Three-Dimensional Image of Cleavage Bodies in Nuclei Is Configured Using Gas Cluster Ion Beam with Time-of-Flight Secondary Ion Mass Spectrometry.

Structural variations of DNA in nuclei are deeply related with development, aging, and diseases through transcriptional regulation. In order to bare cross sections of samples maintaining sub-micron structures, an Ar2500(+)-gas cluster ion beam (GCIB) sputter was recently engineered. By introducing GCIB sputter to time-of-flight secondary ion mass spectrometry (TOF-SIMS), we analyzed the 3D configuration and chemical composition of subnuclear structures of pyramidal cells in the CA2 region in mouse brain hippocampus. Depth profiles of chemicals were analyzed as 3D distributions by combining topographic analyses. Signals corresponding to anions such as CN(-) and PO3(-) were distributed characteristically in the shape of cell organelles. CN(-) signals overlapped DAPI fluorescence signals corresponding to nuclei. The clusters shown by PO3(-) and those of adenine ions were colocalized inside nuclei revealed by the 3D reconstruction. Taking into account their size and their number in each nucleus, those clusters could be in the cleavage bodies, which are a kind of intranuclear structure.

Palmitic acid, verified by lipid profiling using secondary ion mass spectrometry, demonstrates anti-multiple myeloma activity.

Recent studies indicate that lipid metabolic changes affect the survival of multiple myeloma (MM) cells. Time-of-flight secondary ion mass spectrometry (TOF-SIMS), an imaging mass spectrometry technique, is used to visualize the subcellular distribution of biomolecules including lipids. We therefore applied this method to human clinical specimens to analyze the membrane fatty acid composition and determine candidate molecules for MM therapies. We isolated MM cells and normal plasma cells (PCs) from bone marrow aspirates of MM patients and healthy volunteers, respectively, and these separated cells were analyzed by TOF-SIMS. Multiple ions including fatty acids were detected and their ion counts were estimated. In MM cells, the mean intensity of palmitic acid was significantly lower than the mean intensity in PCs. In a cell death assay, palmitic acid reduced U266 cell viability dose-dependently at doses between 50 and 1000 µM. The percentage of apoptotic cells increased from 24h after palmitic acid administration. In contrast, palmitic acid had no effect on the viability of normal peripheral blood mononuclear cells (PBMCs). The results of this study indicated that palmitic acid is a potential candidate for novel therapeutic agents that specifically attack MM cells.

Single-cell time-of-flight secondary ion mass spectrometry reveals that human breast cancer stem cells have significantly lower content of palmitoleic acid compared to their counterpart non-stem cancer cells.

Lipids comprise the primary component of cell membranes. Imaging mass spectrometry is increasingly being used to visualize membranous lipids in clinical specimens, and it has revealed that abnormal lipid metabolism is related to the development of diseases. To characterize cell populations which are rare and sparsely localized in tissues, we conducted time-of-flight secondary ion mass spectrometry (TOF-SIMS) analyses of individual cells sorted by fluorescence activated cell sorting (FACS) and applied the method to analyze breast cancer stem cells (CSCs). TOF-SIMS analyses visualized phosphoric acids and four fatty acid (FA) species in the sorted CD45(-)/CD44(+)/CD24(-) CSCs, and these ions are suspected to have originated from membranous phospholipids as they were uniformly detected from the locus where the cells attached. Integrated ion intensity of palmitoleic acids [FA(16:1)] normalized by phosphoric acid signals were decreased significantly in CSCs as compared to that of CD45(-)/CD44(-)/CD24(+) non-stem cancer cells (NSCCs). This finding was supported by liquid chromatography coupled electrospray ionization-tandem mass spectrometry analysis, which revealed phosphatidylcholine (PC)(16:0/16:1) to be less abundant and PC(16:0/16:0) to be more abundant in CSCs as compared to NSCCs. Therefore, our novel method successfully provided lipid composition analysis of individual cells classified by the expression of a complex combination of cell-surface markers. The lipid compositions of CSCs originating from the heterogeneous cellular populations of clinical specimens were successfully characterized by this method.

The stratum corneum comprises three layers with distinct metal-ion barrier properties.

The stratum corneum (SC), the outermost barrier of mammalian bodies, consists of layers of cornified keratinocytes with intercellular spaces sealed with lipids. The insolubility of the SC has hampered in-depth analysis, and the SC has been considered a homogeneous barrier. Here, we applied time-of-flight secondary ion mass spectrometry to demonstrate that the SC consists of three layers with distinct properties. Arginine, a major component of filaggrin-derived natural moisturizing factors, was concentrated in the middle layer, suggesting that this layer functions in skin hydration. Topical application of metal ions revealed that the outer layer allowed their passive influx and efflux, while the middle and lower layers exhibited distinct barrier properties, depending on the metal tested. Notably, filaggrin deficiency abrogated the lower layer barrier, allowing specific metal ions to permeate viable layers. These findings elucidate the multi-layered barrier function of the SC and its defects in filaggrin-deficient atopic disease patients.

TOF-SIMS imaging of halide/thiocyanate anions and hydrogen sulfide in mouse kidney sections using silver-deposited plates.

