1
|
Hartig J, Young LEA, Grimsley G, Mehta AS, Ippolito JE, Leach RJ, Angel PM, Drake RR. The glycosylation landscape of prostate cancer tissues and biofluids. Adv Cancer Res 2024; 161:1-30. [PMID: 39032948 DOI: 10.1016/bs.acr.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
An overview of the role of glycosylation in prostate cancer (PCa) development and progression is presented, focusing on recent advancements in defining the N-glycome through glycomic profiling and glycoproteomic methodologies. Glycosylation is a common post-translational modification typified by oligosaccharides attached N-linked to asparagine or O-linked to serine or threonine on carrier proteins. These attached sugars have crucial roles in protein folding and cellular recognition processes, such that altered glycosylation is a hallmark of cancer pathogenesis and progression. In the past decade, advancements in N-glycan profiling workflows using Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) technology have been applied to define the spatial distribution of glycans in PCa tissues. Multiple studies applying N-glycan MALDI-MSI to pathology-defined PCa tissues have identified significant alterations in N-glycan profiles associated with PCa progression. N-glycan compositions progressively increase in number, and structural complexity due to increased fucosylation and sialylation. Additionally, significant progress has been made in defining the glycan and glycopeptide compositions of prostatic-derived glycoproteins like prostate-specific antigen in tissues and biofluids. The glycosyltransferases involved in these changes are potential drug targets for PCa, and new approaches in this area are summarized. These advancements will be discussed in the context of the further development of clinical diagnostics and therapeutics targeting glycans and glycoproteins associated with PCa progression. Integration of large scale spatial glycomic data for PCa with other spatial-omic methodologies is now feasible at the tissue and single-cell levels.
Collapse
Affiliation(s)
- Jordan Hartig
- Medical University of South Carolina, Charleston, SC, United States
| | | | - Grace Grimsley
- Medical University of South Carolina, Charleston, SC, United States
| | - Anand S Mehta
- Medical University of South Carolina, Charleston, SC, United States
| | - Joseph E Ippolito
- Washington University School of Medicine in Saint Louis, St. Louis, MO, United States
| | - Robin J Leach
- University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Peggi M Angel
- Medical University of South Carolina, Charleston, SC, United States
| | - Richard R Drake
- Medical University of South Carolina, Charleston, SC, United States.
| |
Collapse
|
2
|
Ikram S, Rege A, Negesse MY, Casanova AG, Reynoird N, Green EM. The SMYD3-MAP3K2 signaling axis promotes tumor aggressiveness and metastasis in prostate cancer. SCIENCE ADVANCES 2023; 9:eadi5921. [PMID: 37976356 PMCID: PMC10656069 DOI: 10.1126/sciadv.adi5921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
Aberrant activation of Ras/Raf/mitogen-activated protein kinase (MAPK) signaling is frequently linked to metastatic prostate cancer (PCa); therefore, the characterization of modulators of this pathway is critical for defining therapeutic vulnerabilities for metastatic PCa. The lysine methyltransferase SET and MYND domain 3 (SMYD3) methylates MAPK kinase kinase 2 (MAP3K2) in some cancers, causing enhanced activation of MAPK signaling. In PCa, SMYD3 is frequently overexpressed and associated with disease severity; however, its molecular function in promoting tumorigenesis has not been defined. We demonstrate that SMYD3 critically regulates tumor-associated phenotypes via its methyltransferase activity in PCa cells and mouse xenograft models. SMYD3-dependent methylation of MAP3K2 promotes epithelial-mesenchymal transition associated behaviors by altering the abundance of the intermediate filament vimentin. Furthermore, activation of the SMYD3-MAP3K2 signaling axis supports a positive feedback loop continually promoting high levels of SMYD3. Our data provide insight into signaling pathways involved in metastatic PCa and enhance understanding of mechanistic functions for SMYD3 to reveal potential therapeutic opportunities for PCa.
