uduman
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alba Font-Tello
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Satyen H Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Academic Haematology, University College London, London, UK
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ekaterina Kim
- Department of Leukemia, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heather Joyal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Leah Billington
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Elizabeth Witten
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mei Zheng
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Teddy Huang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mariano Severgnini
- Center for Immuno-Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Valerie Lefebvre
- Laboratoire d'Hématologie, APHP Hôpital Avicenne, Bobigny, France
| | | | - Catherine Gutierrez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Katia Georgopoulos
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Christopher J Ott
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, CA, USA
| | - Thomas J Kipps
- Division of Hematology-Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, USA
| | - Jan A Burger
- Department of Leukemia, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fanny Baran-Marszak
- INSERM, U978, Université Paris 13, Bobigny, France; Laboratoire d'Hématologie, APHP Hôpital Avicenne, Bobigny, France
| | - Florence Cymbalista
- INSERM, U978, Université Paris 13, Bobigny, France; Laboratoire d'Hématologie, APHP Hôpital Avicenne, Bobigny, France
| | - Ruben D Carrasco
- Harvard Medical School, Boston, MA, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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13
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Koduri V, Duplaquet L, Lampson BL, Wang AC, Sabet AH, Ishoey M, Paulk J, Teng M, Harris IS, Endress JE, Liu X, Dasilva E, Paulo JA, Briggs KJ, Doench JG, Ott CJ, Zhang T, Donovan KA, Fischer ES, Gygi SP, Gray NS, Bradner J, Medin JA, Buhrlage SJ, Oser MG, Kaelin WG. Targeting oncoproteins with a positive selection assay for protein degraders. Sci Adv 2021; 7:7/6/eabd6263. [PMID: 33547076 PMCID: PMC7864573 DOI: 10.1126/sciadv.abd6263] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
Most intracellular proteins lack hydrophobic pockets suitable for altering their function with drug-like small molecules. Recent studies indicate that some undruggable proteins can be targeted by compounds that can degrade them. For example, thalidomide-like drugs (IMiDs) degrade the critical multiple myeloma transcription factors IKZF1 and IKZF3 by recruiting them to the cereblon E3 ubiquitin ligase. Current loss of signal ("down") assays for identifying degraders often exhibit poor signal-to-noise ratios, narrow dynamic ranges, and false positives from compounds that nonspecifically suppress transcription or translation. Here, we describe a gain of signal ("up") assay for degraders. In arrayed chemical screens, we identified novel IMiD-like IKZF1 degraders and Spautin-1, which, unlike the IMiDs, degrades IKZF1 in a cereblon-independent manner. In a pooled CRISPR-Cas9-based screen, we found that CDK2 regulates the abundance of the ASCL1 oncogenic transcription factor. This methodology should facilitate the identification of drugs that directly or indirectly degrade undruggable proteins.
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Affiliation(s)
- Vidyasagar Koduri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Leslie Duplaquet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Benjamin L Lampson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Adam C Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Amin H Sabet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mette Ishoey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mingxing Teng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac S Harris
- Ludwig Cancer Center, Boston, MA 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer E Endress
- Ludwig Cancer Center, Boston, MA 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaoxi Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Linde Program in Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ethan Dasilva
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Linde Program in Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly J Briggs
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - James Bradner
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Jeffrey A Medin
- Departments of Pediatrics and Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Linde Program in Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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14
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Vannam R, Sayilgan J, Ojeda S, Karakyriakou B, Hu E, Kreuzer J, Morris R, Herrera Lopez XI, Rai S, Haas W, Lawrence M, Ott CJ. Targeted degradation of the enhancer lysine acetyltransferases CBP and p300. Cell Chem Biol 2021; 28:503-514.e12. [PMID: 33400925 DOI: 10.1016/j.chembiol.2020.12.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/15/2020] [Accepted: 12/09/2020] [Indexed: 01/10/2023]
Abstract
The enhancer factors CREB-binding protein (CBP) and p300 (also known as KAT3A and KAT3B) maintain gene expression programs through lysine acetylation of chromatin and transcriptional regulators and by scaffolding functions mediated by several protein-protein interaction domains. Small molecule inhibitors that target some of these domains have been developed; however, they cannot completely ablate p300/CBP function in cells. Here we describe a chemical degrader of p300/CBP, dCBP-1. Leveraging structures of ligand-bound p300/CBP domains, we use in silico modeling of ternary complex formation with the E3 ubiquitin ligase cereblon to enable degrader design. dCBP-1 is exceptionally potent at killing multiple myeloma cells and can abolish the enhancer that drives MYC oncogene expression. As an efficient degrader of this unique class of acetyltransferases, dCBP-1 is a useful tool alongside domain inhibitors for dissecting the mechanism by which these factors coordinate enhancer activity in normal and diseased cells.
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Affiliation(s)
- Raghu Vannam
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jan Sayilgan
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Samuel Ojeda
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | | | - Eileen Hu
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Johannes Kreuzer
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - Sumit Rai
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Lawrence
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Christopher J Ott
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA.
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15
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Shirasaki R, Matthews GM, Gandolfi S, de Matos Simoes R, Buckley DL, Raja Vora J, Sievers QL, Brüggenthies JB, Dashevsky O, Poarch H, Tang H, Bariteau MA, Sheffer M, Hu Y, Downey-Kopyscinski SL, Hengeveld PJ, Glassner BJ, Dhimolea E, Ott CJ, Zhang T, Kwiatkowski NP, Laubach JP, Schlossman RL, Richardson PG, Culhane AC, Groen RWJ, Fischer ES, Vazquez F, Tsherniak A, Hahn WC, Levy J, Auclair D, Licht JD, Keats JJ, Boise LH, Ebert BL, Bradner JE, Gray NS, Mitsiades CS. Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins. Cell Rep 2021; 34:108532. [PMID: 33406420 DOI: 10.1016/j.celrep.2020.108532] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 06/14/2019] [Accepted: 11/25/2020] [Indexed: 12/15/2022] Open
Abstract
Heterobifunctional proteolysis-targeting chimeric compounds leverage the activity of E3 ligases to induce degradation of target oncoproteins and exhibit potent preclinical antitumor activity. To dissect the mechanisms regulating tumor cell sensitivity to different classes of pharmacological "degraders" of oncoproteins, we performed genome-scale CRISPR-Cas9-based gene editing studies. We observed that myeloma cell resistance to degraders of different targets (BET bromodomain proteins, CDK9) and operating through CRBN (degronimids) or VHL is primarily mediated by prevention of, rather than adaptation to, breakdown of the target oncoprotein; and this involves loss of function of the cognate E3 ligase or interactors/regulators of the respective cullin-RING ligase (CRL) complex. The substantial gene-level differences for resistance mechanisms to CRBN- versus VHL-based degraders explains mechanistically the lack of cross-resistance with sequential administration of these two degrader classes. Development of degraders leveraging more diverse E3 ligases/CRLs may facilitate sequential/alternating versus combined uses of these agents toward potentially delaying or preventing resistance.
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Affiliation(s)
- Ryosuke Shirasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Geoffrey M Matthews
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara Gandolfi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Ricardo de Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseline Raja Vora
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Quinlan L Sievers
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Johanna B Brüggenthies
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Haley Poarch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Huihui Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Megan A Bariteau
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Yiguo Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Sondra L Downey-Kopyscinski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul J Hengeveld
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Brian J Glassner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tinghu Zhang
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicholas P Kwiatkowski
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob P Laubach
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Robert L Schlossman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Paul G Richardson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Richard W J Groen
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Eric S Fischer
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joan Levy
- Multiple Myeloma Research Foundation, Norwalk, CT, USA
| | | | - Jonathan D Licht
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | | | - Lawrence H Boise
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael S Gray
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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16
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Abstract
For decades, scientists have observed small extrachromosomal DNA fragments in tumor cells, yet comprehensive examination of their structure and function has remained difficult. Three recent studies, published in Nature, Cell, and Nature Genetics, have now shed important light on the architecture, regulatory capacity, and oncogenic nature of tumor-associated extrachromosomal DNA.
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Affiliation(s)
- Christopher J Ott
- Massachusetts General Hospital Center for Cancer Research, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA.
