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Navolić J, Moritz M, Voß H, Schlumbohm S, Schumann Y, Schlüter H, Neumann JE, Hahn J. Direct 3D Sampling of the Embryonic Mouse Head: Layer-wise Nanosecond Infrared Laser (NIRL) Ablation from Scalp to Cortex for Spatially Resolved Proteomics. Anal Chem 2023; 95:17220-17227. [PMID: 37956982 PMCID: PMC10688223 DOI: 10.1021/acs.analchem.3c02637] [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: 06/16/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 11/21/2023]
Abstract
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.
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Affiliation(s)
- Jelena Navolić
- Research
Group Molecular Pathology in Neurooncology, Center for Molecular Neurobiology
(ZMNH), University Medical Center Hamburg−Eppendorf, Falkenried 94, 20251 Hamburg, Germany
| | - Manuela Moritz
- Section/Core
Facility Mass Spectrometry and Proteomics, Center for Diagnostics, University Medical Center Hamburg−Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Hannah Voß
- Section/Core
Facility Mass Spectrometry and Proteomics, Center for Diagnostics, University Medical Center Hamburg−Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Simon Schlumbohm
- High
Performance Computing, Helmut Schmidt University, Holstenhofweg 85, 22043 Hamburg, Germany
| | - Yannis Schumann
- High
Performance Computing, Helmut Schmidt University, Holstenhofweg 85, 22043 Hamburg, Germany
| | - Hartmut Schlüter
- Section/Core
Facility Mass Spectrometry and Proteomics, Center for Diagnostics, University Medical Center Hamburg−Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Julia E. Neumann
- Research
Group Molecular Pathology in Neurooncology, Center for Molecular Neurobiology
(ZMNH), University Medical Center Hamburg−Eppendorf, Falkenried 94, 20251 Hamburg, Germany
- Institute
of Neuropathology, University Medical Center
Hamburg−Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Jan Hahn
- Section/Core
Facility Mass Spectrometry and Proteomics, Center for Diagnostics, University Medical Center Hamburg−Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
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Stadlhofer R, Moritz M, Fuh MM, Heeren J, Zech H, Clauditz TS, Schlüter H, Betz CS, Eggert D, Böttcher A, Hahn J. Lipidome Analysis of Oropharyngeal Tumor Tissues Using Nanosecond Infrared Laser (NIRL) Tissue Sampling and Subsequent Mass Spectrometry. Int J Mol Sci 2023; 24:ijms24097820. [PMID: 37175533 PMCID: PMC10178251 DOI: 10.3390/ijms24097820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
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.
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Affiliation(s)
- Rupert Stadlhofer
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Manuela Moritz
- Section/Core Facility Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marceline M Fuh
- Department of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Jörg Heeren
- Department of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Henrike Zech
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Till S Clauditz
- Department of Pathology, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Section/Core Facility Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Christian S Betz
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Dennis Eggert
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Arne Böttcher
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Jan Hahn
- Section/Core Facility Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
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Luo M, Su T, Wang S, Chen J, Lin T, Cheng Q, Chen Y, Gong M, Yang H, Li F, Zhang Y. Proteomic Landscape of Human Spermatozoa: Optimized Extraction Method and Application. Cells 2022; 11. [PMID: 36552826 DOI: 10.3390/cells11244064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Human spermatozoa proteomics exposed to some physical, biological or chemical stressors is being explored. However, there is a lack of optimized sample preparation methods to achieve in-depth protein coverage for sperm cells. Meanwhile, it is not clear whether antibiotics can regulate proteins to affect sperm quality. Here, we systematically compared a total of six different protein extraction methods based the combination of three commonly used lysis buffers and physical lysis strategies. The urea buffer combined with ultrasonication (UA-ultrasonication) produced the highest protein extraction rate, leading to the deepest coverage of human sperm proteome (5685 protein groups) from healthy human sperm samples. Since the antibiotics, amoxicillin and clarithromycin, have been widely used against H. pylori infection, we conduct a longitudinal study of sperm proteome via data-independent acquisition tandem mass spectrometry (DIA-MS/MS) on an infected patient during on and off therapy with these two drugs. The semen examination and morphological analysis were performed combined with proteomics analysis. Our results indicated that antibiotics may cause an increase in the sperm concentration and the rate of malformed sperm and disrupt proteome expression in sperm. This work provides an optimized extraction method to characterize the in-depth human sperm proteome and to extend its clinical applications.
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Voß H, Moritz M, Pelczar P, Gagliani N, Huber S, Nippert V, Schlüter H, Hahn J. Tissue Sampling and Homogenization with NIRL Enables Spatially Resolved Cell Layer Specific Proteomic Analysis of the Murine Intestine. Int J Mol Sci 2022; 23:ijms23116132. [PMID: 35682811 PMCID: PMC9181169 DOI: 10.3390/ijms23116132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/18/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023] Open
Abstract
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.
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Affiliation(s)
- Hannah Voß
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
| | - Manuela Moritz
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
| | - Penelope Pelczar
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (P.P.); (N.G.); (S.H.)
| | - Nicola Gagliani
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (P.P.); (N.G.); (S.H.)
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany
| | - Samuel Huber
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (P.P.); (N.G.); (S.H.)
| | - Vivien Nippert
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
| | - Hartmut Schlüter
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
- Correspondence: (H.S.); (J.H.); Tel.: +49-1575-6085997 (H.S.); +49-1522-2827168 (J.H.)
| | - Jan Hahn
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
- Correspondence: (H.S.); (J.H.); Tel.: +49-1575-6085997 (H.S.); +49-1522-2827168 (J.H.)
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Dong C, Richardson LT, Solouki T, Murray KK. Infrared Laser Ablation Microsampling with a Reflective Objective. J Am Soc Mass Spectrom 2022; 33:463-470. [PMID: 35104132 PMCID: PMC8895455 DOI: 10.1021/jasms.1c00306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
A Schwarzschild reflective objective with a numerical aperture of 0.3 and working distance of 10 cm was used for laser ablation sampling of tissue for off-line mass spectrometry. The objective focused the laser to a diameter of 5 μm and produced 10 μm ablation spots on thin ink films and tissue sections. Rat brain tissue sections 50 μm thick were ablated in transmission geometry, and the ablated material was captured in a microcentrifuge tube containing solvent. Proteins from ablated tissue sections were quantified with a Bradford assay, which indicated that approximately 300 ng of protein was captured from a 1 mm2 area of ablated tissue. Areas of tissue ranging from 0.01 to 1 mm2 were ablated and captured for bottom-up proteomics. Proteins were extracted from the captured tissue and digested for liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis for peptide and protein identification.
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Affiliation(s)
- Chao Dong
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Luke T. Richardson
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Touradj Solouki
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Kermit K. Murray
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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