1
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Chariou PL, Minnar CM, Tandon M, Guest MR, Chari R, Schlom J, Gameiro SR. Generation of murine tumor models refractory to αPD-1/-L1 therapies due to defects in antigen processing/presentation or IFNγ signaling using CRISPR/Cas9. PLoS One 2024; 19:e0287733. [PMID: 38427670 PMCID: PMC10906908 DOI: 10.1371/journal.pone.0287733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/12/2023] [Indexed: 03/03/2024] Open
Abstract
Immune checkpoint blockade (ICB) targeting the programmed cell death protein 1 (PD-1) and its ligand 1 (PD-L1) fails to provide clinical benefit for most cancer patients due to primary or acquired resistance. Drivers of ICB resistance include tumor antigen processing/presentation machinery (APM) and IFNγ signaling mutations. Thus, there is an unmet clinical need to develop alternative therapies for these patients. To this end, we have developed a CRISPR/Cas9 approach to generate murine tumor models refractory to PD-1/-L1 inhibition due to APM/IFNγ signaling mutations. Guide RNAs were employed to delete B2m, Jak1, or Psmb9 genes in ICB-responsive EMT6 murine tumor cells. B2m was deleted in ICB-responsive MC38 murine colon cancer cells. We report a detailed development and validation workflow including whole exome and Sanger sequencing, western blotting, and flow cytometry to assess target gene deletion. Tumor response to ICB and immune effects of gene deletion were assessed in syngeneic mice. This workflow can help accelerate the discovery and development of alternative therapies and a deeper understanding of the immune consequences of tumor mutations, with potential clinical implications.
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Affiliation(s)
- Paul L. Chariou
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Christine M. Minnar
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Mayank Tandon
- National Cancer Institute, CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Institutes of Health, Bethesda, MD, United States of America
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Mary R. Guest
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Raj Chari
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Sofia R. Gameiro
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
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2
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Hawley RG, Hawley TS. CRISPR-Cas9-Mediated Bioluminescent Tagging of Endogenous Proteins by Fluorescent Protein-Assisted Cell Sorting. Methods Mol Biol 2024; 2779:273-286. [PMID: 38526790 DOI: 10.1007/978-1-0716-3738-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Oncogenic fusion genes are attractive therapeutic targets because of their tumor-specific expression and central "driver" roles in various human cancers. However, oncogenic fusions involving transcription factors such as PAX3-FOXO1 in alveolar fusion gene-positive rhabdomyosarcoma (FP-RMS) have been difficult to inhibit due to the apparent lack of tractable drug-like binding sites comparable to that recognized by Gleevec (imatinib mesylate) on the BCR-ABL1 tyrosine kinase fusion protein. Toward the identification of novel small molecules that selectively target PAX3-FOXO1, we used CRISPR-Cas9-mediated knock-in to append the pro-luminescent HiBiT tag onto the carboxy terminus of the endogenous PAX3-FOXO1 fusion protein in two human FP-RMS cell lines (RH4 and SCMC). HiBiT is an 11-amino acid peptide derived from the NanoLuc luciferase that produces a luminescence signal which is ~100-fold brighter than firefly or Renilla luciferases through high-affinity binding to a complementary NanoLuc peptide fragment called LgBiT. To facilitate single-cell clonal isolation of knock-ins, the homology-directed repair template encoding HiBiT was followed by a P2A self-cleaving peptide for coexpression of an mCherry fluorescent protein as a fluorescence-activated cell sorter (FACS)-selectable marker. HiBiT tagging thus allows highly sensitive luminescence detection of endogenous PAX3-FOXO1 levels permitting quantitative high-throughput screening of large compound libraries for the discovery of PAX3-FOXO1 inhibitors and degraders.
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Affiliation(s)
- Robert G Hawley
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA.
