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• W2914684170 abstract "Methods and technologies for high-throughput analysis of proteins became necessary for a wide range of applications in life sciences. Proteomic profiling provides panoramic pictures of the final molecular actors of biological contexts of interest. Mass spectrometry (MS) at large has entered a new era in the past few years with potential applications for routine pathological diagnostics.1, 2 One year ago, we offered our point of view regarding the most promising proteomic workflows for future applications in tissue-based diagnostics and the prerequisites for a successful translational implementation.3 Today, four approaches appear as possible future cornerstones for histoproteomic diagnostics in institutes of pathology: MALDI profiling and imaging, liquid chromatography-tandem mass spectrometry (LC-MS/MS), and laser microdissection–based microproteomics.3 MALDI profiling was recently demonstrated as a reliable approach for rapid diagnosis with the evaluation of isocitrate dehydrogenase mutational status in diffuse gliomas.4 MALDI imaging allows for close correlation between histological structures and mass spectrometric measurements.5 The analysis of tissue microarrays combined with classification algorithms holds great promise regarding disease diagnosis based on in situ proteomic signatures.6 LC-MS/MS-based shotgun proteomic methods allow for the secure identification of tens of thousands of peptides corresponding to up to thousands of proteins in a single analytical run.7 This approach has a high potential for tissue classification as a high number of biomarkers are identified.8 Microproteomic workflows also represent future valuable methods for molecular pathology. Since tissues are a very heterogeneous mixture of different cell types, laser microdissection has to be performed in order to obtain pure cell populations. Today, it is possible to retrieve thousands of protein identifications from laser-microdissected, formalin-fixed and paraffin-embedded (FFPE) tissue pieces bearing less than 3000 cells.9, 10 Hence, it may be expected that high spatial resolution will meet in-depth proteomic information in the near future. Recent advances in sample processing of tissues for shotgun proteomics directly after laser microdissection represent new perspectives for highly informative molecular imaging.11, 12 In this special issue, experts from all over the world contributed to scientific advances in the field of histoproteomics, with special emphasis on translational pathology. MALDI imaging was used to address a large variety of questions in life sciences and diagnostics. Venkatraman et al. identified and visualized the spatial distribution of amyloid-related proteins in corneas from patients with lattice corneal dystrophy.13 They highlighted the presence of key proteins such as transforming growth factor-beta-induced protein (TGFBIp), apolipoprotein A-I, apolipoprotein A-IV, and apolipoprotein E in amyloid deposits. Scott et al. revealed higher presence of N-glycan polylactosamine in advanced HER2-positive and triple-negative breast cancer tissues by MALDI imaging.14 High-resolution MALDI imaging was performed by Smith et al. to highlight mass spectrometric signatures in glomeruli associated with the response of immunosuppressive treatment in membranous nephropathy.15 Kriegsmann et al. illustrated how MALDI imaging could highlight tissue compartments in a complementary fashion to immunohistochemistry.16 The versatility of MALDI imaging regarding the nature of analyzable samples was demonstrated through the work of Piga et al. who evaluated the time stability of thyroid fine-needle aspiration biopsies through their morphological and proteomic profile.17 Schwamborn et al. analyzed cytology microarrays of malignant peritoneal and pleural effusions from serous ovarian cancer and several non-ovarian carcinomas.18 This study revealed that adenocarcinoma subtyping can be achieved in cytological material with high sensitivity and within the same time frame as routine diagnostic workup while also conserving cytological material. This workflow is an important example of how MALDI imaging could be translated to routine diagnostics. Today, tissue classification methods based on MALDI-MS signatures represent the best promise for a transition into the medical field. Taube et al. illustrated that different types of epithelial ovarian cancer may be classified by MALDI imaging.19 Casadonte et al. constructed a model for the classification of pancreatic ductal adenocarcinoma (pDAC) and pancreatic neuroendocrine tumors (pNETs).20 Cordero Hernandez et al. proposed a new concept for the evaluation of MALDI spectra from tissues in order to improve the classification accuracy and robustness, even across different instrumentation platforms and users.21 In a close future, the combination of multi-level MALDI imaging molecular data will be of particular importance for a better stratification of patients. Balluff et al. used integrative clustering methods on MALDI imaging metabolomic and peptidomic data from a microarray with 46 specimen of esophageal cancer. They detected patient subgroups with different clinical outcome more efficiently than with the single molecular level data.22 LC-MS/MS-based proteomic methods are the most robust and reliable for protein identification and quantification from tissues.7 Le Faouder et al. depicted the proteomic landscape of cholangiocarcinoma using LC-MS/MS-based proteomics in data-dependent acquisition mode.23 Zhu et al. presented an application of pressure cycling technology–sequential window acquisition of all theoretical fragment ion spectra (PCT-SWATH)-MS for the analysis of hepatocellular carcinoma biopsies. From 19 hepatocellular carcinoma patients, they