Lipid analysis of eight human breast cancer cell lines with ToF-SIMS

Abstract

In this work, four triple negative (TN) cell lines, three ER+ and PR+ receptor positive (RP) cell lines, and one ER+, PR+, and HER2+ cell line were chemically distinguished from one another using time-of-flight secondary ion mass spectrometry (ToF-SIMS) and principal component analysis (PCA). PCA scores separation was observed between the individual cell lines within a given classification (TN and RP) and there were distinctly different trends found in the fatty acid and lipid compositions of the two different classifications. These trends indicated that the RP cell lines separated out based on the carbon chain length of the lipids while the TN cell lines showed separation based on cholesterol-related peaks (in the positive ion data). Both cell types separated out by trends in fatty acid chain length and saturation in the negative ions. These chemical differences may be manifestations of unique metabolic processes within each of the different cell lines. Additionally, the HER2+ cell line was distinguished from three other RP cell types as having a unique distribution of fatty acids including anticorrelation to 18-carbon chain fatty acids. As these cell lines could not be grown in the same growth media, a combination of chemical fixation, rinsing, C60 (+) presputtering, and selection of cellular regions-of-interest is also presented as a successful method to acquire ToF-SIMS data from cell lines grown in different media.

An unsupervised MVA method to compare specific regions in human breast tumor tissue samples using ToF-SIMS

“…47 While PCA analysis of the pre- and post-chemotherapy tissues using negative polarity ions similarly shows a trend in the scores related to fatty acids and lipids, the positive ion data results in more overlap of the scores 95% confidence intervals than found for the negative ion data. This is best shown in Supplementary Figure 4 where PC2 vs PC4 scores and corresponding loadings are shown for the positive ion data.…”

“…The presence of large fatty acid droplets, observed as well defined high intensity areas of C16:1 (C 16 H 29 O 2 − , palmitoleic acid, m/z 253.2), 43, 44 C16:0 (C 16 H 31 O 2 − , palmitic acid, m/ z 255.2), 44, 45 C18:2 (C 18 H 29 O 2 − , linoleic acid, m/z 279.2), 44, 46 C18:1 (C 18 H 33 O 2 − , oleic acid, m/z 281.2), 44, 45 and C18:0 (C 18 H 35 O 2 − , stearic acid, m/z 283.2), 13, 44, 45, 47 were occasionally observed in different tissue sections. The strong signal from the fatty acid droplets would dominate PCA and the main variability between the samples would then be related to fatty acid droplets present in that particular tissue slice.…”

Identifying exposition to low oxygen environment in human macrophages using secondary ion mass spectrometry and multivariate analysis

“…The cells were dried overnight in air and analyzed the following day. This method has proven to be an effective sample preparation process to study cells by TOF‐SIMS and obtain a molecular signature (mainly lipids) from cells …”

“…The spectral data were normalized to the sum of the intensities of the peaks for each peak list, then square‐root‐transformed before performing a PCA (Principal Component Analysis) using the JMP software (SAS) . The data preprocessing is done to minimize substrate‐related differences, limit the dynamic range of data and give more weight to high m/z values related to more chemically specific peaks . Criteria used to classify peaks were the Welch t‐test difference (difference between the two compared conditions of the mean value) corrected using the Benjamini‐Hochberg method, and the fold change of the mean between the two compared conditions.…”

“…Frozen and chemically fixated samples can be used which is of critical importance when a clinical application is foreseen. Even if TOF‐SIMS spectra from biological samples can be complex, multivariate analysis has been used with success on various cell types . Successful enhancement of secondary ion signals by direct depositing nanoparticles on sample surfaces, or alternatively using an argon gas cluster ion beam, has further extended the use of TOF‐SIMS for the analysis of biological samples.…”