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3
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Ohara Y, Tang W, Liu H, Yang S, Dorsey TH, Cawley H, Moreno P, Chari R, Guest MR, Azizian A, Gaedcke J, Ghadimi M, Hanna N, Ambs S, Hussain SP. SERPINB3-MYC axis induces the basal-like/squamous subtype and enhances disease progression in pancreatic cancer. Cell Rep 2023; 42:113434. [PMID: 37980563 PMCID: PMC10842852 DOI: 10.1016/j.celrep.2023.113434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/12/2023] [Accepted: 10/30/2023] [Indexed: 11/21/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) exhibits distinct molecular subtypes: classical/progenitor and basal-like/squamous. Our study aimed to identify genes contributing to the development of the basal-like/squamous subtype, known for its aggressiveness. Transcriptome analyses revealed consistent upregulation of SERPINB3 in basal-like/squamous PDAC, correlating with reduced patient survival. SERPINB3 transgene expression in PDAC cells enhanced in vitro invasion and promoted lung metastasis in a mouse PDAC xenograft model. Metabolome analyses unveiled a metabolic signature linked to both SERPINB3 and the basal-like/squamous subtype, characterized by heightened carnitine/acylcarnitine and amino acid metabolism, associated with poor prognosis in patients with PDAC and elevated cellular invasiveness. Further analysis uncovered that SERPINB3 inhibited the cysteine protease calpain, a key enzyme in the MYC degradation pathway, and drove basal-like/squamous subtype and associated metabolic reprogramming through MYC activation. Our findings indicate that the SERPINB3-MYC axis induces the basal-like/squamous subtype, proposing SERPINB3 as a potential diagnostic and therapeutic target for this variant.
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Affiliation(s)
- Yuuki Ohara
- Pancreatic Cancer Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Huaitian Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shouhui Yang
- Pancreatic Cancer Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tiffany H Dorsey
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Helen Cawley
- Pancreatic Cancer Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paloma Moreno
- Pancreatic Cancer Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21701, USA
| | - Mary R Guest
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21701, USA
| | - Azadeh Azizian
- Städtisches Klinikum Karlsruhe, Moltkestraße 90, 76133 Karlsruhe, Germany
| | - Jochen Gaedcke
- Städtisches Klinikum Karlsruhe, Moltkestraße 90, 76133 Karlsruhe, Germany
| | - Michael Ghadimi
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Nader Hanna
- Division of General & Oncologic Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - S Perwez Hussain
- Pancreatic Cancer Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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4
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Ruf B, Bruhns M, Babaei S, Kedei N, Ma L, Revsine M, Benmebarek MR, Ma C, Heinrich B, Subramanyam V, Qi J, Wabitsch S, Green BL, Bauer KC, Myojin Y, Greten LT, McCallen JD, Huang P, Trehan R, Wang X, Nur A, Murphy Soika DQ, Pouzolles M, Evans CN, Chari R, Kleiner DE, Telford W, Dadkhah K, Ruchinskas A, Stovroff MK, Kang J, Oza K, Ruchirawat M, Kroemer A, Wang XW, Claassen M, Korangy F, Greten TF. Tumor-associated macrophages trigger MAIT cell dysfunction at the HCC invasive margin. Cell 2023; 186:3686-3705.e32. [PMID: 37595566 PMCID: PMC10461130 DOI: 10.1016/j.cell.2023.07.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 03/03/2023] [Accepted: 07/17/2023] [Indexed: 08/20/2023]
Abstract
Mucosal-associated invariant T (MAIT) cells represent an abundant innate-like T cell subtype in the human liver. MAIT cells are assigned crucial roles in regulating immunity and inflammation, yet their role in liver cancer remains elusive. Here, we present a MAIT cell-centered profiling of hepatocellular carcinoma (HCC) using scRNA-seq, flow cytometry, and co-detection by indexing (CODEX) imaging of paired patient samples. These analyses highlight the heterogeneity and dysfunctionality of MAIT cells in HCC and their defective capacity to infiltrate liver tumors. Machine-learning tools were used to dissect the spatial cellular interaction network within the MAIT cell neighborhood. Co-localization in the adjacent liver and interaction between niche-occupying CSF1R+PD-L1+ tumor-associated macrophages (TAMs) and MAIT cells was identified as a key regulatory element of MAIT cell dysfunction. Perturbation of this cell-cell interaction in ex vivo co-culture studies using patient samples and murine models reinvigorated MAIT cell cytotoxicity. These studies suggest that aPD-1/aPD-L1 therapies target MAIT cells in HCC patients.