Collapse
Affiliation(s)
- Sabeen Ikram
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Apurv Rege
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Maraki Y. Negesse
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Alexandre G. Casanova
- Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Institute for Advanced Biosciences, Grenoble, France
| | - Nicolas Reynoird
- Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Institute for Advanced Biosciences, Grenoble, France
| | - Erin M. Green
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| |
Collapse
|
3
|
Rittel MF, Schmidt S, Weis CA, Birgin E, van Marwick B, Rädle M, Diehl SJ, Rahbari NN, Marx A, Hopf C. Spatial Omics Imaging of Fresh-Frozen Tissue and Routine FFPE Histopathology of a Single Cancer Needle Core Biopsy: A Freezing Device and Multimodal Workflow. Cancers (Basel) 2023; 15:2676. [PMID: 37345020 DOI: 10.3390/cancers15102676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/16/2023] [Accepted: 05/06/2023] [Indexed: 06/23/2023] Open
Abstract
The complex molecular alterations that underlie cancer pathophysiology are studied in depth with omics methods using bulk tissue extracts. For spatially resolved tissue diagnostics using needle biopsy cores, however, histopathological analysis using stained FFPE tissue and the immunohistochemistry (IHC) of a few marker proteins is currently the main clinical focus. Today, spatial omics imaging using MSI or IRI is an emerging diagnostic technology for the identification and classification of various cancer types. However, to conserve tissue-specific metabolomic states, fast, reliable, and precise methods for the preparation of fresh-frozen (FF) tissue sections are crucial. Such methods are often incompatible with clinical practice, since spatial metabolomics and the routine histopathology of needle biopsies currently require two biopsies for FF and FFPE sampling, respectively. Therefore, we developed a device and corresponding laboratory and computational workflows for the multimodal spatial omics analysis of fresh-frozen, longitudinally sectioned needle biopsies to accompany standard FFPE histopathology of the same biopsy core. As a proof-of-concept, we analyzed surgical human liver cancer specimens using IRI and MSI with precise co-registration and, following FFPE processing, by sequential clinical pathology analysis of the same biopsy core. This workflow allowed for a spatial comparison between different spectral profiles and alterations in tissue histology, as well as a direct comparison for histological diagnosis without the need for an extra biopsy.
Collapse
Affiliation(s)
- Miriam F Rittel
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Stefan Schmidt
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
| | - Cleo-Aron Weis
- Institute of Pathology, University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Emrullah Birgin
- Department of Surgery, University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Björn van Marwick
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
| | - Matthias Rädle
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Steffen J Diehl
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- Clinic of Clinical Radiology and Nuclear Medicine, University Medical Center Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Nuh N Rahbari
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- Department of Surgery, University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Alexander Marx
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- Institute of Pathology, University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| |
Collapse
|
4
|
Høiem TS, Andersen MK, Martin‐Lorenzo M, Longuespée R, Claes BS, Nordborg A, Dewez F, Balluff B, Giampà M, Sharma A, Hagen L, Heeren RM, Bathen TF, Giskeødegård GF, Krossa S, Tessem M. An optimized MALDI MSI protocol for spatial detection of tryptic peptides in fresh frozen prostate tissue. Proteomics 2022; 22:e2100223. [PMID: 35170848 PMCID: PMC9285595 DOI: 10.1002/pmic.202100223] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/19/2022] [Accepted: 02/07/2022] [Indexed: 11/29/2022]
Abstract
MALDI MS imaging (MSI) is a powerful analytical tool for spatial peptide detection in heterogeneous tissues. Proper sample preparation is crucial to achieve high quality, reproducible measurements. Here we developed an optimized protocol for spatially resolved proteolytic peptide detection with MALDI time-of-flight MSI of fresh frozen prostate tissue sections. The parameters tested included four different tissue washes, four methods of protein denaturation, four methods of trypsin digestion (different trypsin densities, sprayers, and incubation times), and five matrix deposition methods (different sprayers, settings, and matrix concentrations). Evaluation criteria were the number of detected and excluded peaks, percentage of high mass peaks, signal-to-noise ratio, spatial localization, and average intensities of identified peptides, all of which were integrated into a weighted quality evaluation scoring system. Based on these scores, the optimized protocol included an ice-cold EtOH+H2 O wash, a 5 min heating step at 95°C, tryptic digestion incubated for 17h at 37°C and CHCA matrix deposited at a final amount of 1.8 μg/mm2 . Including a heat-induced protein denaturation step after tissue wash is a new methodological approach that could be useful also for other tissue types. This optimized protocol for spatial peptide detection using MALDI MSI facilitates future biomarker discovery in prostate cancer and may be useful in studies of other tissue types.