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17
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Guièze R, Liu VM, Rosebrock D, Jourdain AA, Hernández-Sánchez M, Martinez Zurita A, Sun J, Ten Hacken E, Baranowski K, Thompson PA, Heo JM, Cartun Z, Aygün O, Iorgulescu JB, Zhang W, Notarangelo G, Livitz D, Li S, Davids MS, Biran A, Fernandes SM, Brown JR, Lako A, Ciantra ZB, Lawlor MA, Keskin DB, Udeshi ND, Wierda WG, Livak KJ, Letai AG, Neuberg D, Harper JW, Carr SA, Piccioni F, Ott CJ, Leshchiner I, Johannessen CM, Doench J, Mootha VK, Getz G, Wu CJ. Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies. Cancer Cell 2019; 36:369-384.e13. [PMID: 31543463 PMCID: PMC6801112 DOI: 10.1016/j.ccell.2019.08.005] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/04/2019] [Accepted: 08/15/2019] [Indexed: 12/21/2022]
Abstract
Mitochondrial apoptosis can be effectively targeted in lymphoid malignancies with the FDA-approved B cell lymphoma 2 (BCL-2) inhibitor venetoclax, but resistance to this agent is emerging. We show that venetoclax resistance in chronic lymphocytic leukemia is associated with complex clonal shifts. To identify determinants of resistance, we conducted parallel genome-scale screens of the BCL-2-driven OCI-Ly1 lymphoma cell line after venetoclax exposure along with integrated expression profiling and functional characterization of drug-resistant and engineered cell lines. We identified regulators of lymphoid transcription and cellular energy metabolism as drivers of venetoclax resistance in addition to the known involvement by BCL-2 family members, which were confirmed in patient samples. Our data support the implementation of combinatorial therapy with metabolic modulators to address venetoclax resistance.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Animals
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Apoptosis/drug effects
- Apoptosis/genetics
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Bridged Bicyclo Compounds, Heterocyclic/therapeutic use
- Cell Line, Tumor
- Clonal Evolution/drug effects
- Disease Progression
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Energy Metabolism/drug effects
- Energy Metabolism/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Mice
- Middle Aged
- Mitochondria/drug effects
- Mitochondria/pathology
- Myeloid Cell Leukemia Sequence 1 Protein/metabolism
- Oxidative Phosphorylation/drug effects
- Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Sulfonamides/pharmacology
- Sulfonamides/therapeutic use
- Treatment Outcome
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Romain Guièze
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; CHU de Clermont-Ferrand, 63000 Clermont-Ferrand, France; Université Clermont Auvergne, EA7453 CHELTER, 63000 Clermont-Ferrand, France
| | - Vivian M Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Harvard Medical School, Boston, MA 02215, USA
| | | | - Alexis A Jourdain
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - María Hernández-Sánchez
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Instituto de Investigación Biomédica de Salamanca, Centro de Investigación del Cáncer-IBMCC, Universidad de Salamanca, 37007 Salamanca, Spain; Servicio de Hematología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | | | - Jing Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elisa Ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Kaitlyn Baranowski
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA
| | - Philip A Thompson
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Zachary Cartun
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA
| | - Ozan Aygün
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA
| | - Giulia Notarangelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Dimitri Livitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Anat Biran
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Ana Lako
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zoe B Ciantra
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew A Lawlor
- Harvard Medical School, Boston, MA 02215, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02214, USA
| | - Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | | | - William G Wierda
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA
| | - Anthony G Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Donna Neuberg
- Harvard Medical School, Boston, MA 02215, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Christopher J Ott
- Harvard Medical School, Boston, MA 02215, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02214, USA
| | | | | | - John Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02214, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA.
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18
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Viny AD, Bowman RL, Liu Y, Lavallée VP, Eisman SE, Xiao W, Durham BH, Navitski A, Park J, Braunstein S, Alija B, Karzai A, Csete IS, Witkin M, Azizi E, Baslan T, Ott CJ, Pe'er D, Dekker J, Koche R, Levine RL. Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation. Cell Stem Cell 2019; 25:682-696.e8. [PMID: 31495782 DOI: 10.1016/j.stem.2019.08.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 06/19/2019] [Accepted: 08/09/2019] [Indexed: 12/19/2022]
Abstract
Transcriptional regulators, including the cohesin complex member STAG2, are recurrently mutated in cancer. The role of STAG2 in gene regulation, hematopoiesis, and tumor suppression remains unresolved. We show that Stag2 deletion in hematopoietic stem and progenitor cells (HSPCs) results in altered hematopoietic function, increased self-renewal, and impaired differentiation. Chromatin immunoprecipitation (ChIP) sequencing revealed that, although Stag2 and Stag1 bind a shared set of genomic loci, a component of Stag2 binding sites is unoccupied by Stag1, even in Stag2-deficient HSPCs. Although concurrent loss of Stag2 and Stag1 abrogated hematopoiesis, Stag2 loss alone decreased chromatin accessibility and transcription of lineage-specification genes, including Ebf1 and Pax5, leading to increased self-renewal and reduced HSPC commitment to the B cell lineage. Our data illustrate a role for Stag2 in transformation and transcriptional dysregulation distinct from its shared role with Stag1 in chromosomal segregation.
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Affiliation(s)
- Aaron D Viny
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert L Bowman
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yu Liu
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Vincent-Philippe Lavallée
- Center for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shira E Eisman
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wenbin Xiao
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Benjamin H Durham
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anastasia Navitski
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jane Park
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stephanie Braunstein
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Besmira Alija
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Abdul Karzai
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Isabelle S Csete
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew Witkin
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elham Azizi
- Center for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher J Ott
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Dana Pe'er
- Center for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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19
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Sharifnia T, Wawer MJ, Chen T, Huang QY, Weir BA, Sizemore A, Lawlor MA, Goodale A, Cowley GS, Vazquez F, Ott CJ, Francis JM, Sassi S, Cogswell P, Sheppard HE, Zhang T, Gray NS, Clarke PA, Blagg J, Workman P, Sommer J, Hornicek F, Root DE, Hahn WC, Bradner JE, Wong KK, Clemons PA, Lin CY, Kotz JD, Schreiber SL. Small-molecule targeting of brachyury transcription factor addiction in chordoma. Nat Med 2019; 25:292-300. [PMID: 30664779 PMCID: PMC6633917 DOI: 10.1038/s41591-018-0312-3] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022]
Abstract
Chordoma is a primary bone cancer with no approved therapy1. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors2,3. Here we describe the discovery of therapeutically targetable chordoma dependencies via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation. In other cancer types, transcriptional CDK inhibitors have been observed to downregulate highly expressed, enhancer-associated oncogenic transcription factors4,5. In chordoma, we find that T is associated with a 1.5-Mb region containing 'super-enhancers' and is the most highly expressed super-enhancer-associated transcription factor. Notably, transcriptional CDK inhibition leads to preferential and concentration-dependent downregulation of cellular brachyury protein levels in all models tested. In vivo, CDK7/12/13-inhibitor treatment substantially reduces tumor growth. Together, these data demonstrate small-molecule targeting of brachyury transcription factor addiction in chordoma, identify a mechanism of T gene regulation that underlies this therapeutic strategy, and provide a blueprint for applying systematic genetic and chemical screening approaches to discover vulnerabilities in genomically quiet cancers.
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Affiliation(s)
| | | | - Ting Chen
- New York University Langone Medical Center, New York, NY, USA
| | - Qing-Yuan Huang
- New York University Langone Medical Center, New York, NY, USA
- Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Barbara A Weir
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Janssen R&D, Cambridge, MA, USA
| | - Ann Sizemore
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew A Lawlor
- Dana-Farber Cancer Institute, Boston, MA, USA
- Massachusetts General Hospital, Charlestown, MA, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Glenn S Cowley
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Janssen R&D, Spring House, PA, USA
| | | | - Christopher J Ott
- Dana-Farber Cancer Institute, Boston, MA, USA
- Massachusetts General Hospital, Charlestown, MA, USA
| | - Joshua M Francis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Gritstone Oncology, Cambridge, MA, USA
| | - Slim Sassi
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Paul A Clarke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | | | - Francis Hornicek
- Massachusetts General Hospital, Boston, MA, USA
- UCLA Medical Center, Santa Monica, CA, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Dana-Farber Cancer Institute, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Kwok K Wong
- New York University Langone Medical Center, New York, NY, USA
| | | | | | - Joanne D Kotz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Jnana Therapeutics, Boston, MA, USA.