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Affiliation(s)
- Benjamin Ruf
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthias Bruhns
- Department of Internal Medicine I (Gastroenterology, Gastrointestinal Oncology, Hepatology, Infectious Diseases and Geriatrics), University Hospital Tübingen, Tübingen, Germany; Department of Computer Science, University of Tübingen, Tübingen, Germany; University of Tübingen, Interfaculty Institute for Biomedical Informatics (IBMI), Tübingen, Germany; M3 Research Center, University Hospital Tübingen, Tübingen, Germany
| | - Sepideh Babaei
- Department of Internal Medicine I (Gastroenterology, Gastrointestinal Oncology, Hepatology, Infectious Diseases and Geriatrics), University Hospital Tübingen, Tübingen, Germany; University of Tübingen, Interfaculty Institute for Biomedical Informatics (IBMI), Tübingen, Germany; M3 Research Center, University Hospital Tübingen, Tübingen, Germany
| | - Noemi Kedei
- Collaborative Protein Technology Resource, OSTR, Office of the Director, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lichun Ma
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Institutes of Health, National Cancer Institute, Bethesda, MD, USA
| | - Mahler Revsine
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Institutes of Health, National Cancer Institute, Bethesda, MD, USA
| | - Mohamed-Reda Benmebarek
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chi Ma
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bernd Heinrich
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Varun Subramanyam
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan Qi
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Simon Wabitsch
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Benjamin L Green
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kylynda C Bauer
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yuta Myojin
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Layla T Greten
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Justin D McCallen
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Patrick Huang
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rajiv Trehan
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xin Wang
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amran Nur
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dana Qiang Murphy Soika
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marie Pouzolles
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christine N Evans
- Genome Modification Core, Frederick National Lab for Cancer Research, Frederick, MD, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Lab for Cancer Research, Frederick, MD, USA
| | - David E Kleiner
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - William Telford
- Experimental Transplantation and Immunotherapy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kimia Dadkhah
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory, Bethesda, MD, USA
| | - Allison Ruchinskas
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory, Bethesda, MD, USA
| | - Merrill K Stovroff
- MedStar Georgetown Transplant Institute, MedStar Georgetown University Hospital and the Center for Translational Transplant Medicine, Georgetown University Medical Center, Washington, DC, USA
| | - Jiman Kang
- MedStar Georgetown Transplant Institute, MedStar Georgetown University Hospital and the Center for Translational Transplant Medicine, Georgetown University Medical Center, Washington, DC, USA
| | - Kesha Oza
- MedStar Georgetown Transplant Institute, MedStar Georgetown University Hospital and the Center for Translational Transplant Medicine, Georgetown University Medical Center, Washington, DC, USA
| | - Mathuros Ruchirawat
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, Thailand; Center of Excellence on Environmental Health and Toxicology, Office of the Higher Education Commission, Ministry of Education, Bangkok, Thailand
| | - Alexander Kroemer
- MedStar Georgetown Transplant Institute, MedStar Georgetown University Hospital and the Center for Translational Transplant Medicine, Georgetown University Medical Center, Washington, DC, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Institutes of Health, National Cancer Institute, Bethesda, MD, USA; NCI CCR Liver Cancer Program, National Institutes of Health, Bethesda, MD, USA
| | - Manfred Claassen
- Department of Internal Medicine I (Gastroenterology, Gastrointestinal Oncology, Hepatology, Infectious Diseases and Geriatrics), University Hospital Tübingen, Tübingen, Germany; Department of Computer Science, University of Tübingen, Tübingen, Germany; University of Tübingen, Interfaculty Institute for Biomedical Informatics (IBMI), Tübingen, Germany; M3 Research Center, University Hospital Tübingen, Tübingen, Germany
| | - Firouzeh Korangy
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tim F Greten
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; NCI CCR Liver Cancer Program, National Institutes of Health, Bethesda, MD, USA.
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5
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Negi H, Osei-Amponsa V, Ibrahim B, Evans CN, Sullenberger C, Loncarek J, Chari R, Walters KJ. An engineered cell line with a hRpn1-attached handle to isolate proteasomes. J Biol Chem 2023; 299:104948. [PMID: 37354974 PMCID: PMC10372910 DOI: 10.1016/j.jbc.2023.104948] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
Regulated protein degradation in eukaryotes is performed by the 26S proteasome, which contains a 19-subunit regulatory particle (RP) that binds, processes, and translocates substrates to a 28-subunit hollow core particle (CP) where proteolysis occurs. In addition to its intrinsic subunits, myriad proteins interact with the proteasome transiently, including factors that assist and/or regulate its degradative activities. Efforts to identify proteasome-interacting components and/or to solve its structure have relied on over-expression of a tagged plasmid, establishing stable cell lines, or laborious purification protocols to isolate native proteasomes from cells. Here, we describe an engineered human cell line, derived from colon cancer HCT116 cells, with a biotin handle on the RP subunit hRpn1/PSMD2 (proteasome 26S subunit, non-ATPase 2) for purification of 26S proteasomes. A 75-residue sequence from Propionibacterium shermanii that is biotinylated in mammalian cells was added following a tobacco etch virus protease cut site at the C terminus of hRpn1. We tested and found that 26S proteasomes can be isolated from this modified HCT116 cell line by using a simple purification protocol. More specifically, biotinylated proteasomes were purified from the cell lysates by using neutravidin agarose resin and released from the resin following incubation with tobacco etch virus protease. The purified proteasomes had equivalent activity in degrading a model ubiquitinated substrate, namely ubiquitinated p53, compared to commercially available bovine proteasomes that were purified by fractionation. In conclusion, advantages of this approach to obtain 26S proteasomes over others is the simple purification protocol and that all cellular proteins, including the tagged hRpn1 subunit, remain at endogenous stoichiometry.
