MIPS Molecular Imaging Program at Stanford

Bioengineering/Radiology 222B - Winter 2012
Chemistry of Molecular Probes for Imaging in Living Subjects

Course Syllabus

CLASSES: Mondays & Fridays 9-10:50 AM, Alway M112

Week Monday Instructor Friday Instructor
1 1/9 Cox-2 as a molecular target for cancer imaging: Development of PET, SPECT and optical probes
L. Marnett
Lecture notes
1/13 PET/SPECT Radiochemistry I: Introduction and General Radiochemistry
F. Chin
Lecture notes

Molecular Imaging: Principles and Practice Chapters 20, 21, 29

2 1/16 School holiday: no class 1/20 PET/SPECT Radiochemistry II: Research and Clinical Applications
F. Chin
Lecture notes

Molecular Imaging: Principles and Practice Chapters 20, 21, 29

3 1/23 Apoptosis or angiogenesis imaging
F. Blankenberg
Lecture notes

Blankenberg F. Multimodality Molecular Imaging of Apoptosis in Oncology. AJR 2011:197.
Blankenberg F. Role of Radionuclide Imaging in Trials of Antiangiogenic Therapy. Academic Radiology 2000;7(10).
Colamussi P. New Insights on Flow-Independent Mechanisms of 99mTcHMpAO Retention in Nervous Tissue: In Vitro Study. JNM 1999;40(9).
Enns GM. Initial experience in the treatment of inherited mitochondrial disease with EPI-743. Molecular Genetics and Metabolism 2012:105.
Neirinckx R. Technetium-99m d,l-HM-PAO: A New Rathopharmaceutical for SPECT Imaging of Regional Cerebral Blood Perfusion. JNM 1987:28(2).
Smith C. Transmembrane voltage regulates binding of annexin V and lactadherin to cells with exposed phosphatidylserine. BMC Biochem 2009;10(5).
Shrader W. α-Tocotrienol quinone modulates oxidative stress response and the biochemistry of aging. Bioorganic & Medicinal Chemistry Letters 2011:21.
Tait J. Improved Detection of Cell Death In Vivo with Annexin V Radiolabeled by Site-Specific Methods. JNM 2006:47(9).

1/27 Peptide and Protein Probes for PET Imaging
M. Namavari
Lecture notes

Cheng Z. Small-animal PET imaging of human epidermal growth factor receptor type 2 expression with site-specific 18F-labeled protein scaffold molecules. JNM 2008;49(5).
Cheng Z. 64Cu-labeled affibody molecules for imaging of HER2 expressing tumors. MIB 2010;12(3).
Namavari M. A novel method for direct site-specific radiolabeling of peptides using [18F]FDG. Bioconjug Chem. 2009;20(3).
Namavari M. Direct site-specific radiolabeling of an Affibody protein with 4-[18F]fluorobenzaldehyde via oxime chemistry. MIB 2008;10(4).
Miao Z. A novel 18F-labeled two-helix scaffold protein for PET imaging of HER2-positive tumor. EJNM 2011;38(11).

4 1/30 Hyperpolarized MRS
S. Bohndiek
Lecture notes

Ardenkjaer-Larsen JH. Increase in signal-to-noise ratio of >10,000 times in liquid-state NMR. PNAS 2003:100(18).
Gallagher FA. Hyperpolarized 13C MRI and PET: In Vivo Tumor Biochemistry. JNM 2011:52(9).
Kurhanewicz J. Analysis of Cancer Metabolism by Imaging Hyperpolarized Nuclei: Prospects for Translation to Clinical Research. Neoplasia 2011:13(2).

2/3 MR probes and reporter genes
K. Ziv
Lecture notes

Cohen B. MRI detection of transcriptional regulation of gene expression in transgenic mice. Nature Med 2007;13(4):498-503.
Gilad AA. MRI Reporter Genes. JNM 2008;49(12):1905-8.
Weissleder R. Molecular Imaging. Radiology 2001;219:316–333.

5 2/6 MR Probes and Particles
B. Rutt
Lecture notes 1
Lecture notes 2

Corot C. Recent advances in iron oxide nanocrystal technology for medical imaging. Adv Drug Del Revs 2006:58;1471–1504.
Gazdzinski LM. Stem Cell Labeling for Delivery and Tracking Using Non-invasive Imaging. MRI Basics and Principles for Cellular Imaging. 2011.
Lee ESM. Magnetic Resonance Tracking of Stem Cells with Iron Oxide Particles. Intracellular Delivery: Fundamentals and Applications, Fundamental Biomedical Technologies. 2011.