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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20
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Ott CJ, Federation AJ, Schwartz LS, Kasar S, Klitgaard JL, Lenci R, Li Q, Lawlor M, Fernandes SM, Souza A, Polaski D, Gadi D, Freedman ML, Brown JR, Bradner JE. Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia. Cancer Cell 2018; 34:982-995.e7. [PMID: 30503705 PMCID: PMC6298230 DOI: 10.1016/j.ccell.2018.11.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 08/16/2018] [Accepted: 10/30/2018] [Indexed: 12/26/2022]
Abstract
Enhancer profiling is a powerful approach for discovering cis-regulatory elements that define the core transcriptional regulatory circuits of normal and malignant cells. Gene control through enhancer activity is often dominated by a subset of lineage-specific transcription factors. By integrating measures of chromatin accessibility and enrichment for H3K27 acetylation, we have generated regulatory landscapes of chronic lymphocytic leukemia (CLL) samples and representative cell lines. With super enhancer-based modeling of regulatory circuits and assessments of transcription factor dependencies, we discover that the essential super enhancer factor PAX5 dominates CLL regulatory nodes and is essential for CLL cell survival. Targeting enhancer signaling via BET bromodomain inhibition disrupts super enhancer-dependent gene expression with selective effects on CLL core regulatory circuitry, conferring potent anti-tumor activity.
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MESH Headings
- Acetylation
- Animals
- Azepines/pharmacology
- Cell Line, Tumor
- Chromatin/drug effects
- Chromatin/genetics
- Chromatin/metabolism
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation, Leukemic/drug effects
- Gene Expression Regulation, Leukemic/genetics
- Histones/metabolism
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Mice, Knockout
- PAX5 Transcription Factor/genetics
- PAX5 Transcription Factor/metabolism
- Protein Binding
- Proteins/antagonists & inhibitors
- Proteins/genetics
- Proteins/metabolism
- Triazoles/pharmacology
- Xenograft Model Antitumor Assays/methods
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Affiliation(s)
- Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th St. Charlestown, Boston, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA.
| | - Alexander J Federation
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Logan S Schwartz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th St. Charlestown, Boston, MA 02129, USA
| | - Siddha Kasar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Josephine L Klitgaard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Romina Lenci
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Qiyuan Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Medical School, Xiamen University, Xiamen 361102, China
| | - Matthew Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th St. Charlestown, Boston, MA 02129, USA
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Amanda Souza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Donald Polaski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Deepti Gadi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA; Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
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21
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Ott CJ. Opportunities for targeting gene regulatory factors in B-cell acute lymphoblastic leukemia. Int J Hematol Oncol 2018; 6:57-59. [PMID: 30302224 DOI: 10.2217/ijh-2017-0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/07/2017] [Indexed: 11/21/2022] Open
Affiliation(s)
- Christopher J Ott
- Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
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22
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Peeken JC, Jutzi JS, Wehrle J, Koellerer C, Staehle HF, Becker H, Schoenwandt E, Seeger TS, Schanne DH, Gothwal M, Ott CJ, Gründer A, Pahl HL. Epigenetic regulation of NFE2 overexpression in myeloproliferative neoplasms. Blood 2018; 131:2065-2073. [PMID: 29519804 PMCID: PMC5934799 DOI: 10.1182/blood-2017-10-810622] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/27/2018] [Indexed: 12/23/2022] Open
Abstract
The transcription factor "nuclear factor erythroid 2" (NFE2) is overexpressed in the majority of patients with myeloproliferative neoplasms (MPNs). In murine models, elevated NFE2 levels cause an MPN phenotype with spontaneous leukemic transformation. However, both the molecular mechanisms leading to NFE2 overexpression and its downstream targets remain incompletely understood. Here, we show that the histone demethylase JMJD1C constitutes a novel NFE2 target gene. JMJD1C levels are significantly elevated in polycythemia vera (PV) and primary myelofibrosis patients; concomitantly, global H3K9me1 and H3K9me2 levels are significantly decreased. JMJD1C binding to the NFE2 promoter is increased in PV patients, decreasing both H3K9me2 levels and binding of the repressive heterochromatin protein-1α (HP1α). Hence, JMJD1C and NFE2 participate in a novel autoregulatory loop. Depleting JMJD1C expression significantly reduced cytokine-independent growth of an MPN cell line. Independently, NFE2 is regulated through the epigenetic JAK2 pathway by phosphorylation of H3Y41. This likewise inhibits HP1α binding. Treatment with decitabine lowered H3Y41ph and augmented H3K9me2 levels at the NFE2 locus in HEL cells, thereby increasing HP1α binding, which normalized NFE2 expression selectively in JAK2V617F-positive cell lines.
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Affiliation(s)
| | - Jonas S Jutzi
- Division of Molecular Hematology
- Spemann Graduate School of Biology and Medicine (SGBM)
- Faculty of Biology, and
| | - Julius Wehrle
- Division of Molecular Hematology
- Berta Ottenstein Program, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | | | | | | | | | | | - Christopher J Ott
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA; and
- Department of Medicine, Harvard Medical School, Charlestown, MA
| | | | - Heike L Pahl
- Division of Molecular Hematology
- Spemann Graduate School of Biology and Medicine (SGBM)
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23
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Koo SJ, Fernández-Montalván AE, Badock V, Ott CJ, Holton SJ, von Ahsen O, Toedling J, Vittori S, Bradner JE, Gorjánácz M. ATAD2 is an epigenetic reader of newly synthesized histone marks during DNA replication. Oncotarget 2018; 7:70323-70335. [PMID: 27612420 PMCID: PMC5342555 DOI: 10.18632/oncotarget.11855] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/21/2016] [Indexed: 02/02/2023] Open
Abstract
ATAD2 (ATPase family AAA domain-containing protein 2) is a chromatin regulator harboring an AAA+ ATPase domain and a bromodomain, previously proposed to function as an oncogenic transcription co-factor. Here we suggest that ATAD2 is also required for DNA replication. ATAD2 is co-expressed with genes involved in DNA replication in various cancer types and predominantly expressed in S phase cells where it localized on nascent chromatin (replication sites). Our extensive biochemical and cellular analyses revealed that ATAD2 is recruited to replication sites through a direct interaction with di-acetylated histone H4 at K5 and K12, indicative of newly synthesized histones during replication-coupled chromatin reassembly. Similar to ATAD2-depletion, ectopic expression of ATAD2 mutants that are deficient in binding to these di-acetylation marks resulted in reduced DNA replication and impaired loading of PCNA onto chromatin, suggesting relevance of ATAD2 in DNA replication. Taken together, our data show a novel function of ATAD2 in cancer and for the first time identify a reader of newly synthesized histone di-acetylation-marks during replication.
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Affiliation(s)
| | | | | | - Christopher J Ott
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Sarah Vittori
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Present address: Novartis Institute for BioMedical Research, Cambridge, MA, USA
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24
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Abstract
In this issue of Cancer Cell, Qu et al. describe the chromatin accessibility profiles of cutaneous T cell lymphoma, with dynamic assessments of response and resistance to histone deacetylase inhibitor therapy. Their "personal regulome" analysis framework reveals chromatin features that may be predictive of clinical response to epigenetic therapy.