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Affiliation(s)
- Hitendra Negi
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Vasty Osei-Amponsa
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Bishoy Ibrahim
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Christine N Evans
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Catherine Sullenberger
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Jadranka Loncarek
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.
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6
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Li J, Chen Z, Kim G, Luo J, Hori S, Wu C. Cathepsin W restrains peripheral regulatory T cells for mucosal immune quiescence. SCIENCE ADVANCES 2023; 9:eadf3924. [PMID: 37436991 DOI: 10.1126/sciadv.adf3924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
Peripheral regulatory T (pTreg) cells are a key T cell lineage for mucosal immune tolerance and anti-inflammatory responses, and interleukin-2 receptor (IL-2R) signaling is critical for Treg cell generation, expansion, and maintenance. The expression of IL-2R on pTreg cells is tightly regulated to ensure proper induction and function of pTreg cells without a clear molecular mechanism. We here demonstrate that Cathepsin W (CTSW), a cysteine proteinase highly induced in pTreg cells under transforming growth factor-β stimulation is essential for the restraint of pTreg cell differentiation in an intrinsic manner. Loss of CTSW results in elevated pTreg cell generation, protecting the animals from intestinal inflammation. Mechanistically, CTSW inhibits IL-2R signaling in pTreg cells by cytosolic interaction with and process of CD25, repressing signal transducer and activator of transcription 5 activation to restrain pTreg cell generation and maintenance. Hence, our data indicate that CTSW acts as a gatekeeper to calibrate pTreg cell differentiation and function for mucosal immune quiescence.
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Affiliation(s)
- Jian Li
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Zuojia Chen
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Girak Kim
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jialie Luo
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shohei Hori
- Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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7
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Radoua A, Pernon B, Pernet N, Jean C, Elmallah M, Guerrache A, Constantinescu AA, Hadj Hamou S, Devy J, Micheau O. ptARgenOM-A Flexible Vector For CRISPR/CAS9 Nonviral Delivery. SMALL METHODS 2023:e2300069. [PMID: 37156748 DOI: 10.1002/smtd.202300069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/11/2023] [Indexed: 05/10/2023]
Abstract
Viral-mediated delivery of the CRISPR-Cas9 system is one the most commonly used techniques to modify the genome of a cell, with the aim of analyzing the function of the targeted gene product. While these approaches are rather straightforward for membrane-bound proteins, they can be laborious for intracellular proteins, given that selection of full knockout (KO) cells often requires the amplification of single-cell clones. Moreover, viral-mediated delivery systems, besides the Cas9 and gRNA, lead to the integration of unwanted genetic material, such as antibiotic resistance genes, introducing experimental biases. Here, an alternative non-viral delivery approach is presented for CRISPR/Cas9, allowing efficient and flexible selection of KO polyclonal cells. This all-in-one mammalian CRISPR-Cas9 expression vector, ptARgenOM, encodes the gRNA and the Cas9 linked to a ribosomal skipping peptide sequence followed by the enhanced green fluorescent protein and the puromycin N-acetyltransferase, allowing for transient, expression-dependent selection and enrichment of isogenic KO cells. After evaluation using more than 12 distinct targets in 6 cell lines, ptARgenOM is found to be efficient in producing KO cells, reducing the time required to obtain a polyclonal isogenic cell line by 4-6 folds. Altogether ptARgenOM provides a simple, fast, and cost-effective delivery tool for genome editing.