Collapse
Affiliation(s)
- Therese S. Høiem
- Department of Circulation and Medical ImagingNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
| | - Maria K. Andersen
- Department of Circulation and Medical ImagingNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
| | - Marta Martin‐Lorenzo
- Maastricht MultiModal Molecular Imaging Institute (M4I)Maastricht UniversityMaastrichtNetherlands
| | - Rémi Longuespée
- Department of Clinical Pharmacology and PharmacoepidemiologyHeidelberg University HospitalHeidelbergGermany
| | - Britt S.R. Claes
- Maastricht MultiModal Molecular Imaging Institute (M4I)Maastricht UniversityMaastrichtNetherlands
| | - Anna Nordborg
- Department of Biotechnology and NanomedicineSINTEF IndustryTrondheimNorway
| | - Frédéric Dewez
- Maastricht MultiModal Molecular Imaging Institute (M4I)Maastricht UniversityMaastrichtNetherlands
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging Institute (M4I)Maastricht UniversityMaastrichtNetherlands
| | - Marco Giampà
- Department of Clinical and Molecular MedicineNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
| | - Animesh Sharma
- Department of Clinical and Molecular MedicineNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
- PROMEC Core Facility for Proteomics and ModomicsNTNU ‐ Norwegian University of Science and Technology and the Central Norway Regional Health Authority NorwayTrondheimNorway
| | - Lars Hagen
- Department of Clinical and Molecular MedicineNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
- PROMEC Core Facility for Proteomics and ModomicsNTNU ‐ Norwegian University of Science and Technology and the Central Norway Regional Health Authority NorwayTrondheimNorway
- Clinic of Laboratory MedicineSt. Olavs HospitalTrondheim University HospitalTrondheimNorway
| | - Ron M.A. Heeren
- Maastricht MultiModal Molecular Imaging Institute (M4I)Maastricht UniversityMaastrichtNetherlands
| | - Tone F. Bathen
- Department of Circulation and Medical ImagingNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
- Department of radiology and nuclear medicineSt. Olavs HospitalTrondheim University HospitalTrondheimNorway
| | - Guro F. Giskeødegård
- K.G. Jebsen Center for Genetic EpidemiologyDepartment of Public Health and NursingNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
| | - Sebastian Krossa
- Department of Circulation and Medical ImagingNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
| | - May‐Britt Tessem
- Department of Circulation and Medical ImagingNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
- Department of SurgerySt. Olavs HospitalTrondheim University HospitalTrondheimNorway
| |
Collapse
|
5
|
Föll MC, Volkmann V, Enderle-Ammour K, Timme S, Wilhelm K, Guo D, Vitek O, Bronsert P, Schilling O. Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: a case study of an urothelial cancer cohort analyzed in the Galaxy framework. Clin Proteomics 2022; 19:8. [PMID: 35439943 PMCID: PMC9016955 DOI: 10.1186/s12014-022-09347-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 04/04/2022] [Indexed: 11/24/2022] Open
Abstract
Background Mass spectrometry imaging (MSI) derives spatial molecular distribution maps directly from clinical tissue specimens and thus bears great potential for assisting pathologists with diagnostic decisions or personalized treatments. Unfortunately, progress in translational MSI is often hindered by insufficient quality control and lack of reproducible data analysis. Raw data and analysis scripts are rarely publicly shared. Here, we demonstrate the application of the Galaxy MSI tool set for the reproducible analysis of a urothelial carcinoma dataset. Methods Tryptic peptides were imaged in a cohort of 39 formalin-fixed, paraffin-embedded human urothelial cancer tissue cores with a MALDI-TOF/TOF device. The complete data analysis was performed in a fully transparent and reproducible manner on the European Galaxy Server. Annotations of tumor and stroma were performed by a pathologist and transferred to the MSI data to allow for supervised classifications of tumor vs. stroma tissue areas as well as for muscle-infiltrating and non-muscle infiltrating urothelial carcinomas. For putative peptide identifications, m/z features were matched to the MSiMass list. Results Rigorous quality control in combination with careful pre-processing enabled reduction of m/z shifts and intensity batch effects. High classification accuracy was found for both, tumor vs. stroma and muscle-infiltrating vs. non-muscle infiltrating urothelial tumors. Some of the most discriminative m/z features for each condition could be assigned a putative identity: stromal tissue was characterized by collagen peptides and tumor tissue by histone peptides. Immunohistochemistry confirmed an increased histone H2A abundance in the tumor compared to the stroma tissues. The muscle-infiltration status was distinguished via MSI by peptides from intermediate filaments such as cytokeratin 7 in non-muscle infiltrating carcinomas and vimentin in muscle-infiltrating urothelial carcinomas, which was confirmed by immunohistochemistry. To make the study fully reproducible and to advocate the criteria of FAIR (findability, accessibility, interoperability, and reusability) research data, we share the raw data, spectra annotations as well as all Galaxy histories and workflows. Data are available via ProteomeXchange with identifier PXD026459 and Galaxy results via https://github.com/foellmelanie/Bladder_MSI_Manuscript_Galaxy_links. Conclusion Here, we show that translational MSI data analysis in a fully transparent and reproducible manner is possible and we would like to encourage the community to join our efforts.