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Affiliation(s)
- Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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25
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Winter GE, Mayer A, Buckley DL, Erb MA, Roderick JE, Vittori S, Reyes JM, di Iulio J, Souza A, Ott CJ, Roberts JM, Zeid R, Scott TG, Paulk J, Lachance K, Olson CM, Dastjerdi S, Bauer S, Lin CY, Gray NS, Kelliher MA, Churchman LS, Bradner JE. BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment. Mol Cell 2017; 67:5-18.e19. [PMID: 28673542 DOI: 10.1016/j.molcel.2017.06.004] [Citation(s) in RCA: 278] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/14/2017] [Accepted: 06/02/2017] [Indexed: 12/19/2022]
Abstract
Processive elongation of RNA Polymerase II from a proximal promoter paused state is a rate-limiting event in human gene control. A small number of regulatory factors influence transcription elongation on a global scale. Prior research using small-molecule BET bromodomain inhibitors, such as JQ1, linked BRD4 to context-specific elongation at a limited number of genes associated with massive enhancer regions. Here, the mechanistic characterization of an optimized chemical degrader of BET bromodomain proteins, dBET6, led to the unexpected identification of BET proteins as master regulators of global transcription elongation. In contrast to the selective effect of bromodomain inhibition on transcription, BET degradation prompts a collapse of global elongation that phenocopies CDK9 inhibition. Notably, BRD4 loss does not directly affect CDK9 localization. These studies, performed in translational models of T cell leukemia, establish a mechanism-based rationale for the development of BET bromodomain degradation as cancer therapy.
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Affiliation(s)
- Georg E Winter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andreas Mayer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Michael A Erb
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Justine E Roderick
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sarah Vittori
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jaime M Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Julia di Iulio
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda Souza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Rhamy Zeid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Thomas G Scott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kate Lachance
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Calla M Olson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Shiva Dastjerdi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sophie Bauer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Charles Y Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Michelle A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.
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26
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27
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Abstract
Cancer cell hallmarks are underpinned by transcriptional programmes operating in the context of a dynamic and complicit epigenomic environment. Somatic alterations of chromatin modifiers are among the most prevalent cancer perturbations. There is a pressing need for targeted chemical probes to dissect these complex, interconnected gene regulatory circuits. Validated chemical probes empower mechanistic research while providing the pharmacological proof of concept that is required to translate drug-like derivatives into therapy for cancer patients. In this Review, we describe chemical probe development for epigenomic effector proteins that are linked to cancer pathogenesis. By annotating these reagents, we aim to share our perspectives on an informative 'epigenomic toolbox' of broad utility to the research community.
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Affiliation(s)
- Jake Shortt
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville 3052, Australia
- School of Clinical Sciences at Monash Health, Monash University, Clayton 3168, Australia
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, USA
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville 3052, Australia
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, USA
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, USA
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28
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Koblan LW, Buckley DL, Ott CJ, Fitzgerald ME, Ember SWJ, Zhu JY, Liu S, Roberts JM, Remillard D, Vittori S, Zhang W, Schonbrunn E, Bradner JE. Assessment of Bromodomain Target Engagement by a Series of BI2536 Analogues with Miniaturized BET-BRET. ChemMedChem 2016; 11:2575-2581. [PMID: 27862999 DOI: 10.1002/cmdc.201600502] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 10/21/2016] [Indexed: 01/27/2023]
Abstract
Evaluating the engagement of a small molecule ligand with a protein target in cells provides useful information for chemical probe optimization and pharmaceutical development. While several techniques exist that can be performed in a low-throughput manner, systematic evaluation of large compound libraries remains a challenge. In-cell engagement measurements are especially useful when evaluating compound classes suspected to target multiple cellular factors. In this study we used a bioluminescent resonant energy transfer assay to assess bromodomain engagement by a compound series containing bromodomain- and kinase-biasing polypharmacophores based on the known dual BRD4 bromodomain/PLK1 kinase inhibitor BI2536. With this assay, we discovered several novel agents with bromodomain-selective specificity profiles and cellular activity. Thus, this platform aids in distinguishing molecules whose cellular activity is difficult to assess due to polypharmacologic effects.
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Affiliation(s)
- Luke W Koblan
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, 02142, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, 02142, USA
| | - Mark E Fitzgerald
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, 02142, USA
- C4 Therapeutics, Cambridge, MA, 02142, USA
| | - Stuart W J Ember
- Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, 33612, USA
- Reaction Biology Corporation, Malvern, PA, 19355, USA
| | - Jin-Yi Zhu
- Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Shuai Liu
- Department of Chemistry, University of Massachusetts-Boston, Boston, MA, 02125, USA
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David Remillard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sarah Vittori
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, 02142, USA
| | - Wei Zhang
- Department of Chemistry, University of Massachusetts-Boston, Boston, MA, 02125, USA
| | - Ernst Schonbrunn
- Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, 02142, USA
- Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA
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29
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Koblan LW, Buckley DL, Ott CJ, Fitzgerald ME, Ember SWJ, Zhu J, Liu S, Roberts JM, Remillard D, Vittori S, Zhang W, Schonbrunn E, Bradner JE. Back Cover: Assessment of Bromodomain Target Engagement by a Series of BI2536 Analogues with Miniaturized BET‐BRET (ChemMedChem 23/2016). ChemMedChem 2016. [DOI: 10.1002/cmdc.201600587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Luke W. Koblan
- Center for the Science of Therapeutics Broad Institute Cambridge MA 02142 USA
| | - Dennis L. Buckley
- Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Christopher J. Ott
- Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Center for the Science of Therapeutics Broad Institute Cambridge MA 02142 USA
| | - Mark E. Fitzgerald
- Center for the Science of Therapeutics Broad Institute Cambridge MA 02142 USA
- C4 Therapeutics Cambridge MA 02142 USA
| | - Stuart W. J. Ember
- Drug Discovery Department Moffitt Cancer Center Tampa FL 33612 USA
- Reaction Biology Corporation Malvern PA 19355 USA
| | - Jin‐Yi Zhu
- Drug Discovery Department Moffitt Cancer Center Tampa FL 33612 USA
| | - Shuai Liu
- Department of Chemistry University of Massachusetts-Boston Boston MA 02125 USA
| | - Justin M. Roberts
- Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA
| | - David Remillard
- Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA
| | - Sarah Vittori
- Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA
- Center for the Science of Therapeutics Broad Institute Cambridge MA 02142 USA
| | - Wei Zhang
- Department of Chemistry University of Massachusetts-Boston Boston MA 02125 USA
| | - Ernst Schonbrunn
- Drug Discovery Department Moffitt Cancer Center Tampa FL 33612 USA
| | - James E. Bradner
- Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Center for the Science of Therapeutics Broad Institute Cambridge MA 02142 USA
- Novartis Institutes for Biomedical Research Cambridge MA 02139 USA
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Koo SJ, Fernandez-Montalvan AE, Holton S, von Ahsen O, Badock V, Vittori S, Ott CJ, Bradner JE, Gorjanacz M. Abstract 4539: ATAD2 mediates DNA replication in cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
ATAD2 (ATPase family AAA domain-containing protein 2) is an epigenetic regulator which associates with chromatin through its Bromodomain specialized in Acetyl-Lys binding of histones. ATAD2 was also shown to directly associate with multiple transcription factors such as ERα, AR, E2F and MYC, and is believed to function as an oncogenic transcription factor in breast cancer.
Here, we propose that ATAD2 facilitates DNA replication. ATAD2 is specifically expressed in S and G2 phase during which it co-localizes with newly synthesized DNA. We found ATAD2 on nascent chromatin together with newly synthesized histone H4 acetylated on K12 and Proliferating Cell Nuclear Antigen (PCNA), a central protein coupling replication with chromatin restoration, but not on post-replicative chromatin. In line with these observations depletion of ATAD2 by siRNA led to reduced DNA replication, perturbed loading of PCNA onto chromatin and inhibition of cell proliferation. Interestingly, a brief cycloheximide treatment of the cells to prevent the deposition of newly synthesized histones (e.g. H4K5,12diac) abrogated the recruitment of ATAD2 to nascent chromatin suggesting that ATAD2 might recognize and interact with these histone marks. Indeed, extensive biochemical and biophysical analyses involving TR-FRET, MST (MicroScale Thermophresis), Biocore, and NMR revealed that the bromodomain of ATAD2 preferentially interacts with these marks characteristic of newly synthesized histones. Consequently, overexpression of ATAD2 mutants unable to interact with these marks impaired DNA replication and recruitment of PCNA onto chromatin. Taken together, our data suggest that ATAD2 is essential for DNA replication and thus predicts that it is expressed in cells undergoing S phase. To further strengthen this hypothesis we compared the expression of ATAD2 with the proliferation marker Ki67, and the late S and G2/M marker TOP2A, in various cancer types such as colorectal, gastric, lung, prostate and breast cancers by immunohistochemistry. Indeed ATAD2 expression was restricted to Ki67 and TOP2A expressing areas of tumors, independent of cancer type. Moreover, aggressive tumors, such as triple negative breast cancer and metastatic castration-resistant prostate cancer, showed more intense and abundant expression of ATAD2 whereas slow-growing tumors showed low expression of ATAD2. This research identifies a role for ATAD2 in replication, providing mechanistic and translational support for therapeutic development in cancer.