In vivo imaging of reactive small molecule metabolites with high spatial resolution and specificity could give clues to understanding pathophysiology of various diseases. We herein applied time of flight-secondary ion mass spectrometry (TOF-SIMS) to newly developed silver-deposited plates that were stamped on mouse tissues, and succeeded in visualization of halide (Cl(-), Br(-), and I(-)) and pseudohalide thiocyanate (SCN(-)) anions, a class of substrates for neutrophils/eosinophil peroxidases to produce hypohalous acids (HOX/OX(-) mixture; X: (pseudo)halides), as well as hydrogen sulfide (H(2)S). Forty-micrometer frozen mouse kidney sections on cover glasses were attached to 37 °C preheated silver-deposited plates and incubated at -10 °C for 1 h. After sputter cleaning to remove surface contaminants, the plates were analyzed by TOF-SIMS to identify distribution of Br(-), AgBr(2)(-), I(-), AgI(2)(-), SCN(-), as well as S(2-) and AgS(-) as products of tissue-derived H(2)S. Br(-), AgBr(2)(-), I(-), and SCN(-) anions were mainly distributed in core regions including the inner medulla and inner stripe of the outer medulla (except for I(-)), rather than outer regions such as the cortex and outer stripe of the outer medulla. AgI(2)(-) anion was spread over the whole kidney, although its levels were relatively low. In contrast, S(2-) and AgS(-) anions were mainly present in the outer regions. To our knowledge, this is the first imaging study to reveal the distribution of (pseudo)halides and H(2)S in animal tissue sections.

Detection of characteristic distributions of phospholipid head groups and fatty acids on neurite surface by time-of-flight secondary ion mass spectrometry.

Neurons have a large surface because of their long and thin neurites. This surface is composed of a lipid bilayer. Lipids have not been actively investigated so far because of some technical difficulties, although evidence from cell biology is emerging that lipids contain valuable information about their roles in the central nervous system. Recent progress in techniques, e.g., mass spectrometry, opens a new epoch of lipid research. We show herein the characteristic localization of phospholipid components in neurites by means of time-of-flight secondary ion mass spectrometry. We used explant cultures of mouse superior cervical ganglia, which are widely used by neurite investigation research. In a positive-ion detection mode, phospholipid head group molecules were predominantly detected. The ions of m/z 206.1 [phosphocholine, a common component of phosphatidylcholine (PC) and sphingomyelin (SM)] were evenly distributed throughout the neurites, whereas the ions of m/z 224.1, 246.1 (glycerophosphocholine, a part of PC, but not SM) showed relatively strong intensity on neurites adjacent to soma. In a negative-ion detection mode, fatty acids such as oleic and palmitic acids were mainly detected, showing high intensity on neurites adjacent to soma. Our results suggest that lipid components on the neuritic surface show characteristic distributions depending on neurite region.

Studies of DNA recognition mechanism of transcription factor IRF-4.

Transcription factor IFN regulatory factor-4 (IRF-4) prefers a DNA sequence including CCGAAA, though the consensus DNA-binding sequence of the IRF family proteins is NNGAAA, and the crystal structure of PU.1/IRF-4/DNA (GTGAAA) ternary complex indicates the NN region of DNA does not interact with IRF-4 directly. This suggests that there is an indirect DNA recognition mechanism in IRF-4. In order to account for the sequence preference of IRF-4, we focused on structural properties of DNA duplexes recognized by IRF-4. Here, we performed solution NMR studies on DNA duplexes containing GGGAAA and CCGAAA sequences, and assigned most of proton resonances of DNA 17 mer with GGGAAA. (1)H-(1)H NOESY spectra indicated B-form like structure for GGGAAA. We also assigned imino proton resonances of DNA 17 mer with CCGAAA. For the imino proton region, the (1)H-(1)H NOESY spectra of these two DNA duplexes were similar.

Paramagnetic NMR study of Cu(2+)-IDA complex localization on a protein surface and its application to elucidate long distance information.

The paramagnetic metal chelate complex Cu(2+)-iminodiacetic acid (Cu(2+)-IDA) was mixed with ubiquitin, a small globular protein. Quantitative analyses of (1)H and (15)N chemical shift changes and line broadenings induced by the paramagnetic effects indicated that Cu(2+)-IDA was localized to a histidine residue (His68) on the ubiquitin surface. The distances between the backbone amide proton and the Cu(2+) relaxation center were evaluated from the proton transverse relaxation rates enhanced by the paramagnetic effect. These correlated well with the distances calculated from the crystal structure up to 20 A. Here, we show that a Cu(2+)-IDA is the first paramagnetic reagent that specifically localizes to a histidine residue on the protein surface and gives the long-range distance information.

Solution NMR study of DNA recognition mechanism of IRF4 protein.

Transcription factor IRF-4 prefers the DNA sequence including CCGAAA. The consensus sequence of the IRF family proteins is NNGAAA, and all crystal structures indicate the NN region does not interact with IRF proteins directly. Here the sequence preference of IRF-4 was investigated by NMR and fluorescence antisotropy as an example of the indirect sequence recognition. The 1H-15N HSQC spectra of the IRF-4/DNA complex containing the CCGAAA sequence indicated that the 1:1 complex was formed. The dissociation constants (Kd) for two DNA oligomers containing CCGAAA and GGGAAA were determined by fluorescence antistropy, but their difference was very small.