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Affiliation(s)
- Abdelmnim Radoua
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- INSERM, Université de Bourgogne Franche-Comté (UBFC), UMR1231, LNC, Dijon, 21000, France
| | - Baptiste Pernon
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
| | - Nicolas Pernet
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- INSERM, Université de Bourgogne Franche-Comté (UBFC), UMR1231, LNC, Dijon, 21000, France
| | - Chloé Jean
- UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne (URCA), Reims, Cedex, 51687, France
- Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, UMR 7369 CNRS, Reims, 51687, France
| | - Mohammed Elmallah
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- Chemistry Department, Faculty of Science, Helwan University, Ain Helwan, Cairo, 11795, Egypt
| | - Abderrahmane Guerrache
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- INSERM, Université de Bourgogne Franche-Comté (UBFC), UMR1231, LNC, Dijon, 21000, France
| | | | - Sofiane Hadj Hamou
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
| | - Jérôme Devy
- UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne (URCA), Reims, Cedex, 51687, France
- Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, UMR 7369 CNRS, Reims, 51687, France
| | - Olivier Micheau
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- INSERM, Université de Bourgogne Franche-Comté (UBFC), UMR1231, LNC, Dijon, 21000, France
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8
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Sato G, Kuroda K. Overcoming the Limitations of CRISPR-Cas9 Systems in Saccharomyces cerevisiae: Off-Target Effects, Epigenome, and Mitochondrial Editing. Microorganisms 2023; 11:microorganisms11041040. [PMID: 37110464 PMCID: PMC10145089 DOI: 10.3390/microorganisms11041040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Modification of the genome of the yeast Saccharomyces cerevisiae has great potential for application in biological research and biotechnological advancements, and the CRISPR-Cas9 system has been increasingly employed for these purposes. The CRISPR-Cas9 system enables the precise and simultaneous modification of any genomic region of the yeast to a desired sequence by altering only a 20-nucleotide sequence within the guide RNA expression constructs. However, the conventional CRISPR-Cas9 system has several limitations. In this review, we describe the methods that were developed to overcome these limitations using yeast cells. We focus on three types of developments: reducing the frequency of unintended editing to both non-target and target sequences in the genome, inducing desired changes in the epigenetic state of the target region, and challenging the expansion of the CRISPR-Cas9 system to edit genomes within intracellular organelles such as mitochondria. These developments using yeast cells to overcome the limitations of the CRISPR-Cas9 system are a key factor driving the advancement of the field of genome editing.
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Affiliation(s)
- Genki Sato
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- Department of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
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9
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Chakraborty S, Kopitchinski N, Zuo Z, Eraso A, Awasthi P, Chari R, Mitra A, Tobias IC, Moorthy SD, Dale RK, Mitchell JA, Petros TJ, Rocha PP. Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness. Nat Genet 2023; 55:280-290. [PMID: 36717694 PMCID: PMC10758292 DOI: 10.1038/s41588-022-01295-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 12/20/2022] [Indexed: 01/31/2023]
Abstract
How enhancers activate their distal target promoters remains incompletely understood. Here we dissect how CTCF-mediated loops facilitate and restrict such regulatory interactions. Using an allelic series of mouse mutants, we show that CTCF is neither required for the interaction of the Sox2 gene with distal enhancers, nor for its expression. Insertion of various combinations of CTCF motifs, between Sox2 and its distal enhancers, generated boundaries with varying degrees of insulation that directly correlated with reduced transcriptional output. However, in both epiblast and neural tissues, enhancer contacts and transcriptional induction could not be fully abolished, and insertions failed to disrupt implantation and neurogenesis. In contrast, Sox2 expression was undetectable in the anterior foregut of mutants carrying the strongest boundaries, and these animals fully phenocopied loss of SOX2 in this tissue. We propose that enhancer clusters with a high density of regulatory activity can better overcome physical barriers to maintain faithful gene expression and phenotypic robustness.
