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Briggs EM, Mita P, Sun X, Ha S, Vasilyev N, Leopold ZR, Nudler E, Boeke JD, Logan SK. Unbiased proteomic mapping of the LINE-1 promoter using CRISPR Cas9. Mob DNA 2021; 12:21. [PMID: 34425899 PMCID: PMC8381588 DOI: 10.1186/s13100-021-00249-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/12/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The autonomous retroelement Long Interspersed Element-1 (LINE-1) mobilizes though a copy and paste mechanism using an RNA intermediate (retrotransposition). Throughout human evolution, around 500,000 LINE-1 sequences have accumulated in the genome. Most of these sequences belong to ancestral LINE-1 subfamilies, including L1PA2-L1PA7, and can no longer mobilize. Only a small fraction of LINE-1 sequences, approximately 80 to 100 copies belonging to the L1Hs subfamily, are complete and still capable of retrotransposition. While silenced in most cells, many questions remain regarding LINE-1 dysregulation in cancer cells. RESULTS Here, we optimized CRISPR Cas9 gRNAs to specifically target the regulatory sequence of the L1Hs 5'UTR promoter. We identified three gRNAs that were more specific to L1Hs, with limited binding to older LINE-1 sequences (L1PA2-L1PA7). We also adapted the C-BERST method (dCas9-APEX2 Biotinylation at genomic Elements by Restricted Spatial Tagging) to identify LINE-1 transcriptional regulators in cancer cells. Our LINE-1 C-BERST screen revealed both known and novel LINE-1 transcriptional regulators, including CTCF, YY1 and DUSP1. CONCLUSION Our optimization and evaluation of gRNA specificity and application of the C-BERST method creates a tool for studying the regulatory mechanisms of LINE-1 in cancer. Further, we identified the dual specificity protein phosphatase, DUSP1, as a novel regulator of LINE-1 transcription.
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Affiliation(s)
- Erica M Briggs
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
- Present Address: Opentrons Labworks, Queens, NY, USA
| | - Paolo Mita
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
- Present Address: Opentrons Labworks, Queens, NY, USA
- Institute of Systems Genetics, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Xiaoji Sun
- Institute of Systems Genetics, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Cellarity, Cambridge, MA, USA
| | - Susan Ha
- Department of Urology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
| | - Zev R Leopold
- Department of Urology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA
| | - Jef D Boeke
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
- Institute of Systems Genetics, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Susan K Logan
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA.
- Department of Urology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA.
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Caggia S, Tapadar S, Wu B, Venugopal SV, Garrett AS, Kumar A, Stiffend JS, Davis JS, Oyelere AK, Khan SA. Small Molecule Inhibitors Targeting Gα i2 Protein Attenuate Migration of Cancer Cells. Cancers (Basel) 2020; 12:E1631. [PMID: 32575572 PMCID: PMC7353059 DOI: 10.3390/cancers12061631] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 12/12/2022] Open
Abstract
Heterotrimeric G-proteins are ubiquitously expressed in several cancers, and they transduce signals from activated G-protein coupled receptors. These proteins have numerous biological functions, and they are becoming interesting target molecules in cancer therapy. Previously, we have shown that heterotrimeric G-protein subunit alphai2 (Gαi2) has an essential role in the migration and invasion of prostate cancer cells. Using a structure-based approach, we have synthesized optimized small molecule inhibitors that are able to prevent specifically the activation of the Gαi2 subunit, keeping the protein in its inactive GDP-bound state. We observed that two of the compounds (13 and 14) at 10 μΜ significantly inhibited the migratory behavior of the PC3 and DU145 prostate cancer cell lines. Additionally, compound 14 at 10 μΜ blocked the activation of Gαi2 in oxytocin-stimulated prostate cancer PC3 cells, and inhibited the migratory capability of DU145 cells overexpressing the constitutively active form of Gαi2, under basal and EGF-stimulated conditions. We also observed that the knockdown or inhibition of Gαi2 negatively regulated migration of renal and ovarian cancer cell lines. Our results suggest that small molecule inhibitors of Gαi2 have potential as leads for discovering novel anti-metastatic agents for attenuating the capability of cancer cells to spread and invade to distant sites.
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Affiliation(s)
- Silvia Caggia
- Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA 30314, USA; (S.C.); (S.V.V.); (A.S.G.); (A.K.); (J.S.S.)
| | - Subhasish Tapadar
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30318, USA; (S.T.); (B.W.)
| | - Bocheng Wu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30318, USA; (S.T.); (B.W.)
| | - Smrruthi V. Venugopal
- Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA 30314, USA; (S.C.); (S.V.V.); (A.S.G.); (A.K.); (J.S.S.)
| | - Autumn S. Garrett
- Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA 30314, USA; (S.C.); (S.V.V.); (A.S.G.); (A.K.); (J.S.S.)
| | - Aditi Kumar
- Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA 30314, USA; (S.C.); (S.V.V.); (A.S.G.); (A.K.); (J.S.S.)
| | - Janae S. Stiffend
- Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA 30314, USA; (S.C.); (S.V.V.); (A.S.G.); (A.K.); (J.S.S.)
| | - John S. Davis
- Department of Obstetrics and Gynecology, College of Medicine, University of Nebraska Medical Center and VA Medical Center, Omaha, NE 68198, USA;
| | - Adegboyega K. Oyelere
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30318, USA; (S.T.); (B.W.)
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30318, USA
| | - Shafiq A. Khan
- Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA 30314, USA; (S.C.); (S.V.V.); (A.S.G.); (A.K.); (J.S.S.)
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