2/10 Imaging Protein-Protein Interactions
R. Paulmurugan
Lecture notes 1
Lecture notes 2

Massoud T. Reporter gene imaging of protein–protein interactions in living subjects. Cur Ops in Biotech 2007;18.
Massoud T. Molecular Imaging of Protein-Protein Interactions. Molecular Imaging: Principles & Practice. 2010.
Paulmurugan R. An intramolecular folding sensor for imaging estrogen receptor–ligand interactions. PNAS 2006;103(43).
Paulmurugan R. In Vitro and in Vivo Molecular Imaging of Estrogen Receptor α and β Homo- and Heterodimerization: Exploration of New Modes of Receptor Regulation. Mol Endocrinol 2011;25(12).
Paulmurugan R. Noninvasive imaging of protein-protein interactions in living subjects by using reporter protein complementation and reconstitution strategies. PNAS 2002;99(24).
Ray P. Noninvasive quantitative imaging of protein–protein interactions in living subjects. PNAS 2002;99(5).
Serebriiskii H. Two-Hybrid Protein–Protein Interactions. Encyclopedia of Biological Chemistry, Vol 4. 2004.

6 2/13 GFP from the protein's perspective: excited state dynamics and split GFP
S. Boxer
Lecture notes

Chemical Society Reviews - GFP
Chudakov DM. Fluorescent proteins as a toolkit for in vivo imaging. Trends Biotechnol. 2005;23(12):605-13.
Miyawaki A. Fluorescence imaging of physiological activity in complex systems using GFP-based probes. Curr Opin Neurobiol. 2003;13(5):591-6.
Pakhomov AA. GFP family: structural insights into spectral tuning. Chem Biol. 2008;15(8):755-64.

2/17 Fluorophores and Biosensors Built from DNA
E. Kool
Lecture notes

Dai N. Protease probes built from DNA: multispectral fluorescent DNA-peptide conjugates as caspase chemosensors. Angew Chem Int Ed Engl. 2011;50(22).
Koo CK. Fluorescent DNA chemosensors: identification of bacterial species by their volatile metabolites. Chem Commun (Camb). 2011;47(41).
Teo YN. Polyfluorophores on a DNA backbone: a multicolor set of labels excited at one wavelength. J Am Chem Soc. 2009;131(11).

7 2/20 School holiday: no class 2/24 Activtable probes for molecular imaging
J. Rao
Lecture notes

Razgulin A. Strategies for in vivo imaging of enzyme activity: an overview and recent advances. Chem Soc Rev. 2011;40(7).

8 2/27 Protease Targets for Imaging
M. Bogyo
Lecture notes

Blum G. Noninvasive optical imaging of cysteine protease activity using fluorescently quenched activity-based probes. Nat Chem Biol. 2007;3(10).
Edgington LE. Noninvasive optical imaging of apoptosis by caspase-targeted activity-based probes. Nat Med. 2009;15(8).
Jiang T. Tumor imaging by means of proteolytic activation of cell-penetrating peptides. PNAS 2009;101(51).
Watzke A. Selective activity-based probes for cysteine cathepsins. Angew Chem Int Ed Engl. 2008;47(2).
Weissleder R. In vivo imaging of tumors with protease-activated near-infrared fluorescent probes. Nat Biotechnol. 1999;17(4).

3/2 Contrast and Contrast Agents in X-ray Imaging
T. Graves
Lecture notes
9 3/5 Chemical Probes for Ultrasound and Photoacoustic Imaging
J. Levi
Lecture notes

Dayton PA. Molecular ultrasound imaging using microbubble contrast agents. Front Biosci. 2007;12.
Kim C. In vivo photoacoustic tomography of chemicals: high-resolution functional and molecular optical imaging at new depths. Chem Rev. 2010;110(5).
Klibanov AL. Ligand-carrying gas-filled microbubbles: ultrasound contrast agents for targeted molecular imaging. Bioconjug Chem. 2005;16(1).
Ntziachristos V. Molecular imaging by means of multispectral optoacoustic tomography (MSOT). Chem Rev. 2010;110(5).

3/9 Discovery and Engineering of Peptide and Protein Molecular Imaging Agents using Display Technology
F. Cochran
Lecture notes

Moore S. Cell Surface Display Systems for Protein Engineering. Protein Engineering and Design.
Cochran F. Phage display and molecular imaging: expanding fields of vision in living subjects. Biotechnology and Genetic Engineering Reviews 2010;27:57-94.

10 3/12 Production and Characterization of Engineered Peptide and Protein Molecular Imaging Agents
F. Cochran
Lecture notes

Brinkley M. A brief survey of methods for preparing protein conjugates with dyes, haptens, and cross-linking reagents. Bioconjug Chem. 1992;3(1).
Li K. Chemical modification of M13 bacteriophage and its application in cancer cell imaging. Bioconjug Chem. 2010;21(7).

3/16 The Chemistry of Molecular Probes for Imaging in Living Systems: Crossing Biological Barriers
P. Wender
Lecture notes
Final Presentations
During our allocated Final Exam time
LK 101
Monday, March 19th from 8:30-11:30am

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