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Affiliation(s)
- Shreeta Chakraborty
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Nina Kopitchinski
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Zhenyu Zuo
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Ariel Eraso
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Parirokh Awasthi
- Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD, USA
| | - Raj Chari
- Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD, USA
| | - Apratim Mitra
- Bioinformatics and Scientific Programming Core, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Ian C Tobias
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Sakthi D Moorthy
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Timothy J Petros
- Unit on Cellular and Molecular Neurodevelopment, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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10
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Wang D, Wu W, Callen E, Pavani R, Zolnerowich N, Kodali S, Zong D, Wong N, Noriega S, Nathan WJ, Matos-Rodrigues G, Chari R, Kruhlak MJ, Livak F, Ward M, Caldecott K, Di Stefano B, Nussenzweig A. Active DNA demethylation promotes cell fate specification and the DNA damage response. Science 2022; 378:983-989. [PMID: 36454826 PMCID: PMC10196940 DOI: 10.1126/science.add9838] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Neurons harbor high levels of single-strand DNA breaks (SSBs) that are targeted to neuronal enhancers, but the source of this endogenous damage remains unclear. Using two systems of postmitotic lineage specification-induced pluripotent stem cell-derived neurons and transdifferentiated macrophages-we show that thymidine DNA glycosylase (TDG)-driven excision of methylcytosines oxidized with ten-eleven translocation enzymes (TET) is a source of SSBs. Although macrophage differentiation favors short-patch base excision repair to fill in single-nucleotide gaps, neurons also frequently use the long-patch subpathway. Disrupting this gap-filling process using anti-neoplastic cytosine analogs triggers a DNA damage response and neuronal cell death, which is dependent on TDG. Thus, TET-mediated active DNA demethylation promotes endogenous DNA damage, a process that normally safeguards cell identity but can also provoke neurotoxicity after anticancer treatments.
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Affiliation(s)
- Dongpeng Wang
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Nicholas Zolnerowich
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Srikanth Kodali
- Stem Cells and Regenerative Medicine, Center for Cell and Gene Therapy, Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Santiago Noriega
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - William J. Nathan
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | | | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael J. Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ferenc Livak
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Michael Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Keith Caldecott
- Genome Damage and Stability Centre, University of Sussex, Falmer Brighton, UK
| | - Bruno Di Stefano
- Stem Cells and Regenerative Medicine, Center for Cell and Gene Therapy, Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
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11
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An Evolutionarily Conserved AU-Rich Element in the 3' Untranslated Region of a Transcript Misannotated as a Long Noncoding RNA Regulates RNA Stability. Mol Cell Biol 2022; 42:e0050521. [PMID: 35274990 DOI: 10.1128/mcb.00505-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the primary mechanisms of post-transcriptional gene regulation is the modulation of RNA stability. We recently discovered that LINC00675, a transcript annotated as a long noncoding RNA (lncRNA), is transcriptionally regulated by FOXA1 and encodes a highly conserved small protein that localizes to the endoplasmic reticulum, hence renamed as FORCP (FOXA1-regulated conserved small protein). Here, we show that the endogenous FORCP transcript is rapidly degraded and rendered unstable as a result of 3'UTR-mediated degradation. Surprisingly, although the FORCP transcript is a canonical nonsense-mediated decay (NMD) and microRNA (miRNA) target, we found that it is not degraded by NMD or miRNAs. Targeted deletion of an evolutionarily conserved region in the FORCP 3'UTR using CRISPR/Cas9 significantly increased the stability of the FORCP transcript. Interestingly, this region requires the presence of an immediate downstream 55-nt-long sequence for transcript stability regulation. Functionally, colorectal cancer cells lacking this conserved region expressed from the endogenous FORCP locus displayed decreased proliferation and clonogenicity. These data demonstrate that the FORCP transcript is destabilized via conserved elements within its 3'UTR and emphasize the need to interrogate the function of a given 3'UTR in its native context.
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12
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Lu X, Sabbasani VR, Osei-Amponsa V, Evans CN, King JC, Tarasov SG, Dyba M, Das S, Chan KC, Schwieters CD, Choudhari S, Fromont C, Zhao Y, Tran B, Chen X, Matsuo H, Andresson T, Chari R, Swenson RE, Tarasova NI, Walters KJ. Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma. Nat Commun 2021; 12:7318. [PMID: 34916494 PMCID: PMC8677766 DOI: 10.1038/s41467-021-27570-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Proteasome substrate receptor hRpn13 is a promising anti-cancer target. By integrated in silico and biophysical screening, we identified a chemical scaffold that binds hRpn13 with non-covalent interactions that mimic the proteasome and a weak electrophile for Michael addition. hRpn13 Pru domain binds proteasomes and ubiquitin whereas its DEUBAD domain binds deubiquitinating enzyme UCHL5. NMR revealed lead compound XL5 to interdigitate into a hydrophobic pocket created by lateral movement of a Pru β-hairpin with an exposed end for Proteolysis Targeting Chimeras (PROTACs). Implementing XL5-PROTACs as chemical probes identified a DEUBAD-lacking hRpn13 species (hRpn13Pru) present naturally with cell type-dependent abundance. XL5-PROTACs preferentially target hRpn13Pru, causing its ubiquitination. Gene-editing and rescue experiments established hRpn13 requirement for XL5-PROTAC-triggered apoptosis. These data establish hRpn13 as an anti-cancer target for multiple myeloma and introduce an hRpn13-targeting scaffold that can be optimized for preclinical trials against hRpn13Pru-producing cancer types.