Citation Format: Seong Joo Koo, Amaury Ernesto Fernandez-Montalvan, Simon Holton, Oliver von Ahsen, Volker Badock, Sarah Vittori, Christopher J. Ott, James E. Bradner, Matyas Gorjanacz. ATAD2 mediates DNA replication in cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4539.
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Yang S, Ott CJ, Rossmann MP, Superdock M, Zon LI, Zhou Y. Chromatin immunoprecipitation and an open chromatin assay in zebrafish erythrocytes. Methods Cell Biol 2016; 135:387-412. [PMID: 27443937 DOI: 10.1016/bs.mcb.2016.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Zebrafish is an excellent genetic and developmental model for the study of vertebrate development and disease. Its ability to produce an abundance of transparent, externally developed embryos has facilitated large-scale genetic and chemical screens for the identification of critical genes and chemical factors that modulate developmental pathways. These studies can have profound implications for the diagnosis and treatment of a variety of human diseases. Recent advancements in molecular and genomic studies have provided valuable tools and resources for comprehensive and high-resolution analysis of epigenomes during cell specification and lineage differentiation throughout development. In this chapter, we describe two simple methods to evaluate protein-DNA interaction and chromatin architecture in erythrocytes from adult zebrafish. These are chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) and an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). These techniques, together with gene expression profiling, are useful for analyzing epigenomic regulation of cell specification, differentiation, and function during zebrafish development in both normal and disease models.
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Affiliation(s)
- S Yang
- Boston Children's Hospital, Boston, MA, United States; Dana Farber Cancer Institute, Harvard Stem Cell Institute, Boston, MA, United States; Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, United States
| | - C J Ott
- Dana Farber Cancer Institute, Harvard Stem Cell Institute, Boston, MA, United States
| | - M P Rossmann
- Harvard University, Harvard, Cambridge, MA, United States
| | - M Superdock
- Boston Children's Hospital, Boston, MA, United States; Dana Farber Cancer Institute, Harvard Stem Cell Institute, Boston, MA, United States; Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, United States
| | - L I Zon
- Boston Children's Hospital, Boston, MA, United States; Dana Farber Cancer Institute, Harvard Stem Cell Institute, Boston, MA, United States; Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, United States; Harvard University, Harvard, Cambridge, MA, United States
| | - Y Zhou
- Boston Children's Hospital, Boston, MA, United States; Dana Farber Cancer Institute, Harvard Stem Cell Institute, Boston, MA, United States; Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, United States; Harvard University, Harvard, Cambridge, MA, United States
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32
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Mallon JC, Ott CJ, Larson PL, Iuliano EM, Evans DC. Spiclypeus shipporum gen. et sp. nov., a Boldly Audacious New Chasmosaurine Ceratopsid (Dinosauria: Ornithischia) from the Judith River Formation (Upper Cretaceous: Campanian) of Montana, USA. PLoS One 2016; 11:e0154218. [PMID: 27191389 PMCID: PMC4871577 DOI: 10.1371/journal.pone.0154218] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/11/2016] [Indexed: 11/25/2022] Open
Abstract
This study reports on a new ceratopsid, Spiclypeus shipporum gen et sp. nov., from the lower Coal Ridge Member of the Judith River Formation in Montana, USA, which dates to ~76 Ma (upper Campanian). The species is distinguished by rugose dorsal contacts on the premaxillae for the nasals, laterally projecting postorbital horncores, fully fused and anteriorly curled P1 and P2 epiparietals, and a posterodorsally projecting P3 epiparietal. The holotype specimen is also notable for its pathological left squamosal and humerus, which show varied signs of osteomyelitis and osteoarthritis. Although the postorbital horncores of Spiclypeus closely resemble those of the contemporaneous ‘Ceratops’, the horncores of both genera are nevertheless indistinguishable from those of some other horned dinosaurs, including Albertaceratops and Kosmoceratops; ‘Ceratops’ is therefore maintained as a nomen dubium. Cladistic analysis recovers Spiclypeus as the sister taxon to the clade Vagaceratops + Kosmoceratops, and appears transitional in the morphology of its epiparietals. The discovery of Spiclypeus adds to the poorly known dinosaur fauna of the Judith River Formation, and suggests faunal turnover within the formation.
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Affiliation(s)
- Jordan C. Mallon
- Palaeobiology, Canadian Museum of Nature, PO Box 3443 Station “D”, Ottawa, Ontario, K1P 6P4, Canada
- * E-mail:
| | - Christopher J. Ott
- Independent Researcher, PO Box 1515, Appleton, Wisconsin, 54912, United States of America
| | - Peter L. Larson
- Black Hills Institute, 217 Main Street, Hill City, South Dakota, 57745, United States of America
| | - Edward M. Iuliano
- Kadlec Medical Center, 888 Swift Boulevard, Richland, Washington, 99352, United States of America
| | - David C. Evans
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario, M5S 2C6, Canada
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Viny AD, Ott CJ, Spitzer B, Rivas M, Meydan C, Papalexi E, Yelin D, Shank K, Reyes J, Chiu A, Romin Y, Boyko V, Thota S, Maciejewski JP, Melnick A, Bradner JE, Levine RL. Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis. J Exp Med 2015; 212:1819-32. [PMID: 26438361 PMCID: PMC4612085 DOI: 10.1084/jem.20151317] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 09/04/2015] [Indexed: 01/18/2023] Open
Abstract
Cohesin complex members have recently been identified as putative tumor suppressors in hematologic and epithelial malignancies. The cohesin complex guides chromosome segregation; however, cohesin mutant leukemias do not show genomic instability. We hypothesized that reduced cohesin function alters chromatin structure and disrupts cis-regulatory architecture of hematopoietic progenitors. We investigated the consequences of Smc3 deletion in normal and malignant hematopoiesis. Biallelic Smc3 loss induced bone marrow aplasia with premature sister chromatid separation and revealed an absolute requirement for cohesin in hematopoietic stem cell (HSC) function. In contrast, Smc3 haploinsufficiency increased self-renewal in vitro and in vivo, including competitive transplantation. Smc3 haploinsufficiency reduced coordinated transcriptional output, including reduced expression of transcription factors and other genes associated with lineage commitment. Smc3 haploinsufficiency cooperated with Flt3-ITD to induce acute leukemia in vivo, with potentiated Stat5 signaling and altered nucleolar topology. These data establish a dose dependency for cohesin in regulating chromatin structure and HSC function.
