Preloader

Computationally designed dual-color MRI reporters for noninvasive imaging of transgene expression

  • 1.

    Tsien, R. Y. Constructing and exploiting the fluorescent protein paintbox (Nobel Lecture). Angew. Chem. Int. Ed. Engl. 48, 5612–5626 (2009).

    CAS 
    PubMed 

    Google Scholar 

  • 2.

    Chung, K. et al. Structural and molecular interrogation of intact biological systems. Nature 497, 332–337 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 3.

    Genove, G., DeMarco, U., Xu, H., Goins, W. F. & Ahrens, E. T. A new transgene reporter for in vivo magnetic resonance imaging. Nat. Med. 11, 450–454 (2005).

    CAS 
    PubMed 

    Google Scholar 

  • 4.

    Cohen, B. et al. MRI detection of transcriptional regulation of gene expression in transgenic mice. Nat. Med. 13, 498–503 (2007).

    CAS 
    PubMed 

    Google Scholar 

  • 5.

    Schilling, F. et al. MRI measurements of reporter-mediated increases in transmembrane water exchange enable detection of a gene reporter. Nat. Biotechnol. 35, 75–80 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • 6.

    Mukherjee, A., Wu, D., Davis, H. C. & Shapiro, M. G. Non-invasive imaging using reporter genes altering cellular water permeability. Nat. Commun. 7, 13891 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 7.

    Gilad, A. A. et al. Artificial reporter gene providing MRI contrast based on proton exchange. Nat. Biotechnol. 25, 217–219 (2007).

    CAS 
    PubMed 

    Google Scholar 

  • 8.

    Patrick, P. S. et al. Dual-modality gene reporter for in vivo imaging. Proc. Natl Acad. Sci. USA 111, 415–420 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • 9.

    Bar-Shir, A. et al. Transforming thymidine into a magnetic resonance imaging probe for monitoring gene expression. J. Am. Chem. Soc. 135, 1617–1624 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 10.

    Bartelle, B. B., Szulc, K. U., Suero-Abreu, G. A., Rodriguez, J. J. & Turnbull, D. H. Divalent metal transporter, DMT1: a novel MRI reporter protein. Magn. Reson. Med. 70, 842–850 (2013).

    PubMed 

    Google Scholar 

  • 11.

    Tannous, B. A. et al. Metabolic biotinylation of cell surface receptors for in vivo imaging. Nat. Methods 3, 391–396 (2006).

    CAS 
    PubMed 

    Google Scholar 

  • 12.

    Lu, G. J. et al. Acoustically modulated magnetic resonance imaging of gas-filled protein nanostructures. Nat. Mater. 17, 456–463 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 13.

    Mizushima, R. et al. Multiplexed (129)Xe HyperCEST MRI detection of genetically reconstituted bacterial protein nanoparticles in human cancer cells. Contrast Media Mol. Imaging 2020, 5425934 (2020).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 14.

    Shapiro, M. G. et al. Genetically encoded reporters for hyperpolarized xenon magnetic resonance imaging. Nat. Chem. 6, 629–634 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • 15.

    Shaner, N. C. et al. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 22, 1567–1572 (2004).

    CAS 
    PubMed 

    Google Scholar 

  • 16.

    McMahon, M. T. et al. New ‘multicolor’ polypeptide diamagnetic chemical exchange saturation transfer (DIACEST) contrast agents for MRI. Magn. Reson. Med. 60, 803–812 (2008).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 17.

    Liu, G. et al. In vivo multicolor molecular MR imaging using diamagnetic chemical exchange saturation transfer liposomes. Magn. Reson. Med. 67, 1106–1113 (2012).

    CAS 
    PubMed 

    Google Scholar 

  • 18.

    Johansson, M., van Rompay, A. R., Degreve, B., Balzarini, J. & Karlsson, A. Cloning and characterization of the multisubstrate deoxyribonucleoside kinase of Drosophila melanogaster. J. Biol. Chem. 274, 23814–23819 (1999).

    CAS 
    PubMed 

    Google Scholar 

  • 19.

    Black, M. E., Newcomb, T. G., Wilson, H. M. & Loeb, L. A. Creation of drug-specific herpes simplex virus type 1 thymidine kinase mutants for gene therapy. Proc. Natl Acad. Sci. USA 93, 3525–3529 (1996).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 20.

    Bar-Shir, A. et al. Quantification and tracking of genetically engineered dendritic cells for studying immunotherapy. Magn. Reson. Med. 79, 1010–1019 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • 21.

    Bar-Shir, A., Liu, G., Greenberg, M. M., Bulte, J. W. & Gilad, A. A. Synthesis of a probe for monitoring HSV1-tk reporter gene expression using chemical exchange saturation transfer MRI. Nat. Protoc. 8, 2380–2391 (2013).

    CAS 
    PubMed 

    Google Scholar 

  • 22.

    Arner, E. S. & Eriksson, S. Mammalian deoxyribonucleoside kinases. Pharmacol. Ther. 67, 155–186 (1995).

    CAS 
    PubMed 

    Google Scholar 

  • 23.