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Affiliation(s)
- Xiuxiu Lu
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Venkata R Sabbasani
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vasty Osei-Amponsa
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Christine N Evans
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Julianna C King
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Sergey G Tarasov
- Biophysics Resource, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Marzena Dyba
- Biophysics Resource, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, 21702, USA
| | - King C Chan
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, 21702, USA
| | - Charles D Schwieters
- Computational Biomolecular Magnetic Resonance Core, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-5620, USA
| | - Sulbha Choudhari
- Sequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Caroline Fromont
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Yongmei Zhao
- Sequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Bao Tran
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Xiang Chen
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Hiroshi Matsuo
- Basic Science Program, Center for Structural Biology, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, 21702, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Rolf E Swenson
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nadya I Tarasova
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
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13
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Smith CE, Tsai YC, Liang YH, Khago D, Mariano J, Li J, Tarasov SG, Gergel E, Tsai B, Villaneuva M, Clapp ME, Magidson V, Chari R, Byrd RA, Ji X, Weissman AM. A structurally conserved site in AUP1 binds the E2 enzyme UBE2G2 and is essential for ER-associated degradation. PLoS Biol 2021; 19:e3001474. [PMID: 34879065 PMCID: PMC8699718 DOI: 10.1371/journal.pbio.3001474] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 12/23/2021] [Accepted: 11/05/2021] [Indexed: 12/22/2022] Open
Abstract
Endoplasmic reticulum-associated degradation (ERAD) is a protein quality control pathway of fundamental importance to cellular homeostasis. Although multiple ERAD pathways exist for targeting topologically distinct substrates, all pathways require substrate ubiquitination. Here, we characterize a key role for the UBE2G2 Binding Region (G2BR) of the ERAD accessory protein ancient ubiquitous protein 1 (AUP1) in ERAD pathways. This 27-amino acid (aa) region of AUP1 binds with high specificity and low nanomolar affinity to the backside of the ERAD ubiquitin-conjugating enzyme (E2) UBE2G2. The structure of the AUP1 G2BR (G2BRAUP1) in complex with UBE2G2 reveals an interface that includes a network of salt bridges, hydrogen bonds, and hydrophobic interactions essential for AUP1 function in cells. The G2BRAUP1 shares significant structural conservation with the G2BR found in the E3 ubiquitin ligase gp78 and in vitro can similarly allosterically activate ubiquitination in conjunction with ERAD E3s. In cells, AUP1 is uniquely required to maintain normal levels of UBE2G2; this is due to G2BRAUP1 binding to the E2 and preventing its rapid degradation. In addition, the G2BRAUP1 is required for both ER membrane recruitment of UBE2G2 and for its activation at the ER membrane. Thus, by binding to the backside of a critical ERAD E2, G2BRAUP1 plays multiple critical roles in ERAD.
