1
|
Woolman M, Kiyota T, Belgadi SA, Fujita N, Fiorante A, Ramaswamy V, Daniels C, Rutka JT, McIntosh C, Munoz DG, Ginsberg HJ, Aman A, Zarrine-Afsar A. Lipidomic-Based Approach to 10 s Classification of Major Pediatric Brain Cancer Types with Picosecond Infrared Laser Mass Spectrometry. Anal Chem 2024; 96:1019-1028. [PMID: 38190738 PMCID: PMC10809247 DOI: 10.1021/acs.analchem.3c03156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024]
Abstract
Picosecond infrared laser mass spectrometry (PIRL-MS) is shown, through a retrospective patient tissue study, to differentiate medulloblastoma cancers from pilocytic astrocytoma and two molecular subtypes of ependymoma (PF-EPN-A, ST-EPN-RELA) using laser-extracted lipids profiled with PIRL-MS in 10 s of sampling and analysis time. The average sensitivity and specificity values for this classification, taking genomic profiling data as standard, were 96.41 and 99.54%, and this classification used many molecular features resolvable in 10 s PIRL-MS spectra. Data analysis and liquid chromatography coupled with tandem high-resolution mass spectrometry (LC-MS/MS) further allowed us to reduce the molecular feature list to only 18 metabolic lipid markers most strongly involved in this classification. The identified 'metabolite array' was comprised of a variety of phosphatidic and fatty acids, ceramides, and phosphatidylcholine/ethanolamine and could mediate the above-mentioned classification with average sensitivity and specificity values of 94.39 and 98.78%, respectively, at a 95% confidence in prediction probability threshold. Therefore, a rapid and accurate pathology classification of select pediatric brain cancer types from 10 s PIRL-MS analysis using known metabolic biomarkers can now be available to the neurosurgeon. Based on retrospective mining of 'survival' versus 'extent-of-resection' data, we further identified pediatric cancer types that may benefit from actionable 10 s PIRL-MS pathology feedback. In such cases, aggressiveness of the surgical resection can be optimized in a manner that is expected to benefit the patient's overall or progression-free survival. PIRL-MS is a promising tool to drive such personalized decision-making in the operating theater.
Collapse
Affiliation(s)
- Michael Woolman
- Princess
Margaret Cancer Centre, University Health
Network, 101 College
Street, Toronto, Ontario M5G 1L7, Canada
- Department
of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Taira Kiyota
- Ontario
Institute for Cancer Research (OICR), 661 University Ave Suite 510, Toronto, Ontario M5G 0A3, Canada
| | - Siham A. Belgadi
- Department
of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Naohide Fujita
- Arthur
and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - Alexa Fiorante
- Princess
Margaret Cancer Centre, University Health
Network, 101 College
Street, Toronto, Ontario M5G 1L7, Canada
- Department
of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Vijay Ramaswamy
- Department
of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Arthur
and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - Craig Daniels
- Arthur
and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - James T. Rutka
- Arthur
and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
- Department
of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada
| | - Chris McIntosh
- Toronto
General Hospital Research Institute, University Health Network, 200 Elizabeth Street, Toronto, Ontario M5G-2C4, Canada
| | - David G. Munoz
- Keenan
Research Center for Biomedical Science & the Li Ka Shing Knowledge
Institute, St. Michael’s Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
- Department
of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Sixth Floor, Toronto,Ontario M5S 1A8, Canada
| | - Howard J. Ginsberg
- Department
of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada
- Keenan
Research Center for Biomedical Science & the Li Ka Shing Knowledge
Institute, St. Michael’s Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
- Department
of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Sixth Floor, Toronto,Ontario M5S 1A8, Canada
| | - Ahmed Aman
- Ontario
Institute for Cancer Research (OICR), 661 University Ave Suite 510, Toronto, Ontario M5G 0A3, Canada
- Leslie
Dan, Faculty of Pharmacy, University of
Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Arash Zarrine-Afsar
- Princess
Margaret Cancer Centre, University Health
Network, 101 College
Street, Toronto, Ontario M5G 1L7, Canada
- Department
of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Department
of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada
- Keenan
Research Center for Biomedical Science & the Li Ka Shing Knowledge
Institute, St. Michael’s Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
| |
Collapse
|
2
|
Katz L, Kiyota T, Woolman M, Wu M, Pires L, Fiorante A, Ye LA, Leong W, Berman HK, Ghazarian D, Ginsberg HJ, Das S, Aman A, Zarrine-Afsar A. Metabolic Lipids in Melanoma Enable Rapid Determination of Actionable BRAF-V600E Mutation with Picosecond Infrared Laser Mass Spectrometry in 10 s. Anal Chem 2023; 95:14430-14439. [PMID: 37695851 DOI: 10.1021/acs.analchem.3c02901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Rapid molecular profiling of biological tissues with picosecond infrared laser mass spectrometry (PIRL-MS) has enabled the detection of clinically important histologic types and molecular subtypes of human cancers in as little as 10 s of data collection and analysis time. Utilizing an engineered cell line model of actionable BRAF-V600E mutation, we observed statistically significant differences in 10 s PIRL-MS molecular profiles between BRAF-V600E and BRAF-wt cells. Multivariate statistical analyses revealed a list of mass-to-charge (m/z) values most significantly responsible for the identification of BRAF-V600E mutation status in this engineered cell line that provided a highly controlled testbed for this observation. These metabolites predicted BRAF-V600E expression in human melanoma cell lines with greater than 98% accuracy. Through chromatography and tandem mass spectrometry analysis of cell line extracts, a 30-member "metabolite array" was characterized for determination of BRAF-V600E expression levels in subcutaneous melanoma xenografts with an average sensitivity and specificity of 95.6% with 10 s PIRL-MS analysis. This proof-of-principle work warrants a future large-scale study to identify a metabolite array for 10 s determination of actionable BRAF-V600E mutation in human tissue to guide patient care.
Collapse
Affiliation(s)
- Lauren Katz
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Taira Kiyota
- Ontario Institute for Cancer Research (OICR), 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada
| | - Michael Woolman
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Megan Wu
- Peter Gilgan Centre for Research and Learning & Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Layla Pires
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Alexa Fiorante
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Lan Anna Ye
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Wey Leong
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON M5G 2C1, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
| | - Hal K Berman
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON M5G 2C1, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto and the Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON M5G 2C4, Canada
| | - Danny Ghazarian
- Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON M5B 1W8, Canada
| | - Howard J Ginsberg
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
- Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON M5B 1W8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Sixth Floor, Toronto, ON M5S 1A8, Canada
| | - Sunit Das
- Peter Gilgan Centre for Research and Learning & Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
| | - Ahmed Aman
- Ontario Institute for Cancer Research (OICR), 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St, Toronto, ON M5S 3M2, Canada
| | - Arash Zarrine-Afsar
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
- Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON M5B 1W8, Canada
| |
Collapse
|
3
|
Katz L, Woolman M, Kiyota T, Pires L, Zaidi M, Hofer SO, Leong W, Wouters BG, Ghazarian D, Chan AW, Ginsberg HJ, Aman A, Wilson BC, Berman HK, Zarrine-Afsar A. Picosecond Infrared Laser Mass Spectrometry Identifies a Metabolite Array for 10 s Diagnosis of Select Skin Cancer Types: A Proof-of-Concept Feasibility Study. Anal Chem 2022; 94:16821-16830. [DOI: 10.1021/acs.analchem.2c03918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Lauren Katz
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Michael Woolman
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Taira Kiyota
- Ontario Institute for Cancer Research (OICR), 661 University Ave Suite 510, Toronto, Ontario M5G 0A3, Canada
| | - Layla Pires
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, Ontario M5G 2C1, Canada
| | - Mark Zaidi
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Stefan O.P. Hofer
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada
- Division of Plastic and Reconstructive Surgery, Department of Surgery and Surgical Oncology, University Health Network, University of Toronto. Toronto General Hospital, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada
| | - Wey Leong
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, Ontario M5G 2C1, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada
- Department of Surgical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto Ontario M5G 2C1, Canada
| | - Brad G. Wouters
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, Ontario M5G 2C1, Canada
| | - Danny Ghazarian
- Department of Laboratory Medicine and Pathobiology, University of Toronto and University Health Network, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada
| | - An-Wen Chan
- Division of Dermatology, Department of Medicine, University of Toronto, Canada and Women’s College Research Institute, Women’s College Hospital, 76 Grenville St, Toronto, Ontario M5S 1B2, Canada
| | - Howard J. Ginsberg
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada
- Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
| | - Ahmed Aman
- Ontario Institute for Cancer Research (OICR), 661 University Ave Suite 510, Toronto, Ontario M5G 0A3, Canada
- Leslie Dan, Faculty of Pharmacy, University of Toronto, 144 College St, Toronto, Ontario M5S 3M2, Canada
| | - Brian C. Wilson
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, Ontario M5G 2C1, Canada
| | - Hal K. Berman
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, Ontario M5G 2C1, Canada
- Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada
| | - Arash Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada
- Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
| |
Collapse
|
4
|
Katz L, Tata A, Woolman M, Zarrine-Afsar A. Lipid Profiling in Cancer Diagnosis with Hand-Held Ambient Mass Spectrometry Probes: Addressing the Late-Stage Performance Concerns. Metabolites 2021; 11:metabo11100660. [PMID: 34677375 PMCID: PMC8537725 DOI: 10.3390/metabo11100660] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 02/06/2023] Open
Abstract
Untargeted lipid fingerprinting with hand-held ambient mass spectrometry (MS) probes without chromatographic separation has shown promise in the rapid characterization of cancers. As human cancers present significant molecular heterogeneities, careful molecular modeling and data validation strategies are required to minimize late-stage performance variations of these models across a large population. This review utilizes parallels from the pitfalls of conventional protein biomarkers in reaching bedside utility and provides recommendations for robust modeling as well as validation strategies that could enable the next logical steps in large scale assessment of the utility of ambient MS profiling for cancer diagnosis. Six recommendations are provided that range from careful initial determination of clinical added value to moving beyond just statistical associations to validate lipid involvements in disease processes mechanistically. Further guidelines for careful selection of suitable samples to capture expected and unexpected intragroup variance are provided and discussed in the context of demographic heterogeneities in the lipidome, further influenced by lifestyle factors, diet, and potential intersect with cancer lipid pathways probed in ambient mass spectrometry profiling studies.
Collapse
Affiliation(s)
- Lauren Katz
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; (L.K.); (M.W.)
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
| | - Alessandra Tata
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico delle Venezie, Viale Fiume 78, 36100 Vicenza, Italy;
| | - Michael Woolman
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; (L.K.); (M.W.)
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
| | - Arash Zarrine-Afsar
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; (L.K.); (M.W.)
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
- Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, 30 Bond Street, Toronto, ON M5B 1W8, Canada
- Correspondence: ; Tel.: +1-416-581-8473
| |
Collapse
|
5
|
Woolman M, Katz L, Tata A, Basu SS, Zarrine-Afsar A. Breaking Through the Barrier: Regulatory Considerations Relevant to Ambient Mass Spectrometry at the Bedside. Clin Lab Med 2021; 41:221-246. [PMID: 34020761 DOI: 10.1016/j.cll.2021.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rapid characterization of tissue disorder using ambient mass spectrometry (MS) techniques, requiring little to no preanalytical preparations of sampled tissues, has been shown using a variety of ion sources and with many disease classes. A brief overview of ambient MS in clinical applications, the state of the art in regulatory affairs, and recommendations to facilitate adoption for use at the bedside are presented. Unique challenges in the validation of untargeted MS methods and additional safety and compliance requirements for deployment within a clinical setting are further discussed. Development of a harmonized validation strategy for ambient MS methods is emphasized.
Collapse
Affiliation(s)
- Michael Woolman
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Lauren Katz
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Alessandra Tata
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico delle Venezie, Viale Fiume 78, 36100 Vicenza, Italy
| | - Sankha S Basu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Arash Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada; Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada.
| |
Collapse
|
6
|
Woolman M, Katz L, Gopinath G, Kiyota T, Kuzan-Fischer CM, Ferry I, Zaidi M, Peters K, Aman A, McKee T, Fu F, Amara-Belgadi S, Daniels C, Wouters BG, Rutka JT, Ginsberg HJ, McIntosh C, Zarrine-Afsar A. Mass Spectrometry Imaging Reveals a Gradient of Cancer-like Metabolic States in the Vicinity of Cancer Not Seen in Morphometric Margins from Microscopy. Anal Chem 2021; 93:4408-4416. [PMID: 33651938 DOI: 10.1021/acs.analchem.0c04129] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Spatially resolved ambient mass spectrometry imaging methods have gained popularity to characterize cancer sites and their borders using molecular changes in the lipidome. This utility, however, is predicated on metabolic homogeneity at the border, which would create a sharp molecular transition at the morphometric borders. We subjected murine models of human medulloblastoma brain cancer to mass spectrometry imaging, a technique that provides a direct readout of tissue molecular content in a spatially resolved manner. We discovered a distance-dependent gradient of cancer-like lipid molecule profiles in the brain tissue within 1.2 mm of the cancer border, suggesting that a cancer-like state progresses beyond the histologic border, into the healthy tissue. The results were further corroborated using orthogonal liquid chromatography and mass spectrometry (LC-MS) analysis of selected tissue regions subjected to laser capture microdissection. LC-MS/MS analysis for robust identification of the affected molecules implied changes in a number of different lipid classes, some of which are metabolized from the essential docosahexaenoic fatty acid (DHA) present in the interstitial fluid. Metabolic molecular borders are thus not as sharp as morphometric borders, and mass spectrometry imaging can reveal molecular nuances not observed with microscopy. Caution must be exercised in interpreting multimodal imaging results stipulated on a coincidental relationship between metabolic and morphometric borders of cancer, at least within animal models used in preclinical research.
