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Pomplun S, Jbara M, Schissel CK, Wilson Hawken S, Boija A, Li C, Klein I, Pentelute BL. Parallel Automated Flow Synthesis of Covalent Protein Complexes That Can Inhibit MYC-Driven Transcription. ACS CENTRAL SCIENCE 2021; 7:1408-1418. [PMID: 34471684 PMCID: PMC8393199 DOI: 10.1021/acscentsci.1c00663] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Indexed: 06/11/2023]
Abstract
Dysregulation of the transcription factor MYC is involved in many human cancers. The dimeric transcription factor complexes of MYC/MAX and MAX/MAX activate or inhibit, respectively, gene transcription upon binding to the same enhancer box DNA. Targeting these complexes in cancer is a long-standing challenge. Inspired by the inhibitory activity of the MAX/MAX dimer, we engineered covalently linked, synthetic homo- and heterodimeric protein complexes to attenuate oncogenic MYC-driven transcription. We prepared the covalent protein complexes (∼20 kDa, 167-231 residues) in a single shot via parallel automated flow synthesis in hours. The stabilized covalent dimers display DNA binding activity, are intrinsically cell-penetrant, and inhibit cancer cell proliferation in different cell lines. RNA sequencing and gene set enrichment analysis in A549 cancer cells confirmed that the synthetic dimers interfere with MYC-driven transcription. Our results demonstrate the potential of automated flow technology to rapidly deliver engineered synthetic protein complex mimetics that can serve as a starting point in developing inhibitors of MYC-driven cancer cell growth.
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Affiliation(s)
- Sebastian Pomplun
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Muhammad Jbara
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Carly K. Schissel
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Susana Wilson Hawken
- Whitehead
Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ann Boija
- Whitehead
Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Charles Li
- Whitehead
Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Isaac Klein
- Whitehead
Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Center
for Environmental Health Sciences, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Broad Institute
of MIT and Harvard, 415
Main Street, Cambridge, Massachusetts 02142, United States
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Libetti D, Bernardini A, Sertic S, Messina G, Dolfini D, Mantovani R. The Switch from NF-YAl to NF-YAs Isoform Impairs Myotubes Formation. Cells 2020; 9:cells9030789. [PMID: 32214056 PMCID: PMC7140862 DOI: 10.3390/cells9030789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/19/2020] [Accepted: 03/21/2020] [Indexed: 12/19/2022] Open
Abstract
NF-YA, the regulatory subunit of the trimeric transcription factor (TF) NF-Y, is regulated by alternative splicing (AS) generating two major isoforms, “long” (NF-YAl) and “short” (NF-YAs). Muscle cells express NF-YAl. We ablated exon 3 in mouse C2C12 cells by a four-guide CRISPR/Cas9n strategy, obtaining clones expressing exclusively NF-YAs (C2-YAl-KO). C2-YAl-KO cells grow normally, but are unable to differentiate. Myogenin and—to a lesser extent, MyoD— levels are substantially lower in C2-YAl-KO, before and after differentiation. Expression of the fusogenic Myomaker and Myomixer genes, crucial for the early phases of the process, is not induced. Myomaker and Myomixer promoters are bound by MyoD and Myogenin, and Myogenin overexpression induces their expression in C2-YAl-KO. NF-Y inactivation reduces MyoD and Myogenin, but not directly: the Myogenin promoter is CCAAT-less, and the canonical CCAAT of the MyoD promoter is not bound by NF-Y in vivo. We propose that NF-YAl, but not NF-YAs, maintains muscle commitment by indirectly regulating Myogenin and MyoD expression in C2C12 cells. These experiments are the first genetic evidence that the two NF-YA isoforms have functionally distinct roles.
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