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Niedziółka SM, Datta S, Uśpieński T, Baran B, Skarżyńska W, Humke EW, Rohatgi R, Niewiadomski P. The exocyst complex and intracellular vesicles mediate soluble protein trafficking to the primary cilium. Commun Biol 2024; 7:213. [PMID: 38378792 PMCID: PMC10879184 DOI: 10.1038/s42003-024-05817-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 01/15/2024] [Indexed: 02/22/2024] Open
Abstract
The efficient transport of proteins into the primary cilium is a crucial step for many signaling pathways. Dysfunction of this process can lead to the disruption of signaling cascades or cilium assembly, resulting in developmental disorders and cancer. Previous studies on the protein delivery to the cilium were mostly focused on the membrane-embedded receptors. In contrast, how soluble proteins are delivered into the cilium is poorly understood. In our work, we identify the exocyst complex as a key player in the ciliary trafficking of soluble Gli transcription factors. In line with the known function of the exocyst in intracellular vesicle transport, we demonstrate that soluble proteins, including Gli2/3 and Lkb1, can use the endosome recycling machinery for their delivery to the primary cilium. Finally, we identify GTPases: Rab14, Rab18, Rab23, and Arf4 that are involved in vesicle-mediated Gli protein ciliary trafficking. Our data pave the way for a better understanding of ciliary transport and uncover transport mechanisms inside the cell.
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Affiliation(s)
- S M Niedziółka
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - S Datta
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - T Uśpieński
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - B Baran
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - W Skarżyńska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - E W Humke
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- IGM Biosciences, Inc, Mountain View, CA, USA
| | - R Rohatgi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - P Niewiadomski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.
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Baran B, Kosieradzka K, Skarzynska W, Niewiadomski P. MRCKα/β positively regulates Gli protein activity. Cell Signal 2023; 107:110666. [PMID: 37019250 DOI: 10.1016/j.cellsig.2023.110666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023]
Abstract
Posttranslational modifications (PTMs) are key regulatory events for the majority of signaling pathways. Transcription factors are often phosphorylated on multiple residues, which regulates their trafficking, stability, or transcriptional activity. Gli proteins, transcription factors that respond to the Hedgehog pathway, are regulated by phosphorylation, but the sites and the kinases involved have been only partially described. We identified three novel kinases: MRCKα, MRCKβ, and MAP4K5 which physically interact with Gli proteins and directly phosphorylate Gli2 on multiple sites. We established that MRCKα/β kinases regulate Gli proteins, which impacts the transcriptional output of the Hedgehog pathway. We showed that double knockout of MRCKα/β affects Gli2 ciliary and nuclear localization and reduces Gli2 binding to the Gli1 promoter. Our research fills a critical gap in our understanding of the regulation of Gli proteins by describing their activation mechanisms through phosphorylation.
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Thankam FG, Sanchez DJ, Agrawal DK. Design of the lentivirus-driven sustained LR12 delivery system for TREM-1 inhibition for palliating atherosclerosis. Mol Cell Biochem 2022; 477:701-710. [PMID: 35001222 DOI: 10.1007/s11010-021-04321-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/29/2021] [Indexed: 12/17/2022]
Abstract
Triggering Receptor Expressed on Myeloid cells-1 (TREM-1) has been a potential target in the management of pathophysiology and clinical sequelae of atherosclerosis. LR12 peptide effectively blocks ligand-TREM-1 interaction; however, the short half-life of LR12 is a major hurdle in its translational application in atherosclerosis management warranting new methods for sustained bioavailability in clinical applications. The present study reports a novel method of packing the coding sequence of LR12 in a lentiviral system to ensure a sustained expression and bioavailability for effective TREM-1 inhibition. Lentivirus vector systems (LV-LR12 and LV-SP) for the expression of LR12 peptide and SP (scrambled peptide) were successfully designed, constructed, and tested in vitro in smooth muscle cells (SMCs). Viral amounts obtained were 703.6 ± 145.12 and 609.3 ± 145.93 ng/ml p24 for LV-LR12 and LV-SP, respectively which correspond to ~ 107 IFU/ml for both vectors. Dot blot assay revealed significantly increased expression of LR12-FLAG and SP-FLAG in 125 μg total protein which was doubled in 250 μg protein with respect to un-transduced SMCs suggesting the sustained release of LR12/SP as confirmed by ELISA. Cellular expression of LR12-FLAG and SP-FLAG displayed 8.44-fold and 7.55-fold increase, respectively compared to the control SMCs. The findings demonstrated a promising strategy for packing the LR12 coding sequence in lentiviral vector for TREM-1 inhibition for the management of atherosclerosis and other inflammatory diseases.
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Affiliation(s)
- Finosh G Thankam
- Department of Translational Research, Western University of Health Sciences, 309 E. Second Street, Pomona, CA, 91766, USA
| | - David J Sanchez
- Department of Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Devendra K Agrawal
- Department of Translational Research, Western University of Health Sciences, 309 E. Second Street, Pomona, CA, 91766, USA.