    Gambhir, S. S. et al. A mutant herpes simplex virus type 1 thymidine kinase reporter gene shows improved sensitivity for imaging reporter gene expression with positron emission tomography. Proc. Natl Acad. Sci. USA 97, 2785–2790 (2000).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 24.

    Tjuvajev, J. G. et al. Imaging the expression of transfected genes in vivo. Cancer Res. 55, 6126–6132 (1995).

    CAS 
    PubMed 

    Google Scholar 

  • 25.

    Likar, Y. et al. A new pyrimidine-specific reporter gene: a mutated human deoxycytidine kinase suitable for PET during treatment with acycloguanosine-based cytotoxic drugs. J. Nucl. Med. 51, 1395–1403 (2010).

    CAS 
    PubMed 

    Google Scholar 

  • 26.

    Liu, L., Li, Y., Liotta, D. & Lutz, S. Directed evolution of an orthogonal nucleoside analog kinase via fluorescence-activated cell sorting. Nucleic Acids Res. 37, 4472–4481 (2009).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 27.

    Goldenzweig, A. et al. Automated structure- and sequence-based design of proteins for high bacterial expression and stability. Mol Cell 63, 337–346 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 28.

    Meier, S. et al. Non-invasive detection of adeno-associated viral gene transfer using a genetically encoded CEST-MRI reporter gene in the murine heart. Sci. Rep. 8, 4638 (2018).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 29.

    Villano, D. et al. A fast multislice sequence for 3D MRI-CEST pH imaging. Magn. Reson. Med. 85, 1335–1349 (2021).

    CAS 
    PubMed 

    Google Scholar 

  • 30.

    Cohen, O., Huang, S., McMahon, M. T., Rosen, M. S. & Farrar, C. T. Rapid and quantitative chemical exchange saturation transfer (CEST) imaging with magnetic resonance fingerprinting (MRF). Magn. Reson. Med. 80, 2449–2463 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 31.

    Basser, P. J., Pajevic, S., Pierpaoli, C., Duda, J. & Aldroubi, A. In vivo fiber tractography using DT-MRI data. Magn. Reson. Med. 44, 625–632 (2000).

    CAS 
    PubMed 

    Google Scholar 

  • 32.

    Ogawa, S., Lee, T. M., Kay, A. R. & Tank, D. W. Brain magnetic resonance imaging with contrast dependent on blood oxygenation. Proc. Natl Acad. Sci. USA 87, 9868–9872 (1990).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 33.

    Lee, T., Cai, L. X., Lelyveld, V. S., Hai, A. & Jasanoff, A. Molecular-level functional magnetic resonance imaging of dopaminergic signaling. Science 344, 533–535 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • 34.

    Rodrigues, T. B. et al. Magnetic resonance imaging of tumor glycolysis using hyperpolarized 13C-labeled glucose. Nat. Med. 20, 93–97 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • 35.

    Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 36.

    Frey, S. & Gorlich, D. A new set of highly efficient, tag-cleaving proteases for purifying recombinant proteins. J. Chromatogr. A. 1337, 95–105 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • 37.

    Peleg, Y. & Unger, T. Application of high-throughput methodologies to the expression of recombinant proteins in E. coli. Methods Mol. Biol. 426, 197–208 (2008).

    CAS 
    PubMed 

    Google Scholar 

  • 38.

    Unger, T., Jacobovitch, Y., Dantes, A., Bernheim, R. & Peleg, Y. Applications of the restriction free (RF) cloning procedure for molecular manipulations and protein expression. J. Struct. Biol. 172, 34–44 (2010).

    CAS 
    PubMed 

    Google Scholar 

  • 39.

    Lee, J. S. et al. Urea cycle dysregulation generates clinically relevant genomic and biochemical signatures. Cell 174, 1559–1570 e1522 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 40.

    Kim, M., Gillen, J., Landman, B. A., Zhou, J. & van Zijl, P. C. M. Water saturation shift referencing (WASSR) for chemical exchange saturation transfer (CEST) experiments. Magn. Reson. Med. 61, 1441–1450 (2009).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 41.

    Liu, G., Song, X., Chan, K. W. & McMahon, M. T. Nuts and bolts of chemical exchange saturation transfer MRI. NMR Biomed. 26, 810–828 (2013).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 42.

    Liu, G., Li, Y. & Pagel, M. D. Design and characterization of a new irreversible responsive PARACEST MRI contrast agent that detects nitric oxide. Magn. Reson. Med. 58, 1249–1256 (2007).

    CAS 
    PubMed 

    Google Scholar 

  • 43.

    Morales, J. L. & Nocedal, J. Remark on ‘Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound constrained optimization’. ACM Trans. Math. Softw. 38, 1–4 (2011).

    Google Scholar 

  • 44.

    Woessner, D. E., Zhang, S., Merritt, M. E. & Sherry, A. D. Numerical solution of the Bloch equations provides insights into the optimum design of PARACEST agents for MRI. Magn. Reson. Med. 53, 790–799 (2005).

    CAS 
    PubMed 

    Google Scholar 

  • 45.

    Glunde, K., Jie, C. & Bhujwalla, Z. M. Molecular causes of the aberrant choline phospholipid metabolism in breast cancer. Cancer Res. 64, 4270–4276 (2004).

    CAS 
    PubMed 

    Google Scholar 

  • Source link