Collapse
Affiliation(s)
- Michael Woolman
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Lauren Katz
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Georgia Gopinath
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Taira Kiyota
- Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Ontario M5G 0A3, Canada
| | - Claudia M Kuzan-Fischer
- Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Developmental & Stem Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - Isabelle Ferry
- Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Developmental & Stem Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - Mark Zaidi
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.,STTARR Innovation Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Kaitlyn Peters
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Ontario M5G 0A3, Canada.,Leslie Dan Faculty of Pharmacy, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Trevor McKee
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,STTARR Innovation Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Fred Fu
- STTARR Innovation Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Siham Amara-Belgadi
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Craig Daniels
- Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Developmental & Stem Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - Brad G Wouters
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - James T Rutka
- Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada.,Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Howard J Ginsberg
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada.,Keenan Research Center for Biomedical Science & The Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Chris McIntosh
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.,Peter Munk Cardiac Centre, Joint Department of Medical Imaging, University Health Network, Toronto, Ontario M5G 2N2, Canada.,Vector Institute for Artificial Intelligence, Toronto, Ontario M5G 1M1, Canada
| | - Arash Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.,Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada.,Keenan Research Center for Biomedical Science & The Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
| |
Collapse
|
7
|
Katz L, Woolman M, Tata A, Zarrine-Afsar A. Potential impact of tissue molecular heterogeneity on ambient mass spectrometry profiles: a note of caution in choosing the right disease model. Anal Bioanal Chem 2020; 413:2655-2664. [PMID: 33247337 DOI: 10.1007/s00216-020-03054-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
This review provides a summary of known molecular alterations in commonly used cancer models and strives to stipulate how they may affect ambient mass spectrometry profiles. Immortalized cell lines are known to accumulate mutations, and xenografts derived from cell lines are known to contain tumour microenvironment elements from the host animal. While the use of human specimens for mass spectrometry profiling studies is highly encouraged, patient-derived xenografts with low passage numbers could provide an alternative means of amplifying material for ambient MS research when needed. Similarly, genetic preservation of patient tissue seen in some organoid models, further verified by qualitative proteomic and transcriptomic analyses, may argue in favor of organoid suitability for certain ambient profiling studies. However, to choose the appropriate model, pre-evaluation of the model's molecular characteristics in the context of the research question(s) being asked will likely provide the most appropriate strategy to move research forward. This can be achieved by performing comparative ambient MS analysis of the disease model of choice against a small amount of patient tissue to verify concordance. Disease models, however, will continue to be useful tools to orthogonally validate metabolic states of patient tissues through controlled genetic alterations that are not possible with patient specimens.
Collapse
Affiliation(s)
- Lauren Katz
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON, M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Michael Woolman
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON, M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Alessandra Tata
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico delle Venezie, Viale Fiume 78, 36100, Vicenza, Italy
| | - Arash Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON, M5G 1P5, Canada. .,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada. .,Department of Surgery, University of Toronto, 149 College Street, Toronto, ON, M5T 1P5, Canada. .,Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
| |
Collapse
|
8
|
Woolman M, Qiu J, Kuzan-Fischer CM, Ferry I, Dara D, Katz L, Daud F, Wu M, Ventura M, Bernards N, Chan H, Fricke I, Zaidi M, Wouters BG, Rutka JT, Das S, Irish J, Weersink R, Ginsberg HJ, Jaffray DA, Zarrine-Afsar A. In situ tissue pathology from spatially encoded mass spectrometry classifiers visualized in real time through augmented reality. Chem Sci 2020; 11:8723-8735. [PMID: 34123126 PMCID: PMC8163395 DOI: 10.1039/d0sc02241a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Integration between a hand-held mass spectrometry desorption probe based on picosecond infrared laser technology (PIRL-MS) and an optical surgical tracking system demonstrates in situ tissue pathology from point-sampled mass spectrometry data. Spatially encoded pathology classifications are displayed at the site of laser sampling as color-coded pixels in an augmented reality video feed of the surgical field of view. This is enabled by two-way communication between surgical navigation and mass spectrometry data analysis platforms through a custom-built interface. Performance of the system was evaluated using murine models of human cancers sampled in situ in the presence of body fluids with a technical pixel error of 1.0 ± 0.2 mm, suggesting a 84% or 92% (excluding one outlier) cancer type classification rate across different molecular models that distinguish cell-lines of each class of breast, brain, head and neck murine models. Further, through end-point immunohistochemical staining for DNA damage, cell death and neuronal viability, spatially encoded PIRL-MS sampling is shown to produce classifiable mass spectral data from living murine brain tissue, with levels of neuronal damage that are comparable to those induced by a surgical scalpel. This highlights the potential of spatially encoded PIRL-MS analysis for in vivo use during neurosurgical applications of cancer type determination or point-sampling in vivo tissue during tumor bed examination to assess cancer removal. The interface developed herein for the analysis and the display of spatially encoded PIRL-MS data can be adapted to other hand-held mass spectrometry analysis probes currently available. Integration between a hand-held mass spectrometry desorption probe based on picosecond infrared laser technology (PIRL-MS) and an optical surgical tracking system demonstrates in situ tissue pathology from point-sampled mass spectrometry data.![]()
Collapse
Affiliation(s)
- Michael Woolman
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473.,Department of Medical Biophysics, University of Toronto 101 College Street Toronto ON M5G 1L7 Canada
| | - Jimmy Qiu
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473
| | - Claudia M Kuzan-Fischer
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children 686 Bay Street Toronto ON M5G 0A4 Canada.,Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children Toronto ON M5G 1X8 Canada
| | - Isabelle Ferry
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children 686 Bay Street Toronto ON M5G 0A4 Canada.,Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children Toronto ON M5G 1X8 Canada
| | - Delaram Dara
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473
| | - Lauren Katz
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473.,Department of Medical Biophysics, University of Toronto 101 College Street Toronto ON M5G 1L7 Canada
| | - Fowad Daud
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473.,Department of Medical Biophysics, University of Toronto 101 College Street Toronto ON M5G 1L7 Canada
| | - Megan Wu
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children 686 Bay Street Toronto ON M5G 0A4 Canada
| | - Manuela Ventura
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473
| | - Nicholas Bernards
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473
| | - Harley Chan
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473
| | - Inga Fricke
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473
| | - Mark Zaidi
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473
| | - Brad G Wouters
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473.,Department of Medical Biophysics, University of Toronto 101 College Street Toronto ON M5G 1L7 Canada
| | - James T Rutka
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children 686 Bay Street Toronto ON M5G 0A4 Canada.,Department of Surgery, University of Toronto 149 College Street Toronto ON M5T 1P5 Canada.,Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children Toronto ON M5G 1X8 Canada
| | - Sunit Das
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children 686 Bay Street Toronto ON M5G 0A4 Canada.,Department of Surgery, University of Toronto 149 College Street Toronto ON M5T 1P5 Canada.,Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children Toronto ON M5G 1X8 Canada
| | - Jonathan Irish
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473
| | - Robert Weersink
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473
| | - Howard J Ginsberg
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473.,Department of Surgery, University of Toronto 149 College Street Toronto ON M5T 1P5 Canada.,Keenan Research Center for Biomedical Science, The Li Ka Shing Knowledge Institute, St. Michael's Hospital 30 Bond Street Toronto ON M5B 1W8 Canada
| | - David A Jaffray
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473.,Department of Medical Biophysics, University of Toronto 101 College Street Toronto ON M5G 1L7 Canada
| | - Arash Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health, University Health Network 100 College Street, Room 7-207, MaRS Building, Princess Margaret Cancer Research Tower, 7th floor (STTARR) Toronto ON M5G 1P5 Canada +1-416-581-8473.,Department of Medical Biophysics, University of Toronto 101 College Street Toronto ON M5G 1L7 Canada.,Department of Surgery, University of Toronto 149 College Street Toronto ON M5T 1P5 Canada.,Keenan Research Center for Biomedical Science, The Li Ka Shing Knowledge Institute, St. Michael's Hospital 30 Bond Street Toronto ON M5B 1W8 Canada
| |
Collapse
|
9
|
Katz L, Woolman M, Talbot F, Amara-Belgadi S, Wu M, Tortorella S, Das S, Ginsberg HJ, Zarrine-Afsar A. Dual Laser and Desorption Electrospray Ionization Mass Spectrometry Imaging Using the Same Interface. Anal Chem 2020; 92:6349-6357. [PMID: 32275820 DOI: 10.1021/acs.analchem.9b05340] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
For a more comprehensive characterization of molecular heterogeneities of matter, multimodal mass spectrometry imaging must be developed to take advantage of the complementarity of information available through different ionization mechanisms. We report the design, implementation, and performance validation of a laser desorption imaging interface composed of add-on components that adapt a commercial Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) imaging interface for dual imaging of Picosecond Infrared Laser Mass Spectrometry (PIRL-MS) with DESI-MS. The interface utilizes hardware elements and data analysis pipelines already established for DESI-MS imaging, and was further validated in cancer margin assessments using human medulloblastoma cancers. The PIRL-MS images were robust and reproducible across multiple experimental runs on independently prepared xenograft tumors, and could be segmented into cancer and healthy regions in concordance with pathology using a variety of supervised and unsupervised clustering methods. The spectral quality and complexity obtained with this interface were examined with infiltrating and noninfiltrating tumors, and were comparable to other mass spectrometry analysis interfaces. The average PIRL-MS spectra from spatially resolved images could be used for robust cancer m/z model building to classify medulloblastoma cancer from healthy tissue without any misclassifications, an observation that held true over close to 70 sampling data points. While the unsupervised spectral analysis methods suggested a slight suppression of signal in the phospholipid range compared to the hand-held configuration, these changes were insufficient to hamper utility in cancer margin assessment with spatially resolved data obtained with our interface. Dual PIRL-MS and DESI-MS imaging of consecutive sections, as suggested by multivariate loading plots, revealed highly complementary molecular information with m/z values identifiable with one desorption method sufficient to reveal cancer regions being absent in another, further emphasizing the need for effective hardware and software interfaces for dual mass spectrometry imaging.
Collapse
Affiliation(s)
- Lauren Katz
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Michael Woolman
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Francis Talbot
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada
| | - Siham Amara-Belgadi
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada
| | - Megan Wu
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada.,Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario M5G 1 × 8, Canada.,Developmental & Stem Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - Sara Tortorella
- Molecular Horizon Srl, Via Montelino 30, 06084 Bettona (PG), Italy
| | - Sunit Das
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada.,Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario M5G 1 × 8, Canada.,Developmental & Stem Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada.,Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada.,Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Howard J Ginsberg
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada.,Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Arash Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, Ontario M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.,Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada.,Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
| |
Collapse
|
10
|
Woolman M, Kuzan-Fischer CM, Ferry I, Kiyota T, Luu B, Wu M, Munoz DG, Das S, Aman A, Taylor MD, Rutka JT, Ginsberg HJ, Zarrine-Afsar A. Picosecond Infrared Laser Desorption Mass Spectrometry Identifies Medulloblastoma Subgroups on Intrasurgical Timescales. Cancer Res 2019; 79:2426-2434. [DOI: 10.1158/0008-5472.can-18-3411] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/13/2019] [Accepted: 03/14/2019] [Indexed: 11/16/2022]
|
11
|
Woolman M, Zarrine-Afsar A. Platforms for rapid cancer characterization by ambient mass spectrometry: advancements, challenges and opportunities for improvement towards intrasurgical use. Analyst 2019; 143:2717-2722. [PMID: 29786708 DOI: 10.1039/c8an00310f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ambient Mass Spectrometry (MS) analysis is widely used to characterize biological and non-biological samples. Advancements that allow rapid analysis of samples by ambient methods such as Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) and Rapid Evaporative Ionization Mass Spectrometry (REIMS) are discussed. A short, non-comprehensive overview of ambient MS is provided that only contains example applications due to space limitations. A spatially encoded mass spectrometry analysis concept to plan cancer resection is introduced. The application of minimally destructive tissue ablation probes to survey the surgical field for sites of pathology using on-line analysis methods is discussed. The technological challenges that must be overcome for ambient MS to become a robust method for intrasurgical pathology assessments are reviewed.