could identify and quantify about 12 000 peptides that corresponded to 2579 proteins. They could define a subset of 541 proteins that were significantly more abundant in tumor tissues compared to control ones. This study is an important illustration of the capacities of data-independent acquisition methods for biomarker discovery in pathology and their future potential for diagnostics.24 LC-MS/MS-based shotgun proteomics of tissue can now be performed at a very small scale. Microproteomics allowed us to depict the landscape of proteins associated with high-grade squamous intraepithelial lesions (HSIL) of the uterine cervix.25 Such protein maps improve our understanding of the biological background of cervical dysplasia and may contribute to finding new diagnostic or therapeutic targets. In this specific study, we found a nuclear marker—the histone chaperone ASF1B—allowing for the distinction between normal ectocervical epithelium and low- and high-grade dysplastic lesions of the ectocervix. This distinction is highly relevant in pathological diagnostics, since low- and high-grade lesions have different prognosis and lead to different patient monitoring.25 LC-MS/MS also appears very complementary to MALDI imaging, especially for parallel identification of proteins and peptides.26 Hoffmann et al. performed LC-MS/MS analyses of proteins from tissues analyzed by MALDI imaging in order to assign identification of m/z peaks in head and neck cancer.27 Using the dataset for microproteomic profiling of cervical dysplasia,25 we correlated the mass of proteolytic peptides from HSIL biomarker proteins with m/z values found in higher intensity in HSIL by MALDI imaging. We demonstrated that LC-MS/MS-based biomarker discovery data allowed for a more reliable identification of signature m/z values from MALDI imaging.28 With more and more researchers turning toward molecular analysis of clinical samples, it is becoming increasingly important to develop more robust, reliable, and reproducible MS-based proteomic methods. There are still challenges remaining, mainly with regard to sample preparation, automation, standardization, quality control, and data storage/processing. These are crucial problems that first need to be solved before incorporating MS-based approaches into clinical routine. Our consortium evaluated important analytical parameters such as tissue thickness for MALDI imaging analyses of FFPE tissues.29 We also established an updated protocol for bottom-up MALDI imaging analyses of FFPE tissues and tested site-to-site reproducibility and spatial resolution.30 Finally, we evaluated the compatibility of MALDI imaging with current analytical settings for routine molecular diagnostics. We demonstrated that digital polymerase chain reaction and immunohistochemistry can be performed from the same section after analysis by MALDI imaging.31, 32 These findings are important for the implementation of MALDI imaging in routine pathology but also for translational research. It enables the direct correlation of proteomic profiles with the presence of genetic or immunohistochemical markers of interest while preserving precious tissue material. A new sample preparation strategy for MALDI imaging using a bacterial matrix metalloproteinase was presented by Angel et al. to investigate extracellular matrix proteins such as collagen in breast cancer tissues.33 Taverna et al. proposed hydrogel-mediated on-tissue digestion for the proteomic characterization of fresh-frozen as well as FFPE tissues.34 The method holds good promise for quantitative shotgun proteomics while being nondestructive, opening opportunities for combination with other histomolecular methods in pathology. Restellini et al. explored post-translational modification of histones in clinical samples.35 They demonstrated that using alternative digestion approaches improved histone modification mapping. These new approaches may open new paths in clinical epigenomics. In the future, new tools for data sharing and correlation will be needed to combine and summarize the tremendous panel of information that can be retrieved from tissues and clinical data. Rubens et al. introduced new features implemented in their software platform for digital pathology, Cytomine.36 These new developments allow for the correlation of information from normal histology and different molecular imaging modes such as MALDI imaging. It also contains important features such as cell counting that efficiently supports tissue pre-processing for microproteomics.10 All these contributions represent valuable examples of proteomic applications in translational research but also strong hints toward the imminent implementation in the diagnostic field. In addition to the methods presented in this special issue that will find diagnostic applications in institutes of pathology, new sampling and atmospheric pressure ionization technologies have been developed for intraoperative molecular profiling/imaging. Desorption/electrospray ionization,37-40 MasSpec Pen,41 SpiderMass,42, 43 and rapid evaporative ionization mass spectrometry44-47 represent concrete alternatives for another possible evolution of MS-based patient monitoring, within the surgery block. We thank all the authors for their excellent contributions, the reviewers for their wise comments, and the editors of Proteomics Clinical Applications for their efficient guidance and support." @default.
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• W2914684170 date "2019-01-01" @default.
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• W2914684170 title "Proteomics in Pathology: The Special Issue" @default.
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• W2914684170 doi "https://doi.org/10.1002/prca.201800167" @default.
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