Collapse
Affiliation(s)
- Melanie Christine Föll
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106, FreiburgFreiburg, Germany. .,Khoury College of Computer Sciences, Northeastern University, Boston, USA.
| | - Veronika Volkmann
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106, FreiburgFreiburg, Germany
| | - Kathrin Enderle-Ammour
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106, FreiburgFreiburg, Germany
| | - Sylvia Timme
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106, FreiburgFreiburg, Germany.,Core Facility for Histopathology and Digital Pathology, Faculty of Medicine, Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Konrad Wilhelm
- Department of Urology, Center for Surgery, Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Dan Guo
- Khoury College of Computer Sciences, Northeastern University, Boston, USA
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, USA
| | - Peter Bronsert
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106, FreiburgFreiburg, Germany.,German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany.,Tumorbank Comprehensive Cancer Center Freiburg, Freiburg, Germany
| | - Oliver Schilling
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106, FreiburgFreiburg, Germany.,German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
| |
Collapse
|
6
|
Ritschar S, Schirmer E, Hufnagl B, Löder MGJ, Römpp A, Laforsch C. Classification of target tissues of Eisenia fetida using sequential multimodal chemical analysis and machine learning. Histochem Cell Biol 2022; 157:127-137. [PMID: 34750664 PMCID: PMC8847259 DOI: 10.1007/s00418-021-02037-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 12/22/2022]
Abstract
Acquiring comprehensive knowledge about the uptake of pollutants, impact on tissue integrity and the effects at the molecular level in organisms is of increasing interest due to the environmental exposure to numerous contaminants. The analysis of tissues can be performed by histological examination, which is still time-consuming and restricted to target-specific staining methods. The histological approaches can be complemented with chemical imaging analysis. Chemical imaging of tissue sections is typically performed using a single imaging approach. However, for toxicological testing of environmental pollutants, a multimodal approach combined with improved data acquisition and evaluation is desirable, since it may allow for more rapid tissue characterization and give further information on ecotoxicological effects at the tissue level. Therefore, using the soil model organism Eisenia fetida as a model, we developed a sequential workflow combining Fourier transform infrared spectroscopy (FTIR) and matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) for chemical analysis of the same tissue sections. Data analysis of the FTIR spectra via random decision forest (RDF) classification enabled the rapid identification of target tissues (e.g., digestive tissue), which are relevant from an ecotoxicological point of view. MALDI imaging analysis provided specific lipid species which are sensitive to metabolic changes and environmental stressors. Taken together, our approach provides a fast and reproducible workflow for label-free histochemical tissue analyses in E. fetida, which can be applied to other model organisms as well.
Collapse
Affiliation(s)
- Sven Ritschar
- Department of Animal Ecology i and BayCEER, University of Bayreuth, Bayreuth, Germany
| | - Elisabeth Schirmer
- Department of Bioanalytical Sciences and Food Analysis, University of Bayreuth, Bayreuth, Germany
| | - Benedikt Hufnagl
- Institute of Chemical Technologies and Analytics, Vienna, TU, Austria
- Purency GmbH, Walfischgasse 8/34, T1010, Vienna, Austria
| | - Martin G J Löder
- Department of Animal Ecology i and BayCEER, University of Bayreuth, Bayreuth, Germany
| | - Andreas Römpp
- Department of Bioanalytical Sciences and Food Analysis, University of Bayreuth, Bayreuth, Germany.