Collapse
Affiliation(s)
- Michael Woolman
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada.
| | | |
Collapse
|
12
|
Woolman M, Tata A, Dara D, Meens J, D'Arcangelo E, Perez CJ, Saiyara Prova S, Bluemke E, Ginsberg HJ, Ifa D, McGuigan A, Ailles L, Zarrine-Afsar A. Rapid determination of the tumour stroma ratio in squamous cell carcinomas with desorption electrospray ionization mass spectrometry (DESI-MS): a proof-of-concept demonstration. Analyst 2018; 142:3250-3260. [PMID: 28799592 DOI: 10.1039/c7an00830a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Squamous cell carcinomas constitute a major class of head & neck cancers, where the tumour stroma ratio (TSR) carries prognostic information. Patients affected by stroma-rich tumours exhibit a poor prognosis and a higher chance of relapse. As such, there is a need for a technology platform that allows rapid determination of the tumour stroma ratio. In this work, we provide a proof-of-principle demonstration that Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) can be used to determine tumour stroma ratios. Slices from three independent mouse xenograft tumours from the human FaDu cell line were subjected to DESI-MS imaging, staining and detailed analysis using digital pathology methods. Using multivariate statistical methods we compared the MS profiles with those of isolated stromal cells. We found that m/z 773.53 [PG(18:1)(18:1) - H]-, m/z 835.53 [PI(34:1) - H]- and m/z 863.56 [PI(18:1)(18:0) - H]- are biomarker ions that can distinguish FaDu cancer from cancer associated fibroblast (CAF) cells. A comparison with DESI-MS analysis of controlled mixtures of the CAF and FaDu cells showed that the abundance of the biomarker ions above can be used to determine, with an error margin of close to 5% compared with quantitative pathology estimates, TSR values. This proof-of-principle demonstration is encouraging and must be further validated using human samples and a larger sample base. At maturity, DESI-MS thus may become a stand-alone molecular pathology tool providing an alternative rapid cancer assessment without the need for time-consuming staining and microscopy methods, potentially further conserving human resources.
Collapse
Affiliation(s)
- Michael Woolman
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Woolman M, Tata A, Ferry I, Kuzan-Fischer C, Wu M, Das S, Taylor MD, Rutka JT, Ginsberg HJ, Zarrine-Afsar A. Abstract 4118: Rapid, non-subjective characterization of disease in preclinical cancer research using desorption electrospray ionization mass spectrometry. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer tissue smears are routinely used in rapid intraoperative pathology workflows using quick staining methods to characterize cancer in surgical margin assessments or tumor pathology. Mass spectrometry (MS) is a sensitive analytic platform that can detect the presence of cancer from the pattern of cancer-specific molecules present in the mass spectrum of the tissue under examination. In particular, mass spectrometry analysis with desorption electrospray ionization (DESI-MS) is shown to have utility in research models for cancer characterization or even for grading different subclasses of disease based on tumor-specific small molecule lipid or metabolites. DESI does not require extensive tissue preparation, and the data collection and analysis can be done within a few seconds. In this work, we evaluate the combination of rapid DESI-MS detection with rapid tissue smear preparation for research use in preclinical xenograft models of breast cancer and pediatric medulloblastoma requiring only seconds of sampling, and an overall preparation and analysis time of less than one minute. Principal component analysis (PCA) was performed to evaluate the concordance between DESI-MS profiles of breast cancer from tissue slices and smears prepared on various surfaces. PCA suggested no statistical discrimination between DESI-MS profiles of tissue sections and tissue smears prepared on glass, polytetrafluoroethylene (PTFE), and porous PTFE. However, the abundances of cancer biomarker ions varied between sections and smears, with DESI-MS analysis of tissue sections yielding higher ion abundances of cancer biomarkers compared with smears. The coefficient of variance (CV) analysis suggests DESI-MS profiles from tissue smears are as reproducible as the ones from tissue sections. The limit of detection with smear samples from single pixel analysis is comparable to tissue sections that average the signal from a tissue area of 0.01 mm2. The smears prepared on the PTFE surface possessed a higher degree of homogeneity compared with the smears prepared on the glass surface. This allowed single MS scans (~1 s) from random positions across the surface of the smear to be used in rapid cancer typing with good reproducibility, providing useful pathologic information at speeds suitable for research use. Likewise, DESI-MS enabled the rapid classification of subgroups of medulloblastoma in these preclinical models.
Citation Format: Michael Woolman, Alessandra Tata, Isabelle Ferry, Claudia Kuzan-Fischer, Megan Wu, Sunit Das, Michael D. Taylor, James T. Rutka, Howard J. Ginsberg, Arash Zarrine-Afsar. Rapid, non-subjective characterization of disease in preclinical cancer research using desorption electrospray ionization mass spectrometry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4118.
Collapse
Affiliation(s)
| | | | | | | | - Megan Wu
- 2Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sunit Das
- 3University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | |
Collapse
|
14
|
Woolman M, Ferry I, Kuzan-Fischer CM, Wu M, Zou J, Kiyota T, Isik S, Dara D, Aman A, Das S, Taylor MD, Rutka JT, Ginsberg HJ, Zarrine-Afsar A. Rapid determination of medulloblastoma subgroup affiliation with mass spectrometry using a handheld picosecond infrared laser desorption probe. Chem Sci 2017; 8:6508-6519. [PMID: 28989676 PMCID: PMC5628578 DOI: 10.1039/c7sc01974b] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/21/2017] [Indexed: 12/25/2022] Open
Abstract
Medulloblastoma (MB), the most prevalent malignant childhood brain tumour, consists of at least 4 distinct subgroups each of which possesses a unique survival rate and response to treatment. To rapidly determine MB subgroup affiliation in a manner that would be actionable during surgery, we subjected murine xenograft tumours of two MB subgroups (SHH and Group 3) to Mass Spectrometry (MS) profiling using a handheld Picosecond InfraRed Laser (PIRL) desorption probe and interface developed by our group. This platform provides real time MS profiles of tissue based on laser desorbed lipids and small molecules with only 5-10 seconds of sampling. PIRL-MS analysis of ex vivo MB tumours offered a 98% success rate in subgroup determination, observed over 194 PIRL-MS datasets collected from 19 independent tumours (∼10 repetitions each) utilizing 6 different established MB cell lines. Robustness was verified by a 5%-leave-out-and-remodel test. PIRL ablated tissue material was collected on a filter paper and subjected to high resolution LC-MS to provide ion identity assignments for the m/z values that contribute most to the statistical discrimination between SHH and Group 3 MB. Based on this analysis, rapid classification of MB with PIRL-MS utilizes a variety of fatty acid chains, glycerophosphates, glycerophosphoglycerols and glycerophosphocholines rapidly extracted from the tumours. In this work, we provide evidence that 5-10 seconds of sampling from ex vivo MB tissue with PIRL-MS can allow robust tumour subgroup classification, and have identified several biomarker ions responsible for the statistical discrimination of MB Group 3 and the SHH subgroup. The existing PIRL-MS platform used herein offers capabilities for future in vivo use.
Collapse
Affiliation(s)
- Michael Woolman
- Techna Institute for the Advancement of Technology for Health , University Health Network , 100 College Street , Toronto , ON M5G 1P5 , Canada .
- Department of Medical Biophysics , University of Toronto , 101 College Street , Toronto , ON M5G 1L7 , Canada
| | - Isabelle Ferry
- Peter Gilgan Centre for Research and Learning , Hospital for Sick Children , 686 Bay Street , Toronto , ON M5G 0A4 , Canada
- Arthur and Sonia Labatt Brain Tumor Research Centre , The Hospital for Sick Children , Toronto , ON M5G 1X8 , Canada
- Developmental & Stem Cell Biology Program , The Hospital for Sick Children , 686 Bay Street , Toronto , ON M5G 0A4 , Canada
| | - Claudia M Kuzan-Fischer
- Peter Gilgan Centre for Research and Learning , Hospital for Sick Children , 686 Bay Street , Toronto , ON M5G 0A4 , Canada
- Arthur and Sonia Labatt Brain Tumor Research Centre , The Hospital for Sick Children , Toronto , ON M5G 1X8 , Canada
- Developmental & Stem Cell Biology Program , The Hospital for Sick Children , 686 Bay Street , Toronto , ON M5G 0A4 , Canada
| | - Megan Wu
- Peter Gilgan Centre for Research and Learning , Hospital for Sick Children , 686 Bay Street , Toronto , ON M5G 0A4 , Canada
- Arthur and Sonia Labatt Brain Tumor Research Centre , The Hospital for Sick Children , Toronto , ON M5G 1X8 , Canada
- Developmental & Stem Cell Biology Program , The Hospital for Sick Children , 686 Bay Street , Toronto , ON M5G 0A4 , Canada
| | - Jing Zou
- Techna Institute for the Advancement of Technology for Health , University Health Network , 100 College Street , Toronto , ON M5G 1P5 , Canada .
| | - Taira Kiyota
- Drug Discovery Program , Ontario Institute for Cancer Research , 661 University Avenue , Toronto , ON M5G 0A3 , Canada
| | - Semra Isik
- Peter Gilgan Centre for Research and Learning , Hospital for Sick Children , 686 Bay Street , Toronto , ON M5G 0A4 , Canada
| | - Delaram Dara
- Techna Institute for the Advancement of Technology for Health , University Health Network , 100 College Street , Toronto , ON M5G 1P5 , Canada .
| | - Ahmed Aman
- Drug Discovery Program , Ontario Institute for Cancer Research , 661 University Avenue , Toronto , ON M5G 0A3 , Canada
| | - Sunit Das
- Peter Gilgan Centre for Research and Learning , Hospital for Sick Children , 686 Bay Street , Toronto , ON M5G 0A4 , Canada
- Department of Surgery , University of Toronto , 149 College Street , Toronto , ON M5T 1P5 , Canada
- Keenan Research Center for Biomedical Science , The Li Ka Shing Knowledge Institute , St. Michael's Hospital , 30 Bond Street , Toronto , ON M5B 1W8 , Canada
| | - Michael D Taylor
- Peter Gilgan Centre for Research and Learning , Hospital for Sick Children , 686 Bay Street , Toronto , ON M5G 0A4 , Canada
- Department of Surgery , University of Toronto , 149 College Street , Toronto , ON M5T 1P5 , Canada
- Arthur and Sonia Labatt Brain Tumor Research Centre , The Hospital for Sick Children , Toronto , ON M5G 1X8 , Canada
- Developmental & Stem Cell Biology Program , The Hospital for Sick Children , 686 Bay Street , Toronto , ON M5G 0A4 , Canada
| | - James T Rutka
- Peter Gilgan Centre for Research and Learning , Hospital for Sick Children , 686 Bay Street , Toronto , ON M5G 0A4 , Canada
- Department of Surgery , University of Toronto , 149 College Street , Toronto , ON M5T 1P5 , Canada
- Arthur and Sonia Labatt Brain Tumor Research Centre , The Hospital for Sick Children , Toronto , ON M5G 1X8 , Canada
| | - Howard J Ginsberg
- Techna Institute for the Advancement of Technology for Health , University Health Network , 100 College Street , Toronto , ON M5G 1P5 , Canada .
- Department of Surgery , University of Toronto , 149 College Street , Toronto , ON M5T 1P5 , Canada
- Keenan Research Center for Biomedical Science , The Li Ka Shing Knowledge Institute , St. Michael's Hospital , 30 Bond Street , Toronto , ON M5B 1W8 , Canada
- Institute of Biomaterials and Biomedical Engineering , University of Toronto , 164 College Street , Toronto , ON M5S 3G9 , Canada
| | - Arash Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health , University Health Network , 100 College Street , Toronto , ON M5G 1P5 , Canada .
- Department of Medical Biophysics , University of Toronto , 101 College Street , Toronto , ON M5G 1L7 , Canada
- Department of Surgery , University of Toronto , 149 College Street , Toronto , ON M5T 1P5 , Canada
- Keenan Research Center for Biomedical Science , The Li Ka Shing Knowledge Institute , St. Michael's Hospital , 30 Bond Street , Toronto , ON M5B 1W8 , Canada
| |
Collapse
|
15
|
Zarrine-Afsar A, Shrestha B, Tata A, Woolman M, Ventura M, Bernards N, Ganguly M, Ginsberg H, Zheng J, Bluemke E. Abstract 741: Rapid detection of necrosis in breast cancer with ex vivo and in situ mass spectrometry analysis methods. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Necrosis is a form of cell death that is often associated with highly aggressive forms of cancer, is of prognostic value in treatment planning. Mass Spectrometry (MS) is a highly sensitive analytic platform capable of providing a molecular profile of cancer on the basis of mass to charge (m/z) ratio of tissue constituent molecules. MS analysis of ex vivo tissue slices from metastatic murine xenograft tumors from LM2-4 cell line with Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) allowed direct comparisons with histology images to determine the molecular profile of necrotic tissues. The necrotic tissue is characterized by the presence of a ceramide absent from the viable cancer regions. The spatial distribution of this ion fully correlated to necrotic areas from pathology in additional independent tumor samples examined. The same ion was detected from in situ necrotic tissue using tissue aerosols generated by hand-held ablation probes coupled to evaporative ionization interface in only a few seconds of sampling. These developments further establish MS as a novel tool for rapid pathology that is highly complementary to current histology based methods widely used in characterization of cancer in both imaging mode (to provide spatial information on cancer border) and profiling mode (to provide information on cancer type and subtype); all based on unique molecular profile associated with each cancer type and subtype. Current efforts in creating cancer molecular profile libraries will facilitate translation.
