Detecting Spatial and Temporal Distributions of Lipids And
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DETECTING SPATIAL AND TEMPORAL DISTRIBUTIONS OF LIPIDS AND PROTEINS DURING EMBRYO IMPLANTATION BY MALDI IMAGING MASS SPECTROMETRY By Kristin Elizabeth Burnum Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biochemistry December, 2008 Approved: Richard M. Caprioli H. Alex Brown Daniel C. Liebler Jennifer A. Pietenpol Michael R. Waterman This work is dedicated to my parents, Kathy and Steve, who gave me everything ii ACKNOWLEDGEMENTS I would like to thank my mentor, Richard Caprioli, for all his guidance and support throughout my graduate school career. To each of my committee members, Sudhansu K. Dey, H. Alex Brown, Daniel Liebler, Jennifer Pietenpol, and Michael Waterman, thank you for all your guidance and input to help progress this project to its successful completion. This work was supported in part by grants GM58008-9 and DOD W81XWH-05-1-0179 (RMC), HD12304 (SKD), U54 GM69338 (HAB). I would also like to acknowledge support from the NICHD Reproductive Biology Training Grant (2T HD007043-31A2) and the NCI Breast Cancer Research Training Grant (CA78136-07). iii TABLE OF CONTENTS Page DEDICATION ................................................................................................................................... ii ACKNOWLEDGMENTS ................................................................................................................... iii LIST OF TABLES ............................................................................................................................ vii LIST OF FIGURES ......................................................................................................................... viii LIST OF TECHNOLOGICAL ABBREVIATIONS ............................................................................... xi LIST OF BIOLOGICAL ABBREVIATIONS ....................................................................................... xii Chapter I. INTRODUCTION .......................................................................................................................... 1 A. Embryo Implantation ..................................................................................................... 1 B. Imaging Mass Spectrometry .......................................................................................... 2 i. The Technology ........................................................................................................ 4 ii. Reproducibility ......................................................................................................... 8 iii. Data processing and Analysis ................................................................................. 9 iv. Biological Applications of IMS ................................................................................ 10 a. Molecular Images of Disease .................................................................. 11 b. Proteome Response to Drug Administration ........................................... 14 c. In situ Proteomics .................................................................................... 16 d. Phospholipid Imaging .............................................................................. 18 e. New Insights into Biology ........................................................................ 20 C. Summary and Research Objectives ............................................................................. 21 II. STAGES OF MOUSE EMBRYO IMPLANTATION .................................................................... 31 iv III. DETECTING SPATIAL AND TEMPORAL DISTRIBUTIONS OF PHOSPHOLIPIDS DURING EMBRYO IMPLANTATION BY MALDI IMAGING MASS SPECTROMETRY ......................... 35 A. Overview ...................................................................................................................... 35 B. Introduction .................................................................................................................. 36 C. Results ......................................................................................................................... 38 i. Spatial remodeling of phospholipids during early pregnancy ................................... 38 ii. Determining the presence of isobaric ions (same nominal mass but different exact masses) in day 8 implantation sites by FTICR IMS ................................................ 41 iii. In-situ identification of phospholipids by tandem MS .............................................. 42 iv. Distinguishing spatial distribution of isobaric phospholipids (identical masses) in day 8 implantation sites by tandem IMS ................................................................. 42 v. Validation of MALDI IMS phospholipid expression patterns by liquid chromatography-electrospray ionization tandem MS quantitation .......................... 43 vi. Colocalization of arachidonate-containing phospholipids with cyclooxygenase 2 .. 44 D. Discussion .................................................................................................................... 45 E. Materials and Methods ................................................................................................. 47 F. Acknowledgements ...................................................................................................... 50 IV. DETECTING SPATIAL AND TEMPORAL DISTRIBUTIONS OF PROTEINS DURING EMBRYO IMPLANTATION BY MALDI IMAGING MASS SPECTROMETRY ......................... 67 A. Overview ...................................................................................................................... 67 B. Introduction .................................................................................................................. 67 C. Results ......................................................................................................................... 68 i. Protein signatures differ within specific regions of implantation and interimplantation sites ......................................................................................................................... 68 ii. Validation of MALDI IMS protein expression patterns ............................................. 71 a. Correlating protein images with mRNA localization using in situ___ hybridization ............................................................................................ 71 v b. Immunohistochemistry and activity assays confirm protein identification and spatial distribution ............................................................................. 72 c. Isotope Coded Affinity Tag (ICAT) based profiling confirms profiling and imaging mass spectrometry experimental results .................................... 73 iii. Exploring Protein Expression along the Z-axis of a day 6 implantation site ........... 74 iv. Characterizing differential proteome profiles in the Pla2g4a null mice ................... 74 D. Discussion .................................................................................................................... 76 E. Materials and Methods ................................................................................................. 79 F. Acknowledgements ...................................................................................................... 87 IV. CONCLUSIONS AND PERSPECTIVES .............................................................................. 102 A. Discussion of protein and phospholipid localization patterns during early pregnancy 102 B. Future outlook: advancements in IMS ....................................................................... 106 IV. REFERENCES ..................................................................................................................... 118 vi LIST OF TABLES Table Page 1. Assignment of lipid molecular species in MS/MS positive ion mode .................................. 63 2. Assignment of lipid molecular species in MS/MS negative ion mode ................................ 64 3. LC-ESI-MS/MS quantitation of phospholipids in the M and AM poles of day 8 implantation sites ................................................................................................................................... 65 4. Proteins which show differential expression patterns between the various cell types on day 6 of pregnancy ................................................................................................................. 100 vii LIST OF FIGURES Figure Page 1. Mouse embryo implantation ............................................................................................... 24 2. Scheme of a typical direct tissue imaging experiment ....................................................... 25 3. Imaging mass spectrometry analysis of a glioma tumor mouse brain ............................... 26 4. Whole-body protein analysis of rat sagittal tissue section by imaging mass spectrometry 27 5. Examples of on-tissue tryptic digestion and subsequent matrix-assisted laser desorption/ionization imaging mass spectrometry analysis ............................................... 28 6. Imaging mass spectrometry analysis of a sagittal mouse brain to determine the spatial localization of multiple phosphatidylcholine species .......................................................... 29 7. Optical images of a day 6 and day 8 pregnant mouse uterus along with the corresponding ion images ........................................................................................................................