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Affiliation(s)
- Aaron D Viny
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Barbara Spitzer
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Martin Rivas
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065
| | - Cem Meydan
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065
| | - Efthymia Papalexi
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Dana Yelin
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Department of Medicine, Rabin Medical Center, Beilinson Campus, Petah Tikvah 49100, Israel
| | - Kaitlyn Shank
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Jaime Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - April Chiu
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Yevgeniy Romin
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Vitaly Boyko
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Swapna Thota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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Viny AD, Ott CJ, Spitzer B, Rivas M, Meydan C, Papalexi E, Yelin D, Shank K, Reyes J, Chiu A, Romin Y, Boyko V, Thota S, Maciejewski JP, Melnick A, Bradner JE, Levine RL. Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis. J Biophys Biochem Cytol 2015. [DOI: 10.1083/jcb.2111oia226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Ott CJ, Bandaru R, Gill T, Tao J, Chen X, Zhang Y, Bradner JE. Abstract PR12: Selective targeting of MYC mRNA by chemically stabilized antisense oligonucleotides. Mol Cancer Res 2015. [DOI: 10.1158/1557-3125.myc15-pr12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite its well-characterized properties as a proto-oncogene in numerous cancers, direct potent and selective inhibition of MYC or its protein product c-Myc with cell-permeable synthetic agents remains a significant challenge. Systemic inhibition of c-Myc activity in mice by expression of dominant negative MYC transgenes has been shown to dramatically decrease tumor burden with apparently tolerable side effects (Soucek et al, Nature 2008). In order to ultimately realize the goal of therapeutic MYC inhibition in cancer, we have initiated discovery chemistry efforts aimed at inhibiting MYC at the transcriptional, translational, and post-translational level. Here we describe the application of synthetic antisense oligonucleotides designed to target specific sequences of the MYC mRNA (MYCASOs). We have incorporated several chemical features into MYCASOs, including the addition of locked nucleic acid (LNA) bases at the 5' and 3' ends, phosphorothioate linkers, and internal DNA bases in order to increase mRNA target affinity and cleavage, cellular permeability, stability, and systemic distribution in vivo. Treatment of MYC¬-expressing cancer cells with MYCASOs leads to a potent decrease in MYC mRNA and c-Myc protein levels. Cleaved MYC mRNA in MYCASO-treated cells is detected with a sensitive 5' rapid amplification of cDNA ends (RACE) assay. MYCASO-treatment of cancer cell lines leads to significant inhibition of cellular proliferation and induces apoptosis in c-Myc-dependent myeloma and leukemia cell lines while decreasing c-Myc-mediated gene expression. In vivo administration of MYCASOs simply dissolved in saline was performed in mice by tail vein injection. MYCASOs are well tolerated up to 25 mg per kg on a twice-weekly dosing regimen. In a MYC-induced model of hepatocellular carcinoma, MYCASO treatment leads to detectable cleavage of the MYC transcript, decreases c-Myc levels within tumors, and significantly decreases tumor burden. MYCASOs represent a new chemical tool for in vitro and in vivo modulation of c-Myc activity, and promising therapeutic agents for MYC-driven tumors.
Citation Format: Christopher J. Ott, Raj Bandaru, Taylor Gill, Junyan Tao, Xin Chen, Yixian Zhang, James E. Bradner. Selective targeting of MYC mRNA by chemically stabilized antisense oligonucleotides. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr PR12.
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Affiliation(s)
| | | | | | - Junyan Tao
- 3University of California, San Francisco, CA
| | - Xin Chen
- 3University of California, San Francisco, CA
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36
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Ott CJ. Promising new strategies to target gene regulatory factors in T-cell acute lymphoblastic leukemia. Int J Hematol Oncol 2014. [DOI: 10.2217/ijh.14.44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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37
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Knoechel B, Roderick JE, Williamson KE, Zhu J, Lohr JG, Cotton MJ, Gillespie SM, Fernandez D, Ku M, Wang H, Piccioni F, Silver SJ, Jain M, Pearson D, Kluk MJ, Ott CJ, Shultz LD, Brehm MA, Greiner DL, Gutierrez A, Stegmaier K, Kung AL, Root DE, Bradner JE, Aster JC, Kelliher MA, Bernstein BE. An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia. Nat Genet 2014; 46:364-70. [PMID: 24584072 PMCID: PMC4086945 DOI: 10.1038/ng.2913] [Citation(s) in RCA: 279] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 02/06/2014] [Indexed: 12/13/2022]
Abstract
The identification of activating NOTCH1 mutations in T cell acute lymphoblastic leukemia (T-ALL) led to clinical testing of γ-secretase inhibitors (GSIs) that prevent NOTCH1 activation. However, responses to these inhibitors have been transient, suggesting that resistance limits their clinical efficacy. Here we modeled T-ALL resistance, identifying GSI-tolerant 'persister' cells that expand in the absence of NOTCH1 signaling. Rare persisters are already present in naive T-ALL populations, and the reversibility of their phenotype suggests an epigenetic mechanism. Relative to GSI-sensitive cells, persister cells activate distinct signaling and transcriptional programs and exhibit chromatin compaction. A knockdown screen identified chromatin regulators essential for persister viability, including BRD4. BRD4 binds enhancers near critical T-ALL genes, including MYC and BCL2. The BRD4 inhibitor JQ1 downregulates expression of these targets and induces growth arrest and apoptosis in persister cells, at doses well tolerated by GSI-sensitive cells. Consistently, the GSI-JQ1 combination was found to be effective against primary human leukemias in vivo. Our findings establish a role for epigenetic heterogeneity in leukemia resistance that may be addressed by incorporating epigenetic modulators in combination therapy.
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Affiliation(s)
- Birgit Knoechel
- 1] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [4] Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA. [5]
| | - Justine E Roderick
- 1] Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA. [2]
| | - Kaylyn E Williamson
- 1] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, USA. [4] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Jiang Zhu
- 1] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, USA. [4] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Jens G Lohr
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Matthew J Cotton
- 1] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, USA. [4] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Shawn M Gillespie
- 1] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, USA. [4] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Daniel Fernandez
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Biostatistics Graduate Program, Harvard University, Cambridge, Massachusetts, USA
| | - Manching Ku
- 1] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Hongfang Wang
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Serena J Silver
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mohit Jain
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA. [3] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daniel Pearson
- 1] Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA. [2] Biological and Biomedical Sciences Graduate Program, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael J Kluk
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Michael A Brehm
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Dale L Greiner
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Alejandro Gutierrez
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kimberly Stegmaier
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew L Kung
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - James E Bradner
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Michelle A Kelliher
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Bradley E Bernstein
- 1] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, USA. [4] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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Lu G, Middleton RE, Sun H, Naniong M, Ott CJ, Mitsiades CS, Wong KK, Bradner JE, Kaelin WG. The myeloma drug lenalidomide promotes the cereblon-dependent destruction of Ikaros proteins. Science 2013; 343:305-9. [PMID: 24292623 DOI: 10.1126/science.1244917] [Citation(s) in RCA: 1034] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Thalidomide-like drugs such as lenalidomide are clinically important treatments for multiple myeloma and show promise for other B cell malignancies. The biochemical mechanisms underlying their antitumor activity are unknown. Thalidomide was recently shown to bind to, and inhibit, the cereblon ubiquitin ligase. Cereblon loss in zebrafish causes fin defects reminiscent of the limb defects seen in children exposed to thalidomide in utero. Here we show that lenalidomide-bound cereblon acquires the ability to target for proteasomal degradation two specific B cell transcription factors, Ikaros family zinc finger proteins 1 and 3 (IKZF1 and IKZF3). Analysis of myeloma cell lines revealed that loss of IKZF1 and IKZF3 is both necessary and sufficient for lenalidomide's therapeutic effect, suggesting that the antitumor and teratogenic activities of thalidomide-like drugs are dissociable.
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Affiliation(s)
- Gang Lu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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Yigit E, Bischof JM, Zhang Z, Ott CJ, Kerschner JL, Leir SH, Buitrago-Delgado E, Zhang Q, Wang JPZ, Widom J, Harris A. Nucleosome mapping across the CFTR locus identifies novel regulatory factors. Nucleic Acids Res 2013; 41:2857-68. [PMID: 23325854 PMCID: PMC3597660 DOI: 10.1093/nar/gks1462] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/12/2012] [Accepted: 12/14/2012] [Indexed: 12/23/2022] Open
Abstract
Nucleosome positioning on the chromatin strand plays a critical role in regulating accessibility of DNA to transcription factors and chromatin modifying enzymes. Hence, detailed information on nucleosome depletion or movement at cis-acting regulatory elements has the potential to identify predicted binding sites for trans-acting factors. Using a novel method based on enrichment of mononucleosomal DNA by bacterial artificial chromosome hybridization, we mapped nucleosome positions by deep sequencing across 250 kb, encompassing the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR shows tight tissue-specific regulation of expression, which is largely determined by cis-regulatory elements that lie outside the gene promoter. Although multiple elements are known, the repertoire of transcription factors that interact with these sites to activate or repress CFTR expression remains incomplete. Here, we show that specific nucleosome depletion corresponds to well-characterized binding sites for known trans-acting factors, including hepatocyte nuclear factor 1, Forkhead box A1 and CCCTC-binding factor. Moreover, the cell-type selective nucleosome positioning is effective in predicting binding sites for novel interacting factors, such as BAF155. Finally, we identify transcription factor binding sites that are overrepresented in regions where nucleosomes are depleted in a cell-specific manner. This approach recognizes the glucocorticoid receptor as a novel trans-acting factor that regulates CFTR expression in vivo.