Citation Format: Arash Zarrine-Afsar, Bindesh Shrestha, Alessandra Tata, Michael Woolman, Manuela Ventura, Nicholas Bernards, Milan Ganguly, Howard Ginsberg, Jinzi Zheng, Emma Bluemke. Rapid detection of necrosis in breast cancer with ex vivo and in situ mass spectrometry analysis methods [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 741. doi:10.1158/1538-7445.AM2017-741
Collapse
Affiliation(s)
- Arash Zarrine-Afsar
- 1Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, Ontario, Canada
| | | | - Alessandra Tata
- 1Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, Ontario, Canada
| | - Michael Woolman
- 1Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, Ontario, Canada
| | | | - Nicholas Bernards
- 1Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, Ontario, Canada
| | - Milan Ganguly
- 3University Health Network, Toronto, Ontario, Canada
| | | | - Jinzi Zheng
- 3University Health Network, Toronto, Ontario, Canada
| | - Emma Bluemke
- 1Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, Ontario, Canada
| |
Collapse
|
16
|
Woolman M, Gribble A, Bluemke E, Zou J, Ventura M, Bernards N, Wu M, Ginsberg HJ, Das S, Vitkin A, Zarrine-Afsar A. Optimized Mass Spectrometry Analysis Workflow with Polarimetric Guidance for ex vivo and in situ Sampling of Biological Tissues. Sci Rep 2017; 7:468. [PMID: 28352074 PMCID: PMC5428042 DOI: 10.1038/s41598-017-00272-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/14/2017] [Indexed: 02/02/2023] Open
Abstract
Spatially Targeted Mass Spectrometry (MS) analysis using survey scans with an imaging modality often requires consecutive tissue slices, because of the tissue damage during survey scan or due to incompatible sample preparation requirements between the survey modality and MS. We report two spatially targeted MS analysis workflows based on polarized light imaging guidance that use the same tissue sample for survey and targeted analysis. The first workflow is applicable for thin-slice analysis, and uses transmission-polarimetry-guided Desorption ElectroSpray Ionization Mass Spectrometry (DESI-MS), and confirmatory H&E histopathology analysis on the same slice; this is validated using quantitative digital pathology methods. The second workflow explores a polarimetry-guided MS platform for thick tissue assessment by developing reflection-mode polarimetric imaging coupled with a hand-held Picosecond InfraRed Laser (PIRL) MS ablation probe that requires minimal tissue removal to produce detectable signal. Tissue differentiation within 5–10 s of sampling with the hand-held probe is shown using multivariate statistical methods of the MS profiles. Both workflows were tasked with differentiating necrotic cancer sites from viable cancers using a breast tumour model, and their performance was evaluated. The use of the same tissue surface addresses mismatches in guidance due to intrinsic changes in tissue morphology over consecutive sections.
Collapse
Affiliation(s)
- Michael Woolman
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON, M5G 1L7, Canada
| | - Adam Gribble
- Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON, M5G 1L7, Canada
| | - Emma Bluemke
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada
| | - Jing Zou
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada
| | - Manuela Ventura
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada
| | - Nicholas Bernards
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada
| | - Megan Wu
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G-0A4, Canada
| | - Howard J Ginsberg
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada.,Department of Surgery, University of Toronto, 149 College Street, Toronto, ON, M5T-1P5, Canada.,Keenan Research Center for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON, M5B-1W8, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
| | - Sunit Das
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G-0A4, Canada.,Department of Surgery, University of Toronto, 149 College Street, Toronto, ON, M5T-1P5, Canada.,Keenan Research Center for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON, M5B-1W8, Canada
| | - Alex Vitkin
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G-0A4, Canada.,Department of Radiation Oncology, University of Toronto, 610 University Avenue, Toronto, Ontario, M5G 2M9, Canada.,Division of Biophysics and Bioimaging, Ontario Cancer Institute, University Health Network, 610 University Ave, Toronto, ON, M5G 2M9, Canada
| | - Arash Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada. .,Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON, M5G 1L7, Canada. .,Department of Surgery, University of Toronto, 149 College Street, Toronto, ON, M5T-1P5, Canada. .,Keenan Research Center for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON, M5B-1W8, Canada.
| |
Collapse
|
17
|
Woolman M, Tata A, Bluemke E, Dara D, Ginsberg HJ, Zarrine-Afsar A. An Assessment of the Utility of Tissue Smears in Rapid Cancer Profiling with Desorption Electrospray Ionization Mass Spectrometry (DESI-MS). J Am Soc Mass Spectrom 2017; 28:145-153. [PMID: 27730523 DOI: 10.1007/s13361-016-1506-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 08/08/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Mass spectrometry imaging with desorption electrospray ionization mass spectrometry (DESI-MS) is used to characterize cancer from ex vivo slices of tissues. The process is time-consuming. The use of tissue smears for DESI-MS analysis has been proposed as it eliminates the time required to snap-freeze and section the tissue. To assess the utility of tissue smears for rapid cancer characterization, principal component analysis (PCA) was performed to evaluate the concordance between DESI-MS profiles of breast cancer from tissue slices and smears prepared on various surfaces. PCA suggested no statistical discrimination between DESI-MS profiles of tissue sections and tissue smears prepared on glass, polytetrafluoroethylene (PTFE), and porous PTFE. However, the abundances of cancer biomarker ions varied between sections and smears, with DESI-MS analysis of tissue sections yielding higher ion abundances of cancer biomarkers compared with smears. Coefficient of variance (CV) analysis suggests DESI-MS profiles from tissue smears are as reproducible as the ones from tissue sections. The limit of detection with smear samples from single pixel analysis is comparable to tissue sections that average the signal from a tissue area of 0.01 mm2. The smears prepared on the PTFE surface possessed a higher degree of homogeneity compared with the smears prepared on the glass surface. This allowed single MS scans (~1 s) from random positions across the surface of the smear to be used in rapid cancer typing with good reproducibility, providing pathologic information for cancer typing at speeds suitable for clinical utility. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Michael Woolman
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada
| | - Alessandra Tata
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada
| | - Emma Bluemke
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada
| | - Delaram Dara
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada
| | - Howard J Ginsberg
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON, M5T-1P5, Canada
- Keenan Research Center for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON, M5B-1W8, Canada
| | - Arash Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON, M5G-1P5, Canada.
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON, M5T-1P5, Canada.
- Keenan Research Center for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON, M5B-1W8, Canada.
- Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON, M5G 1L7, Canada.
| |
Collapse
|
18
|
Woolman M, Tata A, Dara D, Meens J, D'Arcangelo E, Perez CJ, Prova SS, Bluemke E, Ginsberg HJ, Ifa D, McGuigan A, Ailles L, Zarrine-Afsar A. Correction: Rapid determination of the tumour stroma ratio in squamous cell carcinomas with desorption electrospray ionization mass spectrometry (DESI-MS): a proof-of-concept demonstration. Analyst 2017; 142:3522. [DOI: 10.1039/c7an90066j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correction for ‘Rapid determination of the tumour stroma ratio in squamous cell carcinomas with desorption electrospray ionization mass spectrometry (DESI-MS): a proof-of-concept demonstration’ by Michael Woolman et al., Analyst, 2017, 142, 3250–3260.
Collapse
|
19
|
Bilkey J, Tata A, McKee TD, Porcari AM, Bluemke E, Woolman M, Ventura M, Eberlin MN, Zarrine-Afsar A. Variations in the Abundance of Lipid Biomarker Ions in Mass Spectrometry Images Correlate to Tissue Density. Anal Chem 2016; 88:12099-12107. [PMID: 28193010 DOI: 10.1021/acs.analchem.6b02767] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
While mass spectrometry (MS) imaging is widely used to investigate the molecular composition of ex vivo slices of cancerous tumors, little is known about how variations in the cellular properties of cancer tissue can influence cancer biomarker ion images. To better understand the basis for variations in the abundances of cancer biomarker ions seen in MS images of relatively homogeneous ex vivo tumor samples, sections of snap frozen human breast cancer murine xenografts were subjected to desorption electrospray ionization mass spectrometry (DESI-MS) imaging. Serial sections were then stained with hematoxylin and eosin (H&E) and subjected to detailed morphometric cellular analysis, using a commercial digital pathology platform augmented with custom-tailored image analysis algorithms developed in-house. Gross morphological heterogeneities due to stroma, vasculature, and noncancer cells were mapped in the tumor and found to not correlate with the areas of suppressed cancer biomarker abundance. Instead, the ion abundances of major breast cancer biomarkers were found to correlate with the cytoplasmic area of cancer cells that comprised the tumor tissue. Therefore, detailed cellular analyses can be used to rationalize subtle heterogeneities in ion abundance in MS images, not explained by the presence of gross morphological heterogeneities such as stroma.
Collapse
Affiliation(s)
- Jade Bilkey
- STTARR Innovation Centre, Princess Margaret Cancer Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Alessandra Tata
- Techna Institute for the Advancement of Technology for Health, University Health Network , Toronto, Ontario M5G-1P5, Canada
| | - Trevor D McKee
- STTARR Innovation Centre, Princess Margaret Cancer Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Andreia M Porcari
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas , Campinas, SP Brazil
| | - Emma Bluemke
- Techna Institute for the Advancement of Technology for Health, University Health Network , Toronto, Ontario M5G-1P5, Canada
| | - Michael Woolman
- Techna Institute for the Advancement of Technology for Health, University Health Network , Toronto, Ontario M5G-1P5, Canada
| | - Manuela Ventura
- Techna Institute for the Advancement of Technology for Health, University Health Network , Toronto, Ontario M5G-1P5, Canada
| | - Marcos N Eberlin
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas , Campinas, SP Brazil
| | - Arash Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health, University Health Network , Toronto, Ontario M5G-1P5, Canada.,Department of Medical Biophysics, University of Toronto ,101 College Street Suite 15-701, Toronto, Ontario M5G 1L7, Canada.,Department of Surgery, University of Toronto , 149 College Street, Toronto, Ontario M5T-1P5, Canada.,Keenan Research Centre for Biomedical Science, Li Ka-Shing Knowledge Institute, St. Michael's Hospital , 30 Bond Street, Toronto, Ontario M5B-1W8, Canada
| |
Collapse
|
20
|
Tata A, Gribble A, Ventura M, Ganguly M, Bluemke E, Ginsberg HJ, Jaffray DA, Ifa DR, Vitkin A, Zarrine-Afsar A. Wide-field tissue polarimetry allows efficient localized mass spectrometry imaging of biological tissues. Chem Sci 2016; 7:2162-2169. [PMID: 30155015 PMCID: PMC6090527 DOI: 10.1039/c5sc03782d] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/14/2015] [Indexed: 11/21/2022] Open
Abstract
While mass spectrometers can detect chemical signatures within milliseconds of data acquisition time, the non-targeted nature of mass spectrometry imaging (MSI) necessitates probing the entire surface of the sample to reveal molecular composition even if the information is only sought from a sample subsection. This leads to long analysis times. Here, we used polarimetry to identify, within a biological tissue, areas of polarimetric heterogeneity indicative of cancer. We were then able to target our MS analysis using polarimetry results to either the cancer region itself or to the cancer margin. A tandem of polarimetry and Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI) enables fast (10 fold compared to non-targeted imaging), and accurate pathology assessment (cancer typification in less than 2 minutes compared to 30 minutes for histopathology) of ex vivo tissue slices, without additional sample preparation. This workflow reduces the overall analysis time of MSI as a research tool.
Collapse
Affiliation(s)
- Alessandra Tata
- Techna Institute for the Advancement of Technology for Health , University Health Network , Toronto , ON M5G-1P5 , Canada .
| | - Adam Gribble
- Department of Medical Biophysics , University of Toronto , 101 College Street Suite 15-701 , Toronto , ON M5G 1L7 , Canada
| | - Manuela Ventura
- Techna Institute for the Advancement of Technology for Health , University Health Network , Toronto , ON M5G-1P5 , Canada .
| | - Milan Ganguly
- STTARR Innovation Centre , Princess Margaret Cancer Centre , 101 College Street , Toronto , ON M5G 1L7 , Canada
| | - Emma Bluemke
- Techna Institute for the Advancement of Technology for Health , University Health Network , Toronto , ON M5G-1P5 , Canada .