| | - Christian Laforsch
- Department of Animal Ecology i and BayCEER, University of Bayreuth, Bayreuth, Germany.
| |
Collapse
|
7
|
Proteomic Landscape of Prostate Cancer: The View Provided by Quantitative Proteomics, Integrative Analyses, and Protein Interactomes. Cancers (Basel) 2021; 13:cancers13194829. [PMID: 34638309 PMCID: PMC8507874 DOI: 10.3390/cancers13194829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer is the second most frequent cancer of men worldwide. While the genetic landscapes and heterogeneity of prostate cancer are relatively well-known already, methodological developments now allow for studying basic and dynamic proteomes on a large scale and in a quantitative fashion. This aids in revealing the functional output of cancer genomes. It has become evident that not all aberrations at the genetic and transcriptional level are translated to the proteome. In addition, the proteomic level contains heterogeneity, which increases as the cancer progresses from primary prostate cancer (PCa) to metastatic and castration-resistant prostate cancer (CRPC). While multiple aspects of prostate adenocarcinoma proteomes have been studied, less is known about proteomes of neuroendocrine prostate cancer (NEPC). In this review, we summarize recent developments in prostate cancer proteomics, concentrating on the proteomic landscapes of clinical prostate cancer, cell line and mouse model proteomes interrogating prostate cancer-relevant signaling and alterations, and key prostate cancer regulator interactomes, such as those of the androgen receptor (AR). Compared to genomic and transcriptomic analyses, the view provided by proteomics brings forward changes in prostate cancer metabolism, post-transcriptional RNA regulation, and post-translational protein regulatory pathways, requiring the full attention of studies in the future.
Collapse
|
8
|
Rossiter H, Copic D, Direder M, Gruber F, Zoratto S, Marchetti-Deschmann M, Kremslehner C, Sochorová M, Nagelreiter IM, Mlitz V, Buchberger M, Lengauer B, Golabi B, Sukseree S, Mildner M, Eckhart L, Tschachler E. Autophagy protects murine preputial glands against premature aging, and controls their sebum phospholipid and pheromone profile. Autophagy 2021; 18:1005-1019. [PMID: 34491140 DOI: 10.1080/15548627.2021.1966716] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Preputial glands are large lipid and hormone secreting sebaceous organs of mice, and present a convenient model for the investigation of biological processes in sebocytes. Suppression of ATG7-dependent macroautophagy/autophagy in epithelial cells of murine skin causes enlargement of hair follicle-associated sebaceous glands and alters the lipid profile of sebum. We have now extended these studies to the preputial glands and find that autophagy significantly delays the onset of age-related ductal ectasia, influences lipid droplet morphology and contributes to the complete dissolution of the mature sebocytes during holocrine secretion. Single cell RNA sequencing showed that many genes involved in lipid metabolism and oxidative stress response were downregulated in immature and mature epithelial cells of ATG7-deficient glands. When analyzing the lipid composition of control and mutant glands, we found that levels of all phospholipid classes, except choline plasmalogen, were decreased in the mutant glands, with a concomitant accumulation of diacyl glycerides. Mass spectrometric imaging (MSI) demonstrated that phospholipid species, specifically the dominant phosphatidylcholine (PC 34:1), were decreased in immature and mature sebocytes. In addition, we found a strong reduction in the amounts of the pheromone, palmityl acetate. Thus, autophagy in the preputial gland is not only important for homeostasis of the gland as a whole and an orderly breakdown of cells during holocrine secretion, but also regulates phospholipid and fatty acid metabolism, as well as pheromone production.AbbreviationsATG7: autophagy related 7; BODIPY: boron dipyrromethene; DAG: diacyl glycerides; DBI: diazepam binding inhibitor; GFP: green fluorescent protein; KRT14: keratin 14; HPLC-MS: high performance liquid chromatography-mass spectrometry; LD: lipid droplet; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MSI: mass spectrometric imaging; ORO: Oil Red O; PC: phosphatidylcholine; PE: phosphatidylethanolamine; PG: preputial gland; PLIN2: perilipin 2; PtdIns: phosphatidylinositol; PL: phospholipids; POPC: 1-palmitoyl-2-oleoyl-PC; PS: phosphatidylserine; qRT-PCR: quantitative reverse transcribed PCR; SG: sebaceous gland; scRNAseq: single-cell RNA sequencing; TAG: triacylglycerides; TLC: thin layer chromatography.