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Affiliation(s)
- Erbay Yigit
- Human Molecular Genetics Program, Children’s Memorial Research Center, Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, IL 60614, USA, Department of Molecular Biosciences and Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Jared M. Bischof
- Human Molecular Genetics Program, Children’s Memorial Research Center, Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, IL 60614, USA, Department of Molecular Biosciences and Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Zhaolin Zhang
- Human Molecular Genetics Program, Children’s Memorial Research Center, Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, IL 60614, USA, Department of Molecular Biosciences and Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Christopher J. Ott
- Human Molecular Genetics Program, Children’s Memorial Research Center, Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, IL 60614, USA, Department of Molecular Biosciences and Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Jenny L. Kerschner
- Human Molecular Genetics Program, Children’s Memorial Research Center, Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, IL 60614, USA, Department of Molecular Biosciences and Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Shih-Hsing Leir
- Human Molecular Genetics Program, Children’s Memorial Research Center, Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, IL 60614, USA, Department of Molecular Biosciences and Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Elsy Buitrago-Delgado
- Human Molecular Genetics Program, Children’s Memorial Research Center, Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, IL 60614, USA, Department of Molecular Biosciences and Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Quanwei Zhang
- Human Molecular Genetics Program, Children’s Memorial Research Center, Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, IL 60614, USA, Department of Molecular Biosciences and Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Ji-Ping Z. Wang
- Human Molecular Genetics Program, Children’s Memorial Research Center, Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, IL 60614, USA, Department of Molecular Biosciences and Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Jonathan Widom
- Human Molecular Genetics Program, Children’s Memorial Research Center, Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, IL 60614, USA, Department of Molecular Biosciences and Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Ann Harris
- Human Molecular Genetics Program, Children’s Memorial Research Center, Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, IL 60614, USA, Department of Molecular Biosciences and Department of Statistics, Northwestern University, Evanston, IL 60208, USA
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Abstract
The low levels of CFTR gene expression and paucity of CFTR protein in human airway epithelial cells are not easily reconciled with the pivotal role of the lung in cystic fibrosis pathology. Previous data suggested that the regulatory mechanisms controlling CFTR gene expression might be different in airway epithelium in comparison to intestinal epithelium where CFTR mRNA and protein is much more abundant. Here we examine chromatin structure and modification across the CFTR locus in primary human tracheal (HTE) and bronchial (NHBE) epithelial cells and airway cell lines including 16HBE14o- and Calu3. We identify regions of open chromatin that appear selective for primary airway epithelial cells and show that several of these are enriched for a histone modification (H3K4me1) that is characteristic of enhancers. Consistent with these observations, three of these sites encompass elements that have cooperative enhancer function in reporter gene assays in 16HBE14o- cells. Finally, we use chromosome conformation capture (3C) to examine the three-dimensional structure of nearly 800 kb of chromosome 7 encompassing CFTR and observe long-range interactions between the CFTR promoter and regions far outside the locus in cell types that express high levels of CFTR.
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Affiliation(s)
- Zhaolin Zhang
- Human Molecular Genetic Program, Children's Memorial Research Center, Chicago, IL 60614, USA
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41
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Ott CJ, Harris A. Genomic approaches for the discovery of CFTR regulatory elements. Transcription 2012; 2:23-7. [PMID: 21326906 DOI: 10.4161/trns.2.1.13693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 09/19/2010] [Accepted: 09/20/2010] [Indexed: 12/30/2022] Open
Abstract
Non-coding regions of the human genome contain vast regulatory potential that contributes to the coordination of gene expression. Indeed, regulatory elements can reside large genomic distances from the promoters of genes they control. Here we describe approaches recently used to identify functional elements within the complex CFTR locus.
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Affiliation(s)
- Christopher J Ott
- Human Molecular Genetics Program, Children's Memorial Research Center, Chicago, IL, USA
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Bischof JM, Ott CJ, Leir SH, Gosalia N, Song L, London D, Furey TS, Cotton CU, Crawford GE, Harris A. A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function. Thorax 2012; 67:385-91. [PMID: 22169360 PMCID: PMC3384740 DOI: 10.1136/thoraxjnl-2011-200880] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Distal cell-type-specific regulatory elements may be located at very large distances from the genes that they control and are often hidden within intergenic regions or in introns of other genes. The development of methods that enable mapping of regions of open chromatin genome wide has greatly advanced the identification and characterisation of these elements. METHODS Here we use DNase I hypersensitivity mapping followed by deep sequencing (DNase-seq) to generate a map of open chromatin in primary human tracheal epithelial (HTE) cells and use bioinformatic approaches to characterise the distribution of these sites within the genome and with respect to gene promoters, intronic and intergenic regions. RESULTS Genes with HTE-selective open chromatin at their promoters were associated with multiple pathways of epithelial function and differentiation. The data predict novel cell-type-specific regulatory elements for genes involved in HTE cell function, such as structural proteins and ion channels, and the transcription factors that may interact with them to control gene expression. Moreover, the map of open chromatin can identify the location of potentially critical regulatory elements in genome-wide association studies (GWAS) in which the strongest association is with single nucleotide polymorphisms in non-coding regions of the genome. We demonstrate its relevance to a recent GWAS that identifies modifiers of cystic fibrosis lung disease severity. CONCLUSION Since HTE cells have many functional similarities with bronchial epithelial cells and other differentiated cells in the respiratory epithelium, these data are of direct relevance to elucidating the molecular basis of normal lung function and lung disease.
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Affiliation(s)
- Jared M Bischof
- Human Molecular Genetics Program, Children's Memorial Research Center, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Christopher J Ott
- Human Molecular Genetics Program, Children's Memorial Research Center, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shih-Hsing Leir
- Human Molecular Genetics Program, Children's Memorial Research Center, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nehal Gosalia
- Human Molecular Genetics Program, Children's Memorial Research Center, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lingyun Song
- Institute for Genome Science and Policy, Duke University, Durham, North Carolina, USA
| | - Darin London
- Institute for Genome Science and Policy, Duke University, Durham, North Carolina, USA
| | - Terrence S Furey
- Department of Genetics, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Calvin U Cotton
- Department of Pediatrics, Case Western University, School of Medicine, Cleveland, Ohio, USA
- Department of Physiology and Biophysics, Case Western University, School of Medicine, Cleveland, Ohio, USA
| | - Gregory E Crawford
- Institute for Genome Science and Policy, Duke University, Durham, North Carolina, USA
| | - Ann Harris
- Human Molecular Genetics Program, Children's Memorial Research Center, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Abstract
Access to regulatory elements of the genome can be inhibited by nucleosome core particles arranged along the DNA strand. Hence, sites that are accessible by transcription factors may be located by using nuclease digestion to identify the relative nucleosome occupancy of a genomic region. In order to define novel cis regulatory elements in the ∼2.7-kb promoter region of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, we define its nucleosome occupancy. This profile reveals the precise positions of nucleosome-free regions (NFRs), both cell-type specific and others apparently unrelated to CFTR-expression level and offer the first high-resolution map of the chromatin structure of the entire CFTR promoter in relevant cell types. Several of these NFRs are strongly bound by nuclear factors in a sequence-specific manner, and directly influence CFTR promoter activity. Sequences within the NFR1 and NFR4 elements are highly conserved in many human gene promoters. Moreover, NFR1 contributes to promoter activity of another gene, angiopoietin-like 3 (ANGPTL3), while NFR4 is constitutively nucleosome-free in promoters genome wide. Conserved motifs within NFRs of the CFTR promoter also show a high level of protection from DNase I digestion genome-wide, and likely have important roles in the positioning of nucleosome core particles more generally.