- Department of Medical Biophysics , University of Toronto , 101 College Street Suite 15-701 , Toronto , ON M5G 1L7 , Canada
| | - Howard J Ginsberg
- Techna Institute for the Advancement of Technology for Health , University Health Network , Toronto , ON M5G-1P5 , Canada .
- Department of Surgery , University of Toronto , 149 College Street , Toronto , ON M5T-1P5 , Canada
- Keenan Research Centre for Biomedical Science , Li KaShing Knowledge Institute , St. Michael's Hospital , 30 Bond Street , Toronto , ON M5B-1W8 , Canada
| | - David A Jaffray
- Techna Institute for the Advancement of Technology for Health , University Health Network , Toronto , ON M5G-1P5 , Canada .
- Department of Medical Biophysics , University of Toronto , 101 College Street Suite 15-701 , Toronto , ON M5G 1L7 , Canada
| | - Demian R Ifa
- Department of Chemistry , York University , 4700 Keele Street , Toronto , ON M3J-1P3 , Canada
| | - Alex Vitkin
- Department of Medical Biophysics , University of Toronto , 101 College Street Suite 15-701 , Toronto , ON M5G 1L7 , Canada
- Department of Radiation Oncology , University of Toronto , 610 University Avenue , Toronto , Ontario M5G 2M9 , Canada
- Division of Biophysics and Bioimaging , Ontario Cancer Institute , University Health Network , 610 University Ave , Toronto , ON M5G 2M9 , Canada
| | - Arash Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health , University Health Network , Toronto , ON M5G-1P5 , Canada .
- Department of Medical Biophysics , University of Toronto , 101 College Street Suite 15-701 , Toronto , ON M5G 1L7 , Canada
- Department of Surgery , University of Toronto , 149 College Street , Toronto , ON M5T-1P5 , Canada
- Keenan Research Centre for Biomedical Science , Li KaShing Knowledge Institute , St. Michael's Hospital , 30 Bond Street , Toronto , ON M5B-1W8 , Canada
| |
Collapse
|
21
|
Steffen P, Kwiatkowski M, Robertson WD, Zarrine-Afsar A, Deterra D, Richter V, Schlüter H. Protein species as diagnostic markers. J Proteomics 2016; 134:5-18. [DOI: 10.1016/j.jprot.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/28/2015] [Accepted: 12/09/2015] [Indexed: 02/07/2023]
|
22
|
Kwiatkowski M, Wurlitzer M, Krutilin A, Kiani P, Nimer R, Omidi M, Mannaa A, Bussmann T, Bartkowiak K, Kruber S, Uschold S, Steffen P, Lübberstedt J, Küpker N, Petersen H, Knecht R, Hansen NO, Zarrine-Afsar A, Robertson WD, Miller RJD, Schlüter H. Homogenization of tissues via picosecond-infrared laser (PIRL) ablation: Giving a closer view on the in-vivo composition of protein species as compared to mechanical homogenization. J Proteomics 2016; 134:193-202. [PMID: 26778141 PMCID: PMC4767054 DOI: 10.1016/j.jprot.2015.12.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/22/2015] [Accepted: 12/31/2015] [Indexed: 12/30/2022]
Abstract
Posttranslational modifications and proteolytic processing regulate almost all physiological processes. Dysregulation can potentially result in pathologic protein species causing diseases. Thus, tissue species proteomes of diseased individuals provide diagnostic information. Since the composition of tissue proteomes can rapidly change during tissue homogenization by the action of enzymes released from their compartments, disease specific protein species patterns can vanish. Recently, we described a novel, ultrafast and soft method for cold vaporization of tissue via desorption by impulsive vibrational excitation (DIVE) using a picosecond-infrared-laser (PIRL). Given that DIVE extraction may provide improved access to the original composition of protein species in tissues, we compared the proteome composition of tissue protein homogenates after DIVE homogenization with conventional homogenizations. A higher number of intact protein species was observed in DIVE homogenates. Due to the ultrafast transfer of proteins from tissues via gas phase into frozen condensates of the aerosols, intact protein species were exposed to a lesser extent to enzymatic degradation reactions compared with conventional protein extraction. In addition, total yield of the number of proteins is higher in DIVE homogenates, because they are very homogenous and contain almost no insoluble particles, allowing direct analysis with subsequent analytical methods without the necessity of centrifugation. Biological significance Enzymatic protein modifications during tissue homogenization are responsible for changes of the in-vivo protein species composition. Cold vaporization of tissues by PIRL-DIVE is comparable with taking a snapshot at the time of the laser irradiation of the dynamic changes that occur continuously under in-vivo conditions. At that time point all biomolecules are transferred into an aerosol, which is immediately frozen.
Collapse
Affiliation(s)
- M Kwiatkowski
- University Medical Centre Hamburg-Eppendorf, Institute for Clinical Chemistry, Department for Mass Spectrometric Proteomics, Martinistraße 52, 20246 Hamburg, Germany
| | - M Wurlitzer
- University Medical Centre Hamburg-Eppendorf, Institute for Clinical Chemistry, Department for Mass Spectrometric Proteomics, Martinistraße 52, 20246 Hamburg, Germany
| | - A Krutilin
- University Medical Centre Hamburg-Eppendorf, Institute for Clinical Chemistry, Department for Mass Spectrometric Proteomics, Martinistraße 52, 20246 Hamburg, Germany
| | - P Kiani
- University Medical Centre Hamburg-Eppendorf, Institute for Clinical Chemistry, Department for Mass Spectrometric Proteomics, Martinistraße 52, 20246 Hamburg, Germany
| | - R Nimer
- University Medical Centre Hamburg-Eppendorf, Institute for Clinical Chemistry, Department for Mass Spectrometric Proteomics, Martinistraße 52, 20246 Hamburg, Germany
| | - M Omidi
- University Medical Centre Hamburg-Eppendorf, Institute for Clinical Chemistry, Department for Mass Spectrometric Proteomics, Martinistraße 52, 20246 Hamburg, Germany
| | - A Mannaa
- University Medical Centre Hamburg-Eppendorf, Institute for Clinical Chemistry, Department for Mass Spectrometric Proteomics, Martinistraße 52, 20246 Hamburg, Germany
| | - T Bussmann
- Beiersdorf AG, Research & Development, Unnastrasse 48, 20245, Hamburg, Germany
| | - K Bartkowiak
- University Medical Centre Hamburg-Eppendorf, Department of Tumor Biology, Martinistraße 52, 20246 Hamburg, Germany
| | - S Kruber
- Max Planck Institute for the Structure and Dynamics of Matter, Atomically Resolved Dynamics Division, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - S Uschold
- Max Planck Institute for the Structure and Dynamics of Matter, Atomically Resolved Dynamics Division, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - P Steffen
- University Medical Centre Hamburg-Eppendorf, Institute for Clinical Chemistry, Department for Mass Spectrometric Proteomics, Martinistraße 52, 20246 Hamburg, Germany
| | - J Lübberstedt
- University Medical Centre Hamburg-Eppendorf, Institute for Clinical Chemistry, Department for Mass Spectrometric Proteomics, Martinistraße 52, 20246 Hamburg, Germany
| | - N Küpker
- University Medical Centre Hamburg-Eppendorf, Institute for Clinical Chemistry, Department for Mass Spectrometric Proteomics, Martinistraße 52, 20246 Hamburg, Germany
| | - H Petersen
- University Medical Centre Hamburg-Eppendorf, Department of Otorhinolaryngology, Head and Neck Surgery and Oncology, Martinistraße 52, 20246 Hamburg, Germany
| | - R Knecht
- University Medical Centre Hamburg-Eppendorf, Department of Otorhinolaryngology, Head and Neck Surgery and Oncology, Martinistraße 52, 20246 Hamburg, Germany
| | - N O Hansen
- Max Planck Institute for the Structure and Dynamics of Matter, Atomically Resolved Dynamics Division, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - A Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, ON M5G-1P5, Canada & Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7, Canada
| | - W D Robertson
- Max Planck Institute for the Structure and Dynamics of Matter, Atomically Resolved Dynamics Division, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R J D Miller
- Max Planck Institute for the Structure and Dynamics of Matter, Atomically Resolved Dynamics Division, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - H Schlüter
- University Medical Centre Hamburg-Eppendorf, Institute for Clinical Chemistry, Department for Mass Spectrometric Proteomics, Martinistraße 52, 20246 Hamburg, Germany.
| |
Collapse
|
23
|
Zou J, Talbot F, Tata A, Ermini L, Franjic K, Ventura M, Zheng J, Ginsberg H, Post M, Ifa DR, Jaffray D, Miller RJD, Zarrine-Afsar A. Ambient Mass Spectrometry Imaging with Picosecond Infrared Laser Ablation Electrospray Ionization (PIR-LAESI). Anal Chem 2015; 87:12071-9. [PMID: 26561279 DOI: 10.1021/acs.analchem.5b02756] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A picosecond infrared laser (PIRL) is capable of cutting through biological tissues in the absence of significant thermal damage. As such, PIRL is a standalone surgical scalpel with the added bonus of minimal postoperative scar tissue formation. In this work, a tandem of PIRL ablation with electrospray ionization (PIR-LAESI) mass spectrometry is demonstrated and characterized for tissue molecular imaging, with a limit of detection in the range of 100 nM for reserpine or better than 5 nM for verapamil in aqueous solution. We characterized PIRL crater size using agar films containing Rhodamine. PIR-LAESI offers a 20-30 μm vertical resolution (∼3 μm removal per pulse) and a lateral resolution of ∼100 μm. We were able to detect 25 fmol of Rhodamine in agar ablation experiments. PIR-LAESI was used to map the distribution of endogenous methoxykaempferol glucoronide in zebra plant (Aphelandra squarrosa) leaves producing a localization map that is corroborated by the literature. PIR-LAESI was further used to image the distribution inside mouse kidneys of gadoteridol, an exogenous magnetic resonance contrast agent intravenously injected. Parallel mass spectrometry imaging (MSI) using desorption electrospray ionization (DESI) and matrix assisted laser desorption ionization (MALDI) were performed to corroborate PIR-LAESI images of the exogenous agent. We further show that PIR-LAESI is capable of desorption ionization of proteins as well as phospholipids. This comparative study illustrates that PIR-LAESI is an ion source for ambient mass spectrometry applications. As such, a future PIRL scalpel combined with secondary ionization such as ESI and mass spectrometry has the potential to provide molecular feedback to guide PIRL surgery.