Collapse
Affiliation(s)
| | - Dragan Copic
- Laboratory for Cardiac and Thoracic Diagnosis, Regeneration and Applied Immunology, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Martin Direder
- Laboratory for Cardiac and Thoracic Diagnosis, Regeneration and Applied Immunology, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Florian Gruber
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Samuele Zoratto
- Institute of Chemical Technologies and Analytics, Technical University of Vienna, Vienna, Austria
| | | | | | - Michaela Sochorová
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Ionela-Mariana Nagelreiter
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Center for Brain Research, Department of Molecular Neurosciences, Medical University of Vienna, Vienna, Austria
| | - Veronika Mlitz
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Maria Buchberger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Barbara Lengauer
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Bahar Golabi
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Supawadee Sukseree
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Michael Mildner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Erwin Tschachler
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
9
|
Basu SS, Agar NYR. Bringing Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging to the Clinics. Clin Lab Med 2021; 41:309-324. [PMID: 34020766 DOI: 10.1016/j.cll.2021.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is an emerging analytical technique that promises to change tissue-based diagnostics. This article provides a brief introduction to MALDI MSI as well as clinical diagnostic workflows and opportunities to apply this powerful approach. It describes various MALDI MSI applications, from more clinically mature applications such as cancer to emerging applications such as infectious diseases and drug distribution. In addition, it discusses the analytical considerations that need to be considered when bringing these approaches to different diagnostic problems and settings.
Collapse
Affiliation(s)
- Sankha S Basu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
10
|
Yang YC, Chien MH, Lai TC, Tung MC, Jan YH, Chang WM, Jung SM, Chen MH, Yeh CN, Hsiao M. Proteomics-based identification of TMED9 is linked to vascular invasion and poor prognoses in patients with hepatocellular carcinoma. J Biomed Sci 2021; 28:29. [PMID: 33888099 PMCID: PMC8063382 DOI: 10.1186/s12929-021-00727-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/14/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Due to the difficulties in early diagnosing and treating hepatocellular carcinoma (HCC), prognoses for patients remained poor in the past decade. In this study, we established a screening model to discover novel prognostic biomarkers in HCC patients. METHODS Candidate biomarkers were screened by liquid chromatography with tandem mass spectrometry (LC-MS/MS) analyses of five HCC normal (N)/tumor (T) paired tissues and preliminarily verified them through several in silico database analyses. Expression levels and functional roles of candidate biomarkers were respectively evaluated by immunohistochemical staining in N/T paired tissue (n = 120) and MTS, colony formation, and transwell migration/invasion assays in HCC cell lines. Associations of clinicopathological features and prognoses with candidate biomarkers in HCC patients were analyzed from GEO and TCGA datasets and our recruited cohort. RESULTS We found that the transmembrane P24 trafficking protein 9 (TMED9) protein was elevated in HCC tissues according to a global proteomic analysis. Higher messenger (m)RNA and protein levels of TMED9 were observed in HCC tissues compared to normal liver tissues or pre-neoplastic lesions. The TMED9 mRNA expression level was significantly associated with an advanced stage and a poor prognosis of overall survival (OS, p = 0.00084) in HCC patients. Moreover, the TMED9 protein expression level was positively correlated with vascular invasion (p = 0.026), OS (p = 0.044), and disease-free survival (p = 0.015) in our recruited Taiwanese cohort. In vitro, manipulation of TMED9 expression in HCC cells significantly affected cell migratory, invasive, proliferative, and colony-forming abilities. CONCLUSIONS Ours is the first work to identify an oncogenic role of TMED9 in HCC cells and may provide insights into the application of TMED9 as a novel predictor of clinical outcomes and a potential therapeutic target in patients with HCC.
