Direct 3D Sampling of the Embryonic Mouse Head: Layer-wise Nanosecond Infrared Laser (NIRL) Ablation from Scalp to Cortex for Spatially Resolved Proteomics.

Common workflows in bottom-up proteomics require homogenization of tissue samples to gain access to the biomolecules within the cells. The homogenized tissue samples often contain many different cell types, thereby representing an average of the natural proteome composition, and rare cell types are not sufficiently represented. To overcome this problem, small-volume sampling and spatial resolution are needed to maintain a better representation of the sample composition and their proteome signatures. Using nanosecond infrared laser ablation, the region of interest can be targeted in a three-dimensional (3D) fashion, whereby the spatial information is maintained during the simultaneous process of sampling and homogenization. In this study, we ablated 40 µm thick consecutive layers directly from the scalp through the cortex of embryonic mouse heads and analyzed them by subsequent bottom-up proteomics. Extra- and intracranial ablated layers showed distinct proteome profiles comprising expected cell-specific proteins. Additionally, known cortex markers like SOX2, KI67, NESTIN, and MAP2 showed a layer-specific spatial protein abundance distribution. We propose potential new marker proteins for cortex layers, such as MTA1 and NMRAL1. The obtained data confirm that the new 3D tissue sampling and homogenization method is well suited for investigating the spatial proteome signature of tissue samples in a layerwise manner. Characterization of the proteome composition of embryonic skin and bone structures, meninges, and cortex lamination in situ enables a better understanding of molecular mechanisms of development during embryogenesis and disease pathogenesis.

Lipidome Analysis of Oropharyngeal Tumor Tissues Using Nanosecond Infrared Laser (NIRL) Tissue Sampling and Subsequent Mass Spectrometry.

Ultrashort pulse infrared lasers can simultaneously sample and homogenize biological tissue using desorption by impulsive vibrational excitation (DIVE). With growing attention on alterations in lipid metabolism in malignant disease, mass spectrometry (MS)-based lipidomic analysis has become an emerging topic in cancer research. In this pilot study, we investigated the feasibility of tissue sampling with a nanosecond infrared laser (NIRL) for the subsequent lipidomic analysis of oropharyngeal tissues, and its potential to discriminate oropharyngeal squamous cell carcinoma (OPSCC) from non-tumorous oropharyngeal tissue. Eleven fresh frozen oropharyngeal tissue samples were ablated. The produced aerosols were collected by a glass fiber filter, and the lipidomes were analyzed with mass spectrometry. Data was evaluated by principal component analysis and Welch's t-tests. Lipid profiles comprised 13 lipid classes and up to 755 lipid species. We found significant inter- and intrapatient alterations in lipid profiles for tumor and non-tumor samples (p-value < 0.05, two-fold difference). Thus, NIRL tissue sampling with consecutive MS lipidomic analysis is a feasible and promising approach for the differentiation of OPSCC and non-tumorous oropharyngeal tissue and may provide new insights into lipid composition alterations in OPSCC.

Tissue Sampling and Homogenization with NIRL Enables Spatially Resolved Cell Layer Specific Proteomic Analysis of the Murine Intestine.

For investigating the molecular physiology and pathophysiology in organs, the most exact data should be obtained; if not, organ-specific cell lines are analyzed, or the whole organ is homogenized, followed by the analysis of its biomolecules. However, if the morphological organization of the organ can be addressed, then, in the best case, the composition of molecules in single cells of the target organ can be analyzed. Laser capture microdissection (LCM) is a technique which enables the selection of specific cells of a tissue for further analysis of their molecules. However, LCM is a time-consuming two-dimensional technique, and optimal results are only obtained if the tissue is fixed, e.g., by formalin. Especially for proteome analysis, formalin fixation reduced the number of identifiable proteins, and this is an additional drawback. Recently, it was demonstrated that sampling of fresh-frozen (non-fixed) tissue with an infrared-laser is giving higher yields with respect to the absolute protein amount and number of identifiable proteins than conventional mechanical homogenization of tissues. In this study, the applicability of the infrared laser tissue sampling for the proteome analysis of different cell layers of murine intestine was investigated, using LC-MS/MS-based differential quantitative bottom-up proteomics. By laser ablation, eight consecutive layers of colon tissue were obtained and analyzed. However, a clear distinguishability of protein profiles between ascending, descending, and transversal colon was made, and we identified the different intestinal-cell-layer proteins, which are cell-specific, as confirmed by data from the Human Protein Atlas. Thus, for the first time, sampling directly from intact fresh-frozen tissue with three-dimensional resolution is giving access to the different proteomes of different cell layers of colon tissue.