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Affiliation(s)
- Christopher E. Smith
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Yien Che Tsai
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Yu-He Liang
- Center for Structural Biology, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Domarin Khago
- Center for Structural Biology, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Jennifer Mariano
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Jess Li
- Center for Structural Biology, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Sergey G. Tarasov
- Center for Structural Biology, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Emma Gergel
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Borong Tsai
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Matthew Villaneuva
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Michelle E. Clapp
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - R. Andrew Byrd
- Center for Structural Biology, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Xinhua Ji
- Center for Structural Biology, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Allan M. Weissman
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
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14
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Ruf B, Catania VV, Wabitsch S, Ma C, Diggs LP, Zhang Q, Heinrich B, Subramanyam V, Cui LL, Pouzolles M, Evans CN, Chari R, Sakai S, Oh S, Barry CE, Barber DL, Greten TF. Activating Mucosal-Associated Invariant T Cells Induces a Broad Antitumor Response. Cancer Immunol Res 2021; 9:1024-1034. [PMID: 34193462 DOI: 10.1158/2326-6066.cir-20-0925] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/31/2021] [Accepted: 06/24/2021] [Indexed: 02/06/2023]
Abstract
Mucosal-associated invariant T (MAIT) cells are MR1-restricted innate-like T cells that recognize non-peptide antigens including riboflavin derivates. Although in vitro-activated MAIT cells show antitumor activity, the in vivo role of MAIT cells in cancer is still unclear. Here, we have shown that MAIT cells have antitumor function in vivo when activated by a combination of the synthetic riboflavin synthesis pathway-derived antigen 5-OP-RU [5-(2-oxopropylideneamino)-6-D-ribitylaminouracil] and the Toll-like receptor 9 (TLR9) agonist CpG. Coadministration of 5-OP-RU and CpG induced strong systemic in vivo expansion and activation of MAIT cells with high CD69 expression, pronounced effector memory phenotype, and upregulated levels of effector molecules including IFNγ, granzyme B, and perforin. Activated and expanded MAITs induced a potent and broad antitumor immune response in murine models of liver metastasis and hepatocellular carcinoma, lung metastasis, and subcutaneous tumors in two different mouse strains. Such tumor inhibition was absent in MAIT-deficient Mr1 -/- mice. CRISPR/Cas9-mediated MR1 knockout in tumor cells did not affect efficacy of this MAIT-directed immunotherapy, pointing toward an indirect mechanism of action. Our findings suggest that MAIT cells are an attractive target for cancer immunotherapy.See related Spotlight by Lantz, p. 996.
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Affiliation(s)
- Benjamin Ruf
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Vanessa V Catania
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Simon Wabitsch
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Chi Ma
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Laurence P Diggs
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Qianfei Zhang
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Bernd Heinrich
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Varun Subramanyam
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Linda L Cui
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Marie Pouzolles
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Christine N Evans
- Genome Modification Core, Frederick National Lab for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Raj Chari
- Genome Modification Core, Frederick National Lab for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Shunsuke Sakai
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Daniel L Barber
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Tim F Greten
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland. .,NCI CCR Liver Cancer Program, National Institutes of Health, Bethesda, Maryland
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15
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Abstract
The use of genome editing tools is expanding our understanding of various human diseases by providing insight into gene-disease interactions. Despite the recognized role of toxicants in the development of human health issues and conditions, there is currently limited characterization of their mechanisms of action, and the application of CRISPR-based genome editing to the study of toxicants could help in the identification of novel gene-environment interactions. CRISPR-based functional screens enable identification of cellular mechanisms fundamental for response and susceptibility to a given toxicant. The aim of this review is to inform future directions in the application of CRISPR technologies in toxicological studies. We review and compare different types of CRISPR-based methods including pooled, anchored, combinatorial, and perturb-sequencing screens in vitro, in addition to pooled screenings in model organisms. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
- Amin Sobh
- Department of Medicine, University of Florida Health Cancer Center, University of Florida, Gainesville, Florida
| | - Max Russo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Christopher D Vulpe
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida
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16
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The dystonia gene THAP1 controls DNA double-strand break repair choice. Mol Cell 2021; 81:2611-2624.e10. [PMID: 33857404 DOI: 10.1016/j.molcel.2021.03.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 02/01/2021] [Accepted: 03/19/2021] [Indexed: 12/26/2022]
Abstract
The Shieldin complex shields double-strand DNA breaks (DSBs) from nucleolytic resection. Curiously, the penultimate Shieldin component, SHLD1, is one of the least abundant mammalian proteins. Here, we report that the transcription factors THAP1, YY1, and HCF1 bind directly to the SHLD1 promoter, where they cooperatively maintain the low basal expression of SHLD1, thereby ensuring a proper balance between end protection and resection during DSB repair. The loss of THAP1-dependent SHLD1 expression confers cross-resistance to poly (ADP-ribose) polymerase (PARP) inhibitor and cisplatin in BRCA1-deficient cells and shorter progression-free survival in ovarian cancer patients. Moreover, the embryonic lethality and PARPi sensitivity of BRCA1-deficient mice is rescued by ablation of SHLD1. Our study uncovers a transcriptional network that directly controls DSB repair choice and suggests a potential link between DNA damage and pathogenic THAP1 mutations, found in patients with the neurodevelopmental movement disorder adult-onset torsion dystonia type 6.
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