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Vazquez N, Sanchez L, Marks R, Martinez E, Fanniel V, Lopez A, Salinas A, Flores I, Hirschmann J, Gilkerson R, Schuenzel E, Dearth R, Halaby R, Innis-Whitehouse W, Keniry M. A protocol for custom CRISPR Cas9 donor vector construction to truncate genes in mammalian cells using pcDNA3 backbone. BMC Mol Biol 2018; 19:3. [PMID: 29540148 PMCID: PMC5853148 DOI: 10.1186/s12867-018-0105-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/06/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided adaptive immune systems are found in prokaryotes to defend cells from foreign DNA. CRISPR Cas9 systems have been modified and employed as genome editing tools in wide ranging organisms. Here, we provide a detailed protocol to truncate genes in mammalian cells using CRISPR Cas9 editing. We describe custom donor vector construction using Gibson assembly with the commonly utilized pcDNA3 vector as the backbone. RESULTS We describe a step-by-step method to truncate genes of interest in mammalian cell lines using custom-made donor vectors. Our method employs 2 guide RNAs, mutant Cas9D10A nickase (Cas9 = CRISPR associated sequence 9), and a custom-made donor vector for homologous recombination to precisely truncate a gene of interest with a selectable neomycin resistance cassette (NPTII: Neomycin Phosphotransferase II). We provide a detailed protocol on how to design and construct a custom donor vector using Gibson assembly (and the commonly utilized pcDNA3 vector as the backbone) allowing researchers to obtain specific gene modifications of interest (gene truncation, gene deletion, epitope tagging or knock-in mutation). Selection of mutants in mammalian cell lines with G418 (Geneticin) combined with several screening methods: western blot analysis, polymerase chain reaction, and Sanger sequencing resulted in streamlined mutant isolation. Proof of principle experiments were done in several mammalian cell lines. CONCLUSIONS Here we describe a detailed protocol to employ CRISPR Cas9 genome editing to truncate genes of interest using the commonly employed expression vector pcDNA3 as the backbone for the donor vector. Providing a detailed protocol for custom donor vector design and construction will enable researchers to develop unique genome editing tools. To date, detailed protocols for CRISPR Cas9 custom donor vector construction are limited (Lee et al. in Sci Rep 5:8572, 2015; Ma et al. in Sci Rep 4:4489, 2014). Custom donor vectors are commercially available, but can be expensive. Our goal is to share this protocol to aid researchers in performing genetic investigations that require custom donor vectors for specialized applications (specific gene truncations, knock-in mutations, and epitope tagging applications).
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Affiliation(s)
- Neftali Vazquez
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Lilia Sanchez
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Rebecca Marks
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Eduardo Martinez
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Victor Fanniel
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Alma Lopez
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Andrea Salinas
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Itzel Flores
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Jesse Hirschmann
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Robert Gilkerson
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Erin Schuenzel
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Robert Dearth
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Reginald Halaby
- Department of Biology, Montclair State University, 1 Normal Ave., Montclair, NJ 07043 USA
| | - Wendy Innis-Whitehouse
- School of Medicine, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
| | - Megan Keniry
- Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539 USA
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Guo T, Ochi T, Nakatsugawa M, Kagoya Y, Anczurowski M, Wang CH, Rahman MA, Saso K, Butler MO, Hirano N. Generating De Novo Antigen-specific Human T Cell Receptors by Retroviral Transduction of Centric Hemichain. J Vis Exp 2016. [PMID: 27805596 DOI: 10.3791/54697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
T cell receptors (TCRs) are used clinically to direct the specificity of T cells to target tumors as a promising modality of immunotherapy. Therefore, cloning TCRs specific for various tumor-associated antigens has been the goal of many studies. To elicit an effective T cell response, the TCR must recognize the target antigen with optimal affinity. However, cloning such TCRs has been a challenge and many available TCRs possess sub-optimal affinity for the cognate antigen. In this protocol, we describe a method of cloning de novo high affinity antigen-specific TCRs using existing TCRs by exploiting hemichain centricity. It is known that for some TCRs, each TCRα or TCRβ hemichain do not contribute equally to antigen recognition, and the dominant hemichain is referred to as the centric hemichain. We have shown that by pairing the centric hemichain with counter-chains differing from the original counter-chain, we are able to maintain the antigen specificity, while modulating its interaction strength for the cognate antigen. Thus, the therapeutic potential of a given TCR can be improved by optimizing the pairing between the centric and counter hemichains.
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Affiliation(s)
- Tingxi Guo
- Department of Immunology, University of Toronto; Princess Margaret Cancer Centre, University Health Network
| | - Toshiki Ochi
- Princess Margaret Cancer Centre, University Health Network
| | | | - Yuki Kagoya
- Princess Margaret Cancer Centre, University Health Network
| | - Mark Anczurowski
- Department of Immunology, University of Toronto; Princess Margaret Cancer Centre, University Health Network
| | - Chung-Hsi Wang
- Department of Immunology, University of Toronto; Princess Margaret Cancer Centre, University Health Network
| | | | - Kayoko Saso
- Princess Margaret Cancer Centre, University Health Network
| | - Marcus O Butler
- Department of Immunology, University of Toronto; Princess Margaret Cancer Centre, University Health Network
| | - Naoto Hirano
- Department of Immunology, University of Toronto; Princess Margaret Cancer Centre, University Health Network;
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