Oral HRAS Mutation in Orofacial Nevus Sebaceous Syndrome (Schimmelpenning-Feuerstein-Mims-Syndrome): A Case Report With a Literature Survey.

BACKGROUND/AIM: The aim of this study was to present the long-term course of a patient with nevus sebaceous syndrome (NSS). Recent genetic studies place the syndrome in the emerging group of so-called RASopathies. The focus of the report is on surgical treatment and morphological and genetic findings of the face and oral cavity. CASE REPORT: A female patient was treated for congenital alterations of facial skin and oral mucosa. The oral lesions were removed repeatedly. Eruption of teeth on the lesion sites was made easier by the measures taken. However, after repeated ablation of the affected gingiva, the periodontal papillomatous epithelium re-differentiated into the same reddish, conspicuous, hyperplastic epithelium. The teeth in the affected region showed noticeable changes in position, surface, and shape. A HRAS mutation was detected only in the regions of altered oral epithelia and not in adjacent soft tissues. CONCLUSION: Reports on NSS rarely address oral manifestations. The recorded alterations of oral soft and hard tissues in NSS indicate a topographical relationship between the development of oral mucosa and teeth as well as the long-lasting impact of a sporadic mutation on organ development at this site.

Tissue Sampling and Homogenization in the Sub-Microliter Scale with a Nanosecond Infrared Laser (NIRL) for Mass Spectrometric Proteomics.

It was recently shown that ultrashort pulse infrared (IR) lasers, operating at the wavelength of the OH vibration stretching band of water, are highly efficient for sampling and homogenizing biological tissue. In this study we utilized a tunable nanosecond infrared laser (NIRL) for tissue sampling and homogenization with subsequent liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis for mass spectrometric proteomics. For the first time, laser sampling was performed with murine spleen and colon tissue. An ablation volume of 1.1 × 1.1 × 0.4 mm³ (approximately 0.5 µL) was determined with optical coherence tomography (OCT). The results of bottom-up proteomics revealed proteins with significant abundance differences for both tissue types, which are in accordance with the corresponding data of the Human Protein Atlas. The results demonstrate that tissue sampling and homogenization of small tissue volumes less than 1 µL for subsequent mass spectrometric proteomics is feasible with a NIRL.

Spatial heterogeneity of flesh-cell osmotic potential in sweet cherry affects partitioning of absorbed water.

A fleshy fruit is commonly assumed to resemble a thin-walled pressure vessel containing a homogenous carbohydrate solution. Using sweet cherry (Prunus avium L.) as a model system, we investigate how local differences in cell water potential affect H2O and D2O (heavy water) partitioning. The partitioning of H2O and D2O was mapped non-destructively using magnetic resonance imaging (MRI). The change in size of mesocarp cells due to water movement was monitored by optical coherence tomography (OCT, non-destructive). Osmotic potential was mapped using micro-osmometry (destructive). Virtual sections through the fruit revealed that the H2O distribution followed a net pattern in the outer mesocarp and a radial pattern in the inner mesocarp. These patterns align with the disposition of the vascular bundles. D2O uptake through the skin paralleled the acropetal gradient in cell osmotic potential gradient (from less negative to more negative). Cells in the vicinity of a vascular bundle were of more negative osmotic potential than cells more distant from a vascular bundle. OCT revealed net H2O uptake was the result of some cells loosing volume and other cells increasing volume. H2O and D2O partitioning following uptake is non-uniform and related to the spatial heterogeneity in the osmotic potential of mesocarp cells.

Localized bursting of mesocarp cells triggers catastrophic fruit cracking.