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Affiliation(s)
- Christopher J Ott
- Human Molecular Genetics Program, Children's Memorial Research Center, and Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60614, USA
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McCarthy VA, Ott CJ, Phylactides M, Harris A. Interaction of intestinal and pancreatic transcription factors in the regulation of CFTR gene expression. Biochim Biophys Acta 2009; 1789:709-18. [PMID: 19782160 PMCID: PMC2783911 DOI: 10.1016/j.bbagrm.2009.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 08/14/2009] [Accepted: 09/17/2009] [Indexed: 01/08/2023]
Abstract
The tissue-specific regulation of the cystic fibrosis transmembrane conductance regulator gene (CFTR) is coordinated by intronic and extragenic cis-acting elements that influence its transcriptional activity. The promoter apparently lacks sequences to drive cell type-specific expression. We previously identified a number of intronic elements that were associated with DNase I hypersensitive sites (DHS) and bound the hepatocyte nuclear factor 1 (HNF1) transcription factor. Moreover, we demonstrated the likely involvement of HNF1 in the regulation of CFTR expression in vivo. Here we investigate DHS in introns 16 and 17a of the CFTR gene, which are evident in intestinal and pancreatic cell lines, and determine the transcription factors that interact with these sites. Of particular interest were factors known to interact with HNF1 in coordinated expression of genes in the gastrointestinal tract. We demonstrate that though sequences within these DHS bind HNF1, CDX2, and PBX1 in vitro, only PBX1 show a robust in vivo interaction. These data contribute to our understanding of the complexity of cell-type-specific CFTR regulatory mechanisms.
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Affiliation(s)
- Victoria A McCarthy
- Paediatric Molecular Genetics, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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Ott CJ, Suszko M, Blackledge NP, Wright JE, Crawford GE, Harris A. A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter. J Cell Mol Med 2009; 13:680-92. [PMID: 19449463 PMCID: PMC3822875 DOI: 10.1111/j.1582-4934.2008.00621.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genes can maintain spatiotemporal expression patterns by long-range interactions between cis-acting elements. The cystic fibrosis transmembrane conductance regulator gene (CFTR) is expressed primarily in epithelial cells. An element located within a DNase I-hyper-sensitive site (DHS) 10 kb into the first intron was previously shown to augment CFTR promoter activity in a tissue-specific manner. Here, we reveal the mechanism by which this element influences CFTR transcription. We employed a high-resolution method of mapping DHS using tiled microarrays to accurately locate the intron 1 DHS. Transfection of promoter-reporter constructs demonstrated that the element displays classical tissue-specific enhancer properties and can independently recruit factors necessary for transcription initiation. In vitro DNase I footprinting analysis identified a protected region that corresponds to a conserved, predicted binding site for hepatocyte nuclear factor 1 (HNF1). We demonstrate by electromobility shift assays (EMSA) and chromatin immunoprecipitation (ChIP) that HNF1 binds to this element both in vitro and in vivo. Moreover, using chromosome conformation capture (3C) analysis, we show that this element interacts with the CFTR promoter in CFTR-expressing cells. These data provide the first insight into the three- dimensional (3D) structure of the CFTR locus and confirm the contribution of intronic cis-acting elements to the regulation of CFTR gene expression.
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Affiliation(s)
- Christopher J Ott
- Children's Memorial Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Blackledge NP, Ott CJ, Gillen AE, Harris A. An insulator element 3' to the CFTR gene binds CTCF and reveals an active chromatin hub in primary cells. Nucleic Acids Res 2009; 37:1086-94. [PMID: 19129223 PMCID: PMC2651798 DOI: 10.1093/nar/gkn1056] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Regulation of expression of the CFTR gene is poorly understood. Elements within the basal promoter of the gene do not fully explain CFTR expression patterns, suggesting that cis-regulatory elements are located elsewhere, either within the locus or in adjacent chromatin. We previously mapped DNase I hypersensitive sites (DHS) in 400 kb spanning the CFTR locus including a cluster of sites close to the 3′-end of the gene. Here we focus on a DHS at +6.8 kb from the CFTR translation end-point to evaluate its potential role in regulating expression of the gene. This DHS, which encompasses a consensus CTCF-binding site, was evident in primary human epididymis cells that express abundant CFTR mRNA. We show by DNase I footprinting and electophoretic mobility shift assays that the cis-regulatory element within this DHS binds CTCF in vitro. We further demonstrate that the element functions as an enhancer blocker in a well-established in vivo assay, and by using chromatin immunoprecipitation that it recruits CTCF in vivo. Moreover, we reveal that in primary epididymis cells, the +6.8 kb DHS interacts closely with the CFTR promoter, suggesting that the CFTR locus exists in a looped conformation, characteristic of an active chromatin hub.
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Affiliation(s)
- Neil P Blackledge
- Human Molecular Genetics Program, Children's Memorial Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60614, USA
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Elkahwaji JE, Ott CJ, Janda LM, Hopkins WJ. Mouse model for acute bacterial prostatitis in genetically distinct inbred strains. Urology 2005; 66:883-7. [PMID: 16230175 DOI: 10.1016/j.urology.2005.04.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Revised: 03/17/2005] [Accepted: 04/15/2005] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Prostatitis is a common urologic disease seen in adult men. As many as 50% of men will experience an episode of prostatitis in their lifetime, and 2% to 3% of men will have bacterial prostatitis. Because the pathogenic mechanisms of prostatitis remain unclear, we developed a reproducible mouse model of bacterial prostatitis in which to study the etiology and host factors associated with infection susceptibility. METHODS Male BALB/c, C3H/HeJ, C3H/HeOuJ, C57BL/6J, and (BALB/c x C3H/HeJ)F1 mice 13 weeks old were inoculated intraurethrally with 2 x 10(6) or 2 x 10(8) Escherichia coli. Control mice were inoculated with phosphate-buffered saline. The animals were killed at 5 days after inoculation to assess the intensities of the bladder and prostate infections. RESULTS Significant bladder or prostate infections were not present in the BALB/c, C57BL/6J, or (BALB/c x C3H/HeJ)F1 mice at either inoculum dose. In contrast, both C3H/HeJ and C3H/HeOuJ mice developed high bladder infections and severe, acute prostatitis at both doses. Control mice infected with phosphate-buffered saline had no bladder or prostate infections. The P values were less than 0.01 for the comparison of bladder and prostate colony-forming units between C3H/HeJ or C3H/HeOuJ and BALB/c, C57BL/6J, or F1 mice. CONCLUSIONS The strain-dependent differences in susceptibility indicate that genetic factors may play a major role in the etiology of bacterial prostatitis. Because F1 mice did not develop significant bladder and prostate infections, similar to the BALB/c parents, it appears that infection susceptibility is a recessive trait. The availability of this model will allow us to investigate the immunology, genetics, and histopathologic features of bacterial infection of the prostate.
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Affiliation(s)
- Johny E Elkahwaji
- Division of Urology, Department of Surgery, University of Wisconsin Medical School, Madison, Wisconsin, USA.
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Elkahwaji JE, Uehling DT, Ott CJ, Hopkins WJ. 108: A New Animal Model for Bacterial Prostatitis Induced in Genetically Distinct Mouse Strains. J Urol 2004. [DOI: 10.1016/s0022-5347(18)37370-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Hopkins WJ, Elkahwaji JE, Heisey DM, Ott CJ. Inheritance of susceptibility to induced Escherichia coli bladder and kidney infections in female C3H/HeJ mice. J Infect Dis 2003; 187:418-23. [PMID: 12552425 DOI: 10.1086/367963] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2002] [Revised: 10/09/2002] [Indexed: 11/03/2022] Open
Abstract
In the present study, the inheritance of resistance and susceptibility to bladder and kidney infections in BALB/c, C3H/HeJ, F(1), and backcross mice was investigated, and the number of genes contributing to the phenotypes was estimated. Infections were induced in female mice by intravesical inoculation with Escherichia coli, and the number of bacteria in bladder and kidneys was quantified at 10 days. The (BALB/c x C3H/HeJ) F(1) mice had bladder and kidney infection intensities equivalent to those observed in the resistant BALB/c parents. Twelve percent of the (F(1) x C3H/HeJ) backcross mice had severe bladder infections, similar to the susceptible C3H/HeJ parents. Kidney infections ranging in intensity between those observed in BALB/c and C3H/HeJ parents were present in one-half of the backcross mice. Statistical analyses indicated that >/=1 gene is responsible for the increased susceptibility of C3H/HeJ mice and that the trait appears to be recessive.
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Affiliation(s)
- Walter J Hopkins
- Department of Surgery, University of Wisconsin Medical School, Madison, Wisconsin, USA.
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Affiliation(s)
- C J Ott
- Denver Health Medical Center Emergency Medicine Residency, Denver, CO, USA.
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