title: An unsupervised MVA method to compare specific regions in human breast tumor tissue samples using ToF-SIMS.
abstract: Imaging time-of-flight secondary ion mass spectrometry (ToF-SIMS) and principal component analysis (PCA) were used to investigate two sets of pre- and post-chemotherapy human breast tumor tissue sections to characterize lipids associated with tumor metabolic flexibility and response to treatment. The micron spatial resolution imaging capability of ToF-SIMS provides a powerful approach to attain spatially-resolved molecular and cellular data from cancerous tissues not available with conventional imaging techniques. Three ca. 1 mm(2) areas per tissue section were analyzed by stitching together 200 μm × 200 μm raster area scans. A method to isolate and analyze specific tissue regions of interest by utilizing PCA of ToF-SIMS images is presented, which allowed separation of cellularized areas from stromal areas. These PCA-generated regions of interest were then used as masks to reconstruct representative spectra from specifically stromal or cellular regions. The advantage of this unsupervised selection method is a reduction in scatter in the spectral PCA results when compared to analyzing all tissue areas or analyzing areas highlighted by a pathologist. Utilizing this method, stromal and cellular regions of breast tissue biopsies taken pre- versus post-chemotherapy demonstrate chemical separation using negatively-charged ion species. In this sample set, the cellular regions were predominantly all cancer cells. Fatty acids (i.e. palmitic, oleic, and stearic), monoacylglycerols, diacylglycerols and vitamin E profiles were distinctively different between the pre- and post-therapy tissues. These results validate a new unsupervised method to isolate and interpret biochemically distinct regions in cancer tissues using imaging ToF-SIMS data. In addition, the method developed here can provide a framework to compare a variety of tissue samples using imaging ToF-SIMS, especially where there is section-to-section variability that makes it difficult to use a serial hematoxylin and eosin (H&E) stained section to direct the SIMS analysis.
authors.affiliation: University of Washington, Dept. of Bioengineering, MolES Building, Box 351653, Seattle, WA 98195-1653, USA. lgamble@uw.edu.
authors.forename: Blake M
authors.initials: BM
authors.lastname: Bluestein
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
authors.forename: Fionnuala
authors.initials: F
authors.lastname: Morrish
authors.affiliation: University of Washington, Dept. of Bioengineering, MolES Building, Box 351653, Seattle, WA 98195-1653, USA. lgamble@uw.edu.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Graham
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
authors.forename: Jamie
authors.initials: J
authors.lastname: Guenthoer
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
authors.forename: David
authors.initials: D
authors.lastname: Hockenbery
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
authors.forename: Peggy L
authors.initials: PL
authors.lastname: Porter
authors.affiliation: University of Washington, Dept. of Bioengineering, MolES Building, Box 351653, Seattle, WA 98195-1653, USA. lgamble@uw.edu.
authors.forename: Lara J
authors.initials: LJ
authors.lastname: Gamble
mesh_terms: D001943:Breast Neoplasms / Q000473:pathology*; D006801:Humans; D025341:Principal Component Analysis; D018629:Spectrometry, Mass, Secondary Ion / Q000379:methods*