The so-called rain-cracking of sweet cherry fruit severely threatens commercial production. Simple observation tells us that cuticular microcracking (invisible) always precedes skin macrocracking (visible). The objective here was to investigate how a macrocrack develops. Incubating detached sweet cherry fruit in deionized water induces microcracking. Incubating fruit in D2O and concurrent magnetic resonance imaging demonstrates that water penetration occurs only (principally) through the microcracks, with nondetectable amounts penetrating the intact cuticle. Optical coherence tomography of detached, whole fruit incubated in deionized water, allowed generation of virtual cross-sections through the zone of a developing macrocrack. Outer mesocarp cell volume increased before macrocracks developed but increased at a markedly higher rate thereafter. Little change in mesocarp cell volume occurred in a control zone distant from the crack. As water incubation continued, the cell volume in the crack zone decreased, indicating leaking/bursting of individual mesocarp cells. As incubation continued still longer, the crack propagated between cells both to form a long, deep macrocrack. Outer mesocarp cell turgor did not differ significantly before and after incubation between fruit with or without macrocracks; nor between cells within the crack zone and those in a control zone distant from the macrocrack. The cumulative frequency distribution of the log-transformed turgor pressure of a population of outer mesocarp cells reveals all cell turgor data followed a normal distribution. The results demonstrate that microcracks develop into macrocracks following the volume increase of a few outer mesocarp cells and is soon accompanied by cell bursting.

Measurement of Ex Vivo Porcine Lens Shape During Simulated Accommodation, Before and After fs-Laser Treatment.

PURPOSE: According to Helmholtz, accommodation is based on the flexibility of the crystalline lens, which decreases with age, causing presbyopia. With femtosecond (fs)-lentotomy treatment, it is possible to restore the flexibility of presbyopic lenses. The efficiency of the treatment can be systematically evaluated using the finite element method based on experimental data. The purpose of this study was to quantify the shape change of ex vivo lenses in different accommodation states according to the fs-lentotomy treatment. METHODS: Five lenses with ciliary body excised from ex vivo porcine eyes (age: approximately 6 months, exact age unknown) were stretched in an accommodation device before and after laser treatment. Depending on the accommodation state, the lens shape, reconstructed from lens thickness, diameter, and anterior and posterior curvature, was measured using optical coherence tomography (OCT). The complete lens shape was parameterized and each measured parameter was compared to the results of a control group (n = 5, age: approximately 6 months, exact age unknown) without treatment. RESULTS: The amplitudes of the parameters thickness (+140%), diameter (+54%), and anterior radius of curvature (+57%) significantly increased after treatment (P < 0.05), and showed no significant change for the control group. By contrast, the amplitude of the posterior radius of curvature showed no change after treatment (P > 0.05). CONCLUSIONS: Measurement of the lens shape in different accommodation states was successful and showed significant changes after the treatment. The resulting data will be utilized as input for a finite element model to systematically evaluate the effect of fs-lentotomy treatment in future work.

Low fecal elastase 1 levels do not indicate exocrine pancreatic insufficiency in type-1 diabetes mellitus.

OBJECTIVES: On the basis of very low fecal elastase 1 and very high fecal fat estimations, it has been claimed that exocrine pancreatic insufficiency is frequent in diabetic patients, and that in up to 40% of the patients, pancreatic enzyme substitution would be indicated. Because this would affect millions of diabetic patients worldwide, we evaluated this suggestion by testing exocrine pancreatic function in type-1 diabetes using the criterion standard of exocrine pancreatic function tests, the secretin-cerulein test (SCT). The results of this test were then compared with those of fecal elastase 1 and fecal fat estimations. METHODS: Thirty-three patients with type-1 diabetes mellitus underwent an SCT, a fecal fat estimation, and 2 fecal elastase 1 tests (using both monoclonal and polyclonal antibodies) to evaluate their exocrine pancreatic function. RESULTS: The SCT results were abnormal in 11 of the 33 patients, who showed only mild to moderate exocrine pancreatic insufficiency, and the stimulated lipase secretion was never less than 10% of the level where pancreatic steatorrhea first occurs. The correlation between fecal elastase 1 and SCT showed much lower sensitivity, specificity, and positive and negative predictive values than did the correlation between SCT and fecal fat. Nonpancreatogenic steatorrhea was present in two thirds of the patients and was probably caused by bacterial overgrowth. CONCLUSIONS: Neither low fecal elastase 1 nor raised fecal fat levels reliably indicate exocrine pancreatic insufficiency in type-1 diabetes and therefore should not be used as an indicator for expensive pancreatic enzyme substitution.