Collapse
Affiliation(s)
- Jing Zou
- Department of Physics, University of Toronto , 60 St George Street, Toronto, Ontario M5S 1A7, Canada
| | - Francis Talbot
- Department of Chemistry, University of Toronto , 80 St George Street, Toronto, Ontario M5S 3H6, Canada
| | - Alessandra Tata
- Department of Chemistry, York University , 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,Techna Institute for the Advancement of Technology for Health, University Health Network , Toronto, Ontario M5G 1P5, Canada
| | - Leonardo Ermini
- Program in Physiology and Experimental Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children , Toronto, Ontario M5G 0A4, Canada
| | - Kresimir Franjic
- Department of Physics, University of Toronto , 60 St George Street, Toronto, Ontario M5S 1A7, Canada
| | - Manuela Ventura
- Techna Institute for the Advancement of Technology for Health, University Health Network , Toronto, Ontario M5G 1P5, Canada
| | - Jinzi Zheng
- Techna Institute for the Advancement of Technology for Health, University Health Network , Toronto, Ontario M5G 1P5, Canada
| | - Howard Ginsberg
- Department of Surgery, University of Toronto , 149 College Street, Toronto, Ontario M5T 1P5, Canada.,Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital , 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
| | - Martin Post
- Program in Physiology and Experimental Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children , Toronto, Ontario M5G 0A4, Canada.,Institute of Medical Science, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Demian R Ifa
- Department of Chemistry, York University , 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - David Jaffray
- Techna Institute for the Advancement of Technology for Health, University Health Network , Toronto, Ontario M5G 1P5, Canada.,Department of Medical Biophysics, University of Toronto , 101 College Street Suite 15-701, Toronto, Ontario M5G 1L7, Canada
| | - R J Dwayne Miller
- Department of Physics, University of Toronto , 60 St George Street, Toronto, Ontario M5S 1A7, Canada.,Department of Chemistry, University of Toronto , 80 St George Street, Toronto, Ontario M5S 3H6, Canada.,Max Planck Institute for the Structure and Dynamics of Matter , Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Arash Zarrine-Afsar
- Techna Institute for the Advancement of Technology for Health, University Health Network , Toronto, Ontario M5G 1P5, Canada.,Department of Surgery, University of Toronto , 149 College Street, Toronto, Ontario M5T 1P5, Canada.,Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital , 30 Bond Street, Toronto, Ontario M5B 1W8, Canada.,Department of Medical Biophysics, University of Toronto , 101 College Street Suite 15-701, Toronto, Ontario M5G 1L7, Canada
| |
Collapse
|
24
|
Czar MF, Zosel F, König I, Nettels D, Wunderlich B, Schuler B, Zarrine-Afsar A, Jockusch RA. Gas-Phase FRET Efficiency Measurements To Probe the Conformation of Mass-Selected Proteins. Anal Chem 2015; 87:7559-65. [DOI: 10.1021/acs.analchem.5b01591] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Martin F. Czar
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Franziska Zosel
- Biochemisches
Institut, Universität Zürich, Zürich, CH-8057, Switzerland
| | - Iwo König
- Biochemisches
Institut, Universität Zürich, Zürich, CH-8057, Switzerland
| | - Daniel Nettels
- Biochemisches
Institut, Universität Zürich, Zürich, CH-8057, Switzerland
| | - Bengt Wunderlich
- Biochemisches
Institut, Universität Zürich, Zürich, CH-8057, Switzerland
| | - Benjamin Schuler
- Biochemisches
Institut, Universität Zürich, Zürich, CH-8057, Switzerland
| | | | - Rebecca A. Jockusch
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| |
Collapse
|
25
|
Abstract
Mapping intratumoral heterogeneity such as vasculature and margins is important during intraoperative applications. Desorption electrospray ionization mass spectrometry (DESI-MS) has demonstrated potential for intraoperative tumor imaging using validated MS profiles. The clinical translation of DESI-MS into a universal label-free imaging technique thus requires access to MS profiles characteristic to tumors and healthy tissues. Here, we developed contrast agent mass spectrometry imaging (CA-MSI) that utilizes a magnetic resonance imaging (MRI) contrast agent targeted to disease sites, as a label, to reveal tumor heterogeneity in the absence of known MS profiles. Human breast cancer tumors grown in mice were subjected to CA-MSI using Gadoteridol revealing tumor margins and vasculature from the localization of [Gadoteridol+K](+) and [Gadoteridol+Na](+) adducts, respectively. The localization of the [Gadoteridol+K](+) adduct as revealed through DESI-MS complements the in vivo MRI results. DESI-MS imaging is therefore possible for tumors for which no characteristic MS profiles are established. Further DESI-MS imaging of the flux of the contrast agent through mouse kidneys was performed indicating secretion of the intact label.
Collapse
Affiliation(s)
- Alessandra Tata
- †Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, Ontario M5G-1P5, Canada.,‡Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J-1P3, Canada
| | - Jinzi Zheng
- †Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, Ontario M5G-1P5, Canada
| | - Howard J Ginsberg
- §Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T-1P5, Canada.,⊥Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B-1W8, Canada
| | - David A Jaffray
- †Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, Ontario M5G-1P5, Canada.,∥Department of Medical Biophysics, University of Toronto, 101 College Street, Suite 15-701, Toronto, Ontario M5G 1L7, Canada
| | - Demian R Ifa
- ‡Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J-1P3, Canada
| | - Arash Zarrine-Afsar
- †Techna Institute for the Advancement of Technology for Health, University Health Network, Toronto, Ontario M5G-1P5, Canada.,§Department of Surgery, University of Toronto, 149 College Street, Toronto, Ontario M5T-1P5, Canada.,⊥Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B-1W8, Canada.,∥Department of Medical Biophysics, University of Toronto, 101 College Street, Suite 15-701, Toronto, Ontario M5G 1L7, Canada
| |
Collapse
|
26
|
König I, Zarrine-Afsar A, Aznauryan M, Soranno A, Wunderlich B, Dingfelder F, Stüber JC, Plückthun A, Nettels D, Schuler B. Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells. Nat Methods 2015; 12:773-9. [PMID: 26147918 DOI: 10.1038/nmeth.3475] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/22/2015] [Indexed: 12/18/2022]
Abstract
Single-molecule methods have become widely used for quantifying the conformational heterogeneity and structural dynamics of biomolecules in vitro. Their application in vivo, however, has remained challenging owing to shortcomings in the design and reproducible delivery of labeled molecules, the range of applicable analysis methods, and suboptimal cell culture conditions. By addressing these limitations in an integrated approach, we demonstrate the feasibility of probing protein dynamics from milliseconds down to the nanosecond regime in live eukaryotic cells with confocal single-molecule Förster resonance energy transfer (FRET) spectroscopy. We illustrate the versatility of the approach by determining the dimensions and submicrosecond chain dynamics of an intrinsically disordered protein; by detecting even subtle changes in the temperature dependence of protein stability, including in-cell cold denaturation; and by quantifying the folding dynamics of a small protein. The methodology opens possibilities for assessing the effect of the cellular environment on biomolecular conformation, dynamics and function.
Collapse
Affiliation(s)
- Iwo König
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Mikayel Aznauryan
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andrea Soranno
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Bengt Wunderlich
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Fabian Dingfelder
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Jakob C Stüber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| |
Collapse
|
27
|
Rosenzweig R, Moradi S, Zarrine-Afsar A, Glover JR, Kay LE. Unraveling the mechanism of protein disaggregation through a ClpB-DnaK interaction. Science 2013; 339:1080-3. [PMID: 23393091 DOI: 10.1126/science.1233066] [Citation(s) in RCA: 199] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
HSP-100 protein machines, such as ClpB, play an essential role in reactivating protein aggregates that can otherwise be lethal to cells. Although the players involved are known, including the DnaK/DnaJ/GrpE chaperone system in bacteria, details of the molecular interactions are not well understood. Using methyl-transverse relaxation-optimized nuclear magnetic resonance spectroscopy, we present an atomic-resolution model for the ClpB-DnaK complex, which we verified by mutagenesis and functional assays. ClpB and GrpE compete for binding to the DnaK nucleotide binding domain, with GrpE binding inhibiting disaggregation. DnaK, in turn, plays a dual role in both disaggregation and subsequent refolding of polypeptide chains as they emerge from the aggregate. On the basis of a combined structural-biochemical analysis, we propose a model for the mechanism of protein aggregate reactivation by ClpB.
Collapse
Affiliation(s)
- Rina Rosenzweig
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| | | | | | | | | |
Collapse
|
28
|
Neudecker P, Robustelli P, Cavalli A, Walsh P, Lundström P, Zarrine-Afsar A, Sharpe S, Vendruscolo M, Kay LE. Structure of an intermediate state in protein folding and aggregation. Science 2012; 336:362-6. [PMID: 22517863 DOI: 10.1126/science.1214203] [Citation(s) in RCA: 299] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein-folding intermediates have been implicated in amyloid fibril formation involved in neurodegenerative disorders. However, the structural mechanisms by which intermediates initiate fibrillar aggregation have remained largely elusive. To gain insight, we used relaxation dispersion nuclear magnetic resonance spectroscopy to determine the structure of a low-populated, on-pathway folding intermediate of the A39V/N53P/V55L (A, Ala; V, Val; N, Asn; P, Pro; L, Leu) Fyn SH3 domain. The carboxyl terminus remains disordered in this intermediate, thereby exposing the aggregation-prone amino-terminal β strand. Accordingly, mutants lacking the carboxyl terminus and thus mimicking the intermediate fail to safeguard the folding route and spontaneously form fibrillar aggregates. The structure provides a detailed characterization of the non-native interactions stabilizing an aggregation-prone intermediate under native conditions and insight into how such an intermediate can derail folding and initiate fibrillation.
Collapse
Affiliation(s)
- Philipp Neudecker
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Zarrine-Afsar A, Barends TRM, Müller C, Fuchs MR, Lomb L, Schlichting I, Miller RJD. Crystallography on a chip. Acta Crystallogr D Biol Crystallogr 2012; 68:321-3. [PMID: 22349234 DOI: 10.1107/s0907444911055296] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2011] [Accepted: 12/22/2011] [Indexed: 11/11/2022]
Abstract
A new chip-based crystal-mounting approach for rapid room-temperature data collection from numerous crystals is described. This work was motivated by the recent development of X-ray free-electron lasers. These novel sources deliver very intense femtosecond X-ray pulses that promise to yield high-resolution diffraction data of nanocrystals before their destruction by radiation damage. Thus, the concept of `diffraction before destruction' requires rapid replenishment of the sample for each exposure. The chip promotes the self-assembly of an array of protein crystals on a surface. Rough features on the surface cause the crystals to adopt random orientations, allowing efficient sampling of reciprocal space.
Collapse
Affiliation(s)
- Arash Zarrine-Afsar
- Max Planck Research Group for Structural Dynamics, Center for Free-Electron Laser Science, Department of Physics, University of Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | | | | | | | | | | | | |
Collapse
|
30
|
Zarrine-Afsar A, Dahesh S, Davidson AR. A residue in helical conformation in the native state adopts a β-strand conformation in the folding transition state despite its high and canonical Φ-value. Proteins 2012; 80:1343-9. [PMID: 22274997 DOI: 10.1002/prot.24030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 12/19/2011] [Accepted: 01/02/2012] [Indexed: 11/10/2022]
Abstract
Delineating structures of the transition states in protein folding reactions has provided great insight into the mechanisms by which proteins fold. The most common method for obtaining this information is Φ-value analysis, which is carried out by measuring the changes in the folding and unfolding rates caused by single amino acid substitutions at various positions within a given protein. Canonical Φ-values range between 0 and 1, and residues displaying high values within this range are interpreted to be important in stabilizing the transition state structure, and to elicit this stabilization through native-like interactions. Although very successful in defining the general features of transition state structures, Φ-value analysis can be confounded when non-native interactions stabilize this state. In addition, direct information on backbone conformation within the transition state is not provided. In the work described here, we have investigated structure formation at a conserved β-bulge (with helical conformation) in the Fyn SH3 domain by characterizing the effects of substituting all natural amino acids at one position within this structural motif. By comparing the effects on folding rates of these substitutions with database-derived local structure propensity values, we have determined that this position adopts a non-native backbone conformation in the folding transition state. This result is surprising because this position displays a high and canonical Φ-value of 0.7. This work emphasizes the potential role of non-native conformations in folding pathways and demonstrates that even positions displaying high and canonical Φ-values may, nevertheless, adopt a non-native conformation in the transition state.
Collapse
Affiliation(s)
- Arash Zarrine-Afsar
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S-1A8, Canada
| | | | | |
Collapse
|
31
|
Zarrine-Afsar A, Zhang Z, Schweiker KL, Makhatadze GI, Davidson AR, Chan HS. Kinetic consequences of native state optimization of surface-exposed electrostatic interactions in the Fyn SH3 domain. Proteins 2011; 80:858-70. [PMID: 22161863 DOI: 10.1002/prot.23243] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 10/24/2011] [Accepted: 10/29/2011] [Indexed: 11/11/2022]
Abstract
Optimization of surface exposed charge-charge interactions in the native state has emerged as an effective means to enhance protein stability; but the effect of electrostatic interactions on the kinetics of protein folding is not well understood. To investigate the kinetic consequences of surface charge optimization, we characterized the folding kinetics of a Fyn SH3 domain variant containing five amino acid substitutions that was computationally designed to optimize surface charge-charge interactions. Our results demonstrate that this optimized Fyn SH3 domain is stabilized primarily through an eight-fold acceleration in the folding rate. Analyses of the constituent single amino acid substitutions indicate that the effects of optimization of charge-charge interactions on folding rate are additive. This is in contrast to the trend seen in folded state stability, and suggests that electrostatic interactions are less specific in the transition state compared to the folded state. Simulations of the transition state using a coarse-grained chain model show that native electrostatic contacts are weakly formed, thereby making the transition state conducive to nonspecific, or even nonnative, electrostatic interactions. Because folding from the unfolded state to the folding transition state for small proteins is accompanied by an increase in charge density, nonspecific electrostatic interactions, that is, generic charge density effects can have a significant contribution to the kinetics of protein folding. Thus, the interpretation of the effects of amino acid substitutions at surface charged positions may be complicated and consideration of only native-state interactions may fail to provide an adequate picture.
Collapse
Affiliation(s)
- Arash Zarrine-Afsar
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | | | | | | | | | | |
Collapse
|
32
|
Zarrine-Afsar A, Müller C, Talbot FO, Miller RJD. Self-Localizing Stabilized Mega-Pixel Picoliter Arrays with Size-Exclusion Sorting Capabilities. Anal Chem 2010; 83:767-73. [DOI: 10.1021/ac1021024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Arash Zarrine-Afsar
- Max Planck Research Group for Structural Dynamics, Department of Physics, University of Hamburg, Centre for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607 Germany, and Departments of Chemistry and Physics, Institute for Optical Sciences, 80 St. George Street, University of Toronto, Toronto, ON, Canada M5S-3H6
| | - Christina Müller
- Max Planck Research Group for Structural Dynamics, Department of Physics, University of Hamburg, Centre for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607 Germany, and Departments of Chemistry and Physics, Institute for Optical Sciences, 80 St. George Street, University of Toronto, Toronto, ON, Canada M5S-3H6
| | - Francis O. Talbot
- Max Planck Research Group for Structural Dynamics, Department of Physics, University of Hamburg, Centre for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607 Germany, and Departments of Chemistry and Physics, Institute for Optical Sciences, 80 St. George Street, University of Toronto, Toronto, ON, Canada M5S-3H6
| | - R. J. Dwayne Miller
- Max Planck Research Group for Structural Dynamics, Department of Physics, University of Hamburg, Centre for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607 Germany, and Departments of Chemistry and Physics, Institute for Optical Sciences, 80 St. George Street, University of Toronto, Toronto, ON, Canada M5S-3H6
| |
Collapse
|
33
|
Zarrine-Afsar A, Lin SL, Neudecker P. Mutational investigation of protein folding transition states by Phi-value analysis and beyond: lessons from SH3 domain folding. Biochem Cell Biol 2010; 88:231-8. [PMID: 20453926 DOI: 10.1139/o09-153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Understanding how proteins adopt their unique native structures requires a complete structural characterization of the rate-limiting transition state(s) along the folding pathway. By definition, transition states are not significantly populated and are only accessible via folding kinetics studies. In this respect, interpreting the kinetic effects of amino acid substitutions (especially to Ala) via Phi-value analysis is the most common method to probe the structure of these transient, yet important states. A critical review of the key assumptions required for rigorous interpretation of Phi values reveals that a multiple substitution strategy in which a position of interest is mutated to a variety of amino acids, and not exclusively to Ala, provides the best means to characterize folding transition states. This approach has proven useful in revealing non-native interactions and (or) conformations in folding transition states. Moreover, by simultaneously examining the folding kinetics of multiple substitutions made at a single surface-exposed position using the Brønsted analysis the backbone conformation in a folding transition state can be investigated. For folding equilibria with exchange rates on the order of milliseconds, the kinetic parameters for Phi-value analysis can be obtained from NMR relaxation dispersion experiments, under fully native conditions, along with a wealth of high-resolution structural information about the states in exchange (native, denatured, and intermediate states that populate the pathway). This additional structural information, which is not readily obtained through stopped-flow based methods, can significantly facilitate the interpretation of Phi values because it often reports on the validity of the assumptions required for a rigorous interpretation of Phi values.
Collapse
Affiliation(s)
- Arash Zarrine-Afsar
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | | | | |
Collapse
|
34
|
Lin SL, Zarrine-Afsar A, Davidson AR. The osmolyte trimethylamine-N-oxide stabilizes the Fyn SH3 domain without altering the structure of its folding transition state. Protein Sci 2009; 18:526-36. [PMID: 19241379 DOI: 10.1002/pro.52] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Trimethylamine-N-oxide (TMAO) is a naturally occurring osmolyte that stabilizes proteins against denaturation. Although the impact of TMAO on the folding thermodynamics of many proteins has been well characterized, far fewer studies have investigated its effects on protein folding kinetics. In particular, no previous studies have used Phi-value analysis to determine whether TMAO may alter the structure of the folding transition state. Here we have measured the effects on folding kinetics of 16 different amino acid substitutions distributed across the structure of the Fyn SH3 domain both in the presence and absence of TMAO. The folding and unfolding rates in TMAO, on average, improved to equivalent degrees, with a twofold increase in the protein folding rate accompanied by a twofold decrease in the unfolding rate. Importantly, TMAO caused little alteration to the Phi-values of the mutants tested, implying that this compound minimally perturbs the folding transition state structure. Furthermore, the solvent accessibility of the transition state was not altered as reflected in an absence of a TMAO-induced change in the denaturant beta(T) (D) factors. Through TMAO-induced folding studies, a beta(T) (TMAO) factor of 0.5 was calculated for this compound, suggesting that the protein backbone, which is the target of action of TMAO, is 50% exposed in the transition state as compared to the native state. This finding is consistent with the equivalent effects of TMAO on the folding and unfolding rates. Through thermodynamic analysis of mutants, we also discovered that the stabilizing effect of TMAO is lessened with increasing temperature.
Collapse
Affiliation(s)
- Sung Lun Lin
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | | | | |
Collapse
|
35
|
Zhang F, Zarrine-Afsar A, Al-Abdul-Wahid MS, Prosser RS, Davidson AR, Woolley GA. Structure-Based Approach to the Photocontrol of Protein Folding. J Am Chem Soc 2009; 131:2283-9. [PMID: 19170498 DOI: 10.1021/ja807938v] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fuzhong Zhang
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto M5S 3H6 Canada, Department of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, M5S 1A8, Canada, and Department of Chemistry, University of Toronto at Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, L5L 1C6, Canada
| | - Arash Zarrine-Afsar
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto M5S 3H6 Canada, Department of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, M5S 1A8, Canada, and Department of Chemistry, University of Toronto at Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, L5L 1C6, Canada
| | - M. Sameer Al-Abdul-Wahid
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto M5S 3H6 Canada, Department of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, M5S 1A8, Canada, and Department of Chemistry, University of Toronto at Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, L5L 1C6, Canada
| | - R. Scott Prosser
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto M5S 3H6 Canada, Department of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, M5S 1A8, Canada, and Department of Chemistry, University of Toronto at Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, L5L 1C6, Canada
| | - Alan R. Davidson
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto M5S 3H6 Canada, Department of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, M5S 1A8, Canada, and Department of Chemistry, University of Toronto at Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, L5L 1C6, Canada
| | - G. Andrew Woolley
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto M5S 3H6 Canada, Department of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, M5S 1A8, Canada, and Department of Chemistry, University of Toronto at Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, L5L 1C6, Canada
| |
Collapse
|
36
|
Schweiker KL, Zarrine-Afsar A, Davidson AR, Makhatadze GI. Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions. Protein Sci 2007; 16:2694-702. [PMID: 18029422 PMCID: PMC2222822 DOI: 10.1110/ps.073091607] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2007] [Revised: 08/29/2007] [Accepted: 08/29/2007] [Indexed: 10/22/2022]
Abstract
Computational design of surface charge-charge interactions has been demonstrated to be an effective way to increase both the thermostability and the stability of proteins. To test the robustness of this approach for proteins with predominantly beta-sheet secondary structure, the chicken isoform of the Fyn SH3 domain was used as a model system. Computational analysis of the optimal distribution of surface charges showed that the increase in favorable energy per substitution begins to level off at five substitutions; hence, the designed Fyn sequence contained four charge reversals at existing charged positions and one introduction of a new charge. Three additional variants were also constructed to explore stepwise contributions of these substitutions to Fyn stability. The thermodynamic stabilities of the variants were experimentally characterized using differential scanning calorimetry and far-UV circular dichroism spectroscopy and are in very good agreement with theoretical predictions from the model. The designed sequence was found to have increased the melting temperature, DeltaT (m) = 12.3 +/- 0.2 degrees C, and stability, DeltaDeltaG(25 degrees C) = 7.1 +/- 2.2 kJ/mol, relative to the wild-type protein. The experimental data suggest that a significant increase in stability can be achieved through a very small number of amino acid substitutions. Consistent with a number of recent studies, the presented results clearly argue for a seminal role of surface charge-charge interactions in determining protein stability and suggest that the optimization of surface interactions can be an attractive strategy to complement algorithms optimizing interactions in the protein core to further enhance protein stability.
Collapse
Affiliation(s)
- Katrina L Schweiker
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
| | | | | | | |
Collapse
|
37
|
Neudecker P, Zarrine-Afsar A, Davidson AR, Kay LE. Phi-value analysis of a three-state protein folding pathway by NMR relaxation dispersion spectroscopy. Proc Natl Acad Sci U S A 2007; 104:15717-22. [PMID: 17898173 PMCID: PMC2000424 DOI: 10.1073/pnas.0705097104] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Indexed: 11/18/2022] Open
Abstract
Experimental studies of protein folding frequently are consistent with two-state folding kinetics. However, recent NMR relaxation dispersion studies of several fast-folding mutants of the Fyn Src homology 3 (SH3) domain have established that folding proceeds through a low-populated on-pathway intermediate, which could not be detected with stopped-flow experiments. The dispersion experiments provide precise kinetic and thermodynamic parameters that describe the folding pathway, along with a detailed site-specific structural characterization of both the intermediate and unfolded states from the NMR chemical shifts that are extracted. Here we describe NMR relaxation dispersion Phi-value analysis of the A39V/N53P/V55L Fyn SH3 domain, where the effects of suitable point mutations on the energy landscape are quantified, providing additional insight into the structure of the folding intermediate along with per-residue structural information of both rate-limiting transition states that was not available from previous studies. In addition to the advantage of delineating the full three-state folding pathway, the use of NMR relaxation dispersion as opposed to stopped-flow kinetics to quantify Phi values facilitates their interpretation because the obtained chemical shifts monitor any potential structural changes along the folding pathway that might be introduced by mutation, a significant concern in their analysis. Phi-Value analysis of several point mutations of A39V/N53P/V55L Fyn SH3 establishes that the beta(3)-beta(4)-hairpin already is formed in the first transition state, whereas strand beta(1), which forms nonnative interactions in the intermediate, does not fully adopt its native conformation until after the final transition state. The results further support the notion that on-pathway intermediates can be stabilized by nonnative contacts.
Collapse
Affiliation(s)
- Philipp Neudecker
- Departments of Medical Genetics and Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 3H6
| | - Arash Zarrine-Afsar
- Departments of Medical Genetics and Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
| | - Alan R. Davidson
- Departments of Medical Genetics and Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
| | - Lewis E. Kay
- Departments of Medical Genetics and Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 3H6
| |
Collapse
|
38
|
Murphy JM, Korzhnev DM, Ceccarelli DF, Briant DJ, Zarrine-Afsar A, Sicheri F, Kay LE, Pawson T. Conformational instability of the MARK3 UBA domain compromises ubiquitin recognition and promotes interaction with the adjacent kinase domain. Proc Natl Acad Sci U S A 2007; 104:14336-41. [PMID: 17726107 PMCID: PMC1964837 DOI: 10.1073/pnas.0703012104] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Par-1/MARK protein kinases play a pivotal role in establishing cellular polarity. This family of kinases contains a unique domain architecture, in which a ubiquitin-associated (UBA) domain is located C-terminal to the kinase domain. We have used a combination of x-ray crystallography and NMR dynamics experiments to understand the interaction of the human (h) MARK3 UBA domain with the adjacent kinase domain as compared with ubiquitin. The x-ray crystal structure of the linked hMARK3 kinase and UBA domains establishes that the UBA domain forms a stable intramolecular interaction with the N-terminal lobe of the kinase domain. However, solution-state NMR studies of the isolated UBA domain indicate that it is highly dynamic, undergoing conformational transitions that can be explained by a folding-unfolding equilibrium. NMR titration experiments indicated that the hMARK3 UBA domain has a detectable but extremely weak affinity for mono ubiquitin, which suggests that conformational instability of the isolated hMARK3 UBA domain attenuates binding to ubiquitin despite the presence of residues typically involved in ubiquitin recognition. Our data identify a molecular mechanism through which the hMARK3 UBA domain has evolved to bind the kinase domain, in a fashion that stabilizes an open conformation of the N- and C-terminal lobes, at the expense of its capacity to engage ubiquitin. These results may be relevant more generally to the 30% of UBA domains that lack significant ubiquitin-binding activity, and they suggest a unique mechanism by which interaction domains may evolve new binding properties.
Collapse
Affiliation(s)
- James M. Murphy
- *Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5; and
| | - Dmitry M. Korzhnev
- Departments of Medical Genetics
- Biochemistry, and
- Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Derek F. Ceccarelli
- *Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5; and
| | - Douglas J. Briant
- *Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5; and
| | | | - Frank Sicheri
- *Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5; and
- Departments of Medical Genetics
| | - Lewis E. Kay
- Departments of Medical Genetics
- Biochemistry, and
- Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- To whom correspondence may be addressed. E-mail: or
| | - Tony Pawson
- *Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5; and
- Departments of Medical Genetics
- To whom correspondence may be addressed. E-mail: or
| |
Collapse
|
39
|
Zarrine-Afsar A, Dahesh S, Davidson AR. Protein folding kinetics provides a context-independent assessment of beta-strand propensity in the Fyn SH3 domain. J Mol Biol 2007; 373:764-74. [PMID: 17850820 DOI: 10.1016/j.jmb.2007.07.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 07/13/2007] [Accepted: 07/26/2007] [Indexed: 11/16/2022]
Abstract
Structural database-derived propensities for amino acids to adopt particular local protein structures, such as alpha-helix and beta-strand, have long been recognized and effectively exploited for the prediction of protein secondary structure. However, the experimental verification of database-derived propensities using mutagenesis studies has been problematic, especially for beta-strand propensities, because local structural preferences are often confounded by non-local interactions arising from formation of the native tertiary structure. Thus, the overall thermodynamic stability of a protein is not always altered in a predictable manner by changes in local structural propensity at a single position. In this study, we have undertaken an investigation of the relationship between beta-strand propensity and protein folding kinetics. By characterizing the effects of a wide variety of amino acid substitutions at two different beta-strand positions in an SH3 domain, we have found that the observed changes in protein folding rates are very well correlated to beta-strand propensities for almost all of the substitutions examined. In contrast, there is little correlation between propensities and unfolding rates. These data indicate that beta-strand conformation is well formed in the structured portion of the SH3 domain transition state, and that local structure propensity strongly influences the stability of the transition state. Since the transition state is known to be packed more loosely than the native state and likely lacks many of the non-local stabilizing interactions seen in the native state, we suggest that folding kinetics studies may generally provide an effective means for the experimental validation of database-derived local structural propensities.
Collapse
Affiliation(s)
- Arash Zarrine-Afsar
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S-1A8
| | | | | |
Collapse
|
40
|
Neudecker P, Zarrine-Afsar A, Choy WY, Muhandiram DR, Davidson AR, Kay LE. Identification of a Collapsed Intermediate with Non-native Long-range Interactions on the Folding Pathway of a Pair of Fyn SH3 Domain Mutants by NMR Relaxation Dispersion Spectroscopy. J Mol Biol 2006; 363:958-76. [PMID: 16989862 DOI: 10.1016/j.jmb.2006.08.047] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Revised: 08/16/2006] [Accepted: 08/17/2006] [Indexed: 11/19/2022]
Abstract
Recent 15N and 13C spin-relaxation dispersion studies of fast-folding mutants of the Fyn SH3 domain have established that folding proceeds through a low-populated on-pathway intermediate (I) where the central beta-sheet is at least partially formed, but without interactions between the NH2- and COOH-terminal beta-strands that exist in the folded state (F). Initial studies focused on mutants where Gly48 is replaced; in an effort to establish whether this intermediate is a general feature of Fyn SH3 folding a series of 15N relaxation experiments monitoring the folding of Fyn SH3 mutants N53P/V55L and A39V/N53P/V55L are reported here. For these mutants as well, folding proceeds through an on-pathway intermediate with similar features to those observed for G48M and G48V Fyn SH3 domains. However, the 15N chemical shifts extracted for the intermediate indicate pronounced non-native contacts between the NH2 and COOH-terminal regions not observed previously. The kinetic parameters extracted for the folding of A39V/N53P/V55L Fyn SH3 from the three-state folding model F<-->I<-->U are in good agreement with folding and unfolding rates extrapolated to zero denaturant obtained from stopped-flow experiments analyzed in terms of a simplified two-state folding reaction. The folding of the triple mutant was studied over a wide range of temperatures, establishing that there is no difference in heat capacities between F and I states. This confirms a compact folding intermediate structure, which is supported by the 15N chemical shifts of the I state extracted from the dispersion data. The temperature-dependent relaxation data simplifies data analysis because at low temperatures (< 25 degrees C) the unfolded state (U) is negligibly populated relative to I and F. A comparison between parameters extracted at low temperatures where the F<-->I exchange model is appropriate with those from the more complex, three-state model at higher temperatures has been used to validate the protocol for analysis of three-site exchange relaxation data.
Collapse
Affiliation(s)
- Philipp Neudecker
- Departments of Medical Genetics and Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | | | | | | | | | | |
Collapse
|
41
|
Korzhnev DM, Neudecker P, Zarrine-Afsar A, Davidson AR, Kay LE. Abp1p and Fyn SH3 domains fold through similar low-populated intermediate states. Biochemistry 2006; 45:10175-83. [PMID: 16922492 DOI: 10.1021/bi0611560] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Src homology 3 (SH3) domains are small modules that are thought to fold via a two-state mechanism, without the accumulation of significant populations of intermediate states. Relaxation dispersion NMR studies of the folding of G48V and G48M mutants of the Fyn SH3 domain have established that, at least for these modules, folding proceeds through the formation of a transient on-pathway intermediate with an equilibrium population of 1-2% that can be readily detected [Korzhnev, D. M., et al. (2004) Nature 430, 586-590]. To investigate the generality of this result, we present an (15)N relaxation dispersion NMR study of a pair of additional SH3 domains, including a G48V mutant of a stabilized Abp1p SH3 domain that shares 36% sequence identity with the Fyn SH3 module, and a A39V/N53P/V55L mutant Fyn SH3 domain. A transient folding intermediate is detected for both of the proteins studied here, and the dispersion data are well fit to a folding model of the form F <--> I <--> U, where F, I, and U correspond to folded, intermediate, and unfolded states, respectively. The temperature dependencies of the folding/unfolding rate constants were obtained so that the thermodynamic properties of each of F, I, and U could be established. The detection of I states in folding pathways of all SH3 domains examined to date via relaxation dispersion NMR spectroscopy indicates that such intermediates may well be a conserved feature in the folding of such domains in general but that their transient nature along with their low population makes detection difficult using more well-established approaches to the study of folding.
Collapse
Affiliation(s)
- Dmitry M Korzhnev
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | | | | | | | | |
Collapse
|
42
|
Zarrine-Afsar A, Mittermaier A, Kay LE, Davidson AR. Protein stabilization by specific binding of guanidinium to a functional arginine-binding surface on an SH3 domain. Protein Sci 2006; 15:162-70. [PMID: 16373478 PMCID: PMC2242360 DOI: 10.1110/ps.051829106] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Guanidinium hydrochloride (GuHCl) at low concentrations significantly stabilizes the Fyn SH3 domain. In this work, we have demonstrated that this stabilizing effect is manifested through a dramatic (five- to sixfold) decrease in the unfolding rate of the domain with the folding rate being affected minimally. This behavior contrasts to the effect of NaCl, which stabilizes this domain by accelerating the folding rate. These data imply that the stabilizing effect of GuHCl is not predominantly ionic in nature. Through NMR studies, we have identified a specific binding site for guanidinium, and we have determined a dissociation constant of 90 mM for this interaction. The guanidinium-binding site overlaps with a functionally important arginine-binding pocket on the domain surface, and we have shown that GuHCl is a specific inhibitor of the peptide-binding activity of the domain. A different SH3 domain possessing a similar arginine-binding pocket is also thermodynamically stabilized by GuHCl. These data suggest that many proteins that normally interact with arginine-containing ligands may also be able to specifically interact with guanidinium. Thus, some caution should be used when using GuHCl as a denaturant in protein folding studies. Since arginine-mediated interactions are often important in the energetics of protein-protein interactions, our observations could be relevant for the design of small molecule inhibitors of protein-protein interactions.
Collapse
|
43
|
Maxwell KL, Wildes D, Zarrine-Afsar A, De Los Rios MA, Brown AG, Friel CT, Hedberg L, Horng JC, Bona D, Miller EJ, Vallée-Bélisle A, Main ERG, Bemporad F, Qiu L, Teilum K, Vu ND, Edwards AM, Ruczinski I, Poulsen FM, Kragelund BB, Michnick SW, Chiti F, Bai Y, Hagen SJ, Serrano L, Oliveberg M, Raleigh DP, Wittung-Stafshede P, Radford SE, Jackson SE, Sosnick TR, Marqusee S, Davidson AR, Plaxco KW. Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci 2005; 14:602-16. [PMID: 15689503 PMCID: PMC2279278 DOI: 10.1110/ps.041205405] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Recent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. Our ability to test and refine these relationships has been limited, however, by a variety of difficulties associated with the comparison of folding and unfolding rates, thermodynamics, and structure across diverse sets of proteins. These difficulties include the wide, potentially confounding range of experimental conditions and methods employed to date and the difficulty of obtaining correct and complete sequence and structural details for the characterized constructs. The lack of a single approach to data analysis and error estimation, or even of a common set of units and reporting standards, further hinders comparative studies of folding. In an effort to overcome these problems, we define here a "consensus" set of experimental conditions (25 degrees C at pH 7.0, 50 mM buffer), data analysis methods, and data reporting standards that we hope will provide a benchmark for experimental studies. We take the first step in this initiative by describing the folding kinetics of 30 apparently two-state proteins or protein domains under the consensus conditions. The goal of our efforts is to set uniform standards for the experimental community and to initiate an accumulating, self-consistent data set that will aid ongoing efforts to understand the folding process.
Collapse
Affiliation(s)
- Karen L Maxwell
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
Theoretical and experimental studies of protein folding have suggested that the topology of the native state may be the most important factor determining the folding pathway of a protein, independent of its specific amino acid sequence. To test this concept, many experimental studies have been carried out with the aim of comparing the folding pathways of proteins that possess similar tertiary structures, but divergent sequences. Many of these studies focus on quantitative comparisons of folding transition state structures, as determined by Phi(f) value analysis of folding kinetic data. In some of these studies, folding transition state structures are found to be highly conserved, whereas in others they are not. We conclude that folds displaying more conserved transition state structures may have the most restricted number of possible folding pathways and that folds displaying low transition state structural conservation possess many potential pathways for reaching the native state.
Collapse
Affiliation(s)
- Arash Zarrine-Afsar
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | | |
Collapse
|
45
|
Abstract
Over the past decade, the "protein engineering method" has been used to investigate the folding pathways of more than 20 different proteins. This method involves measuring the folding and unfolding rates of mutant proteins with single amino acid substitutions spread across the sequence. Comparison of folding rates of the mutant proteins to that of the wild-type protein allows the calculation of the phi value, which can be used to evaluate the stabilizing contribution of an amino acid side chain to the structure of the folding transition state. Here, we review the methodology for analysing data collected in protein engineering folding kinetics studies. We discuss the calculation of folding rates and kinetic m values, the estimation of errors in folding kinetics experiments, phi value calculation including potential pitfalls of the analysis, Brønsted plots, detecting Hammond behaviour, and the analysis of curved chevron plots.
Collapse
Affiliation(s)
- Arash Zarrine-Afsar
- Department of Biochemistry, University of Toronto, Toronto, Ont. M5S 1A8, Canada
| | | |
Collapse
|
46
|
Zarrine-Afsar A, Krylov SN. Use of capillary electrophoresis and endogenous fluorescent substrate to monitor intracellular activation of protein kinase A. Anal Chem 2004; 75:3720-4. [PMID: 14572035 DOI: 10.1021/ac034463+] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we demonstrate for the first time the use of an endogenous multiphosphorylatable substrate for monitoring the intracellular activation of kinase with capillary electrophoresis. First, we devised a novel PCR-based strategy for controlled generation of short multirepeat DNA sequences and applied this method to generate a green fluorescence protein (GFP)-tagged protein substrate containing eight phosphorylation sites for protein kinase A (PKA). The protein substrate was transiently expressed in C2C12 rat myoblast cells, and intracellular PKA was then activated by adding [8]-bromo-cyclic AMP to the cell culture medium. Phosphorylated product and nonphosphorylated substrate present in the crude cell extract were separated by capillary zone electrophoresis and detected with laser-induced fluorescence of the GFP tag. The identities of two electrophoretic peaks were confirmed by both phosphorylation of the substrate and dephosphorylation of the product in vitro. The proposed method was applied to monitoring the activation of PKA in single myoblast cells. It advantageously allowed us to avoid microinjection of the substrate, the procedure that is both hard to perform and excessively invasive when applied to small mammalian cells.
Collapse
|
47
|
Di Nardo AA, Korzhnev DM, Stogios PJ, Zarrine-Afsar A, Kay LE, Davidson AR. Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation. Proc Natl Acad Sci U S A 2004; 101:7954-9. [PMID: 15148398 PMCID: PMC419538 DOI: 10.1073/pnas.0400550101] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Through a mutagenic investigation of Gly-48, a highly conserved position in the Src homology 3 domain, we have discovered a series of amino acid substitutions that are highly destabilizing, yet dramatically accelerate protein folding, some up to 10-fold compared with the wild-type rate. The unique folding properties of these mutants allowed for accurate measurement of their folding and unfolding rates in water with no denaturant by using an NMR spin relaxation dispersion technique. A strong correlation was found between beta-sheet propensity and the folding rates of the Gly-48 mutants, even though Gly-48 lies in an unusual non-beta-strand backbone conformation in the native state. This finding indicates that the accelerated folding rates of the Gly-48 mutants are the result of stabilization of a nonnative beta-strand conformation in the transition-state structure at this position, thus providing the first, to our knowledge, experimentally elucidated example of a mechanism by which folding can occur fastest through a nonnative conformation. We also demonstrate that residues that are most stabilizing in the transition-state structure are most destabilizing in the native state, and also cause the greatest reductions in in vitro functional activity. These data indicate that the unusual native conformation of the Gly-48 position is important for function, and that evolutionary selection for function can result in a domain that folds at a rate far below the maximum possible.
Collapse
Affiliation(s)
- Ariel A Di Nardo
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | | | | | | | | | | |
Collapse
|