Collapse
Affiliation(s)
- Yi-Chieh Yang
- Department of Medical Research, Tungs' Taichung Metro Harbor Hospital, Taichung, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan.,Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Ming-Hsien Chien
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan. .,Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan. .,Traditional Herbal Medicine Research Center, Taipei Medical University Hospital, Taipei, Taiwan. .,TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Tsung-Ching Lai
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Min-Che Tung
- Department of Medical Research, Tungs' Taichung Metro Harbor Hospital, Taichung, Taiwan
| | - Yi-Hua Jan
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Wei-Ming Chang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.,School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Shih-Ming Jung
- Department of Pathology, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan
| | - Ming-Huang Chen
- Department of Oncology, Taipei Veterans General Hospital and School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan. .,School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Chun-Nan Yeh
- Department of General Surgery and Liver Research Center, Linkou Branch, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, 333, Taiwan.
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan. .,Department of Biochemistry, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
| |
Collapse
|
11
|
Abstract
Mass spectrometry imaging (MSI) is a label-free molecular imaging technique allowing an untargeted detection of a broad range of biomolecules and xenobiotics. MSI enables imaging of the spatial distribution of proteins, peptides, lipids and metabolites from a wide range of samples. To date, this technique is commonly applied to tissue sections in cancer diagnostics and biomarker development, but also molecular histology in general. Advances in the methodology and bioinformatics improved the resolution of MS images below the single cell level and increased the flexibility of the workflow. However, MSI-based research in virology is just starting to gain momentum and its full potential has not been exploited yet. In this review, we discuss the main applications of MSI in virology. We review important aspects of matrix-assisted laser desorption/ionization (MALDI) MSI, the most widely used MSI technique in virology. In addition, we summarize relevant literature on MSI studies that aim to unravel virus-host interactions and virus pathogenesis, to elucidate antiviral drug kinetics and to improve current viral disease diagnostics. Collectively, these studies strongly improve our general understanding of virus-induced changes in the proteome, metabolome and metabolite distribution in host tissues of humans, animals and plants upon infection. Furthermore, latest MSI research provided important insights into the drug distribution and distribution kinetics, especially in antiretroviral research. Finally, MSI-based investigations of oncogenic viruses greatly increased our knowledge on tumor mass signatures and facilitated the identification of cancer biomarkers.
Collapse
Affiliation(s)
- Luca D Bertzbach
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | | | - Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
| |
Collapse
|
12
|
Dannhorn A, Kazanc E, Ling S, Nikula C, Karali E, Serra MP, Vorng JL, Inglese P, Maglennon G, Hamm G, Swales J, Strittmatter N, Barry ST, Sansom OJ, Poulogiannis G, Bunch J, Goodwin RJ, Takats Z. Universal Sample Preparation Unlocking Multimodal Molecular Tissue Imaging. Anal Chem 2020; 92:11080-11088. [PMID: 32519547 DOI: 10.1021/acs.analchem.0c00826] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A new tissue sample embedding and processing method is presented that provides downstream compatibility with numerous different histological, molecular biology, and analytical techniques. The methodology is based on the low temperature embedding of fresh frozen specimens into a hydrogel matrix composed of hydroxypropyl methylcellulose (HPMC) and polyvinylpyrrolidone (PVP) and sectioning using a cryomicrotome. The hydrogel was expected not to interfere with standard tissue characterization methods, histologically or analytically. We assessed the compatibility of this protocol with various mass spectrometric imaging methods including matrix-assisted laser desorption ionization (MALDI), desorption electrospray ionization (DESI) and secondary ion mass spectrometry (SIMS). We also demonstrated the suitability of the universal protocol for extraction based molecular biology techniques such as rt-PCR. The integration of multiple analytical modalities through this universal sample preparation protocol offers the ability to study tissues at a systems biology level and directly linking results to tissue morphology and cellular phenotype.
Collapse
Affiliation(s)
- Andreas Dannhorn
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, U.K
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences (CPSS), AstraZeneca, Cambridge, U.K
| | - Emine Kazanc
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, U.K
| | - Stephanie Ling
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences (CPSS), AstraZeneca, Cambridge, U.K
| | - Chelsea Nikula
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington TW11 0LW, U.K
| | - Evdoxia Karali
- The Institute for Cancer Research (ICR), London SW7 3RP, U.K
| | - Maria Paola Serra
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences (CPSS), AstraZeneca, Cambridge, U.K
| | - Jean-Luc Vorng
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington TW11 0LW, U.K
| | - Paolo Inglese
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, U.K
| | - Gareth Maglennon
- Oncology Safety, Clinical Pharmacology and Safety Sciences (CPSS), AstraZeneca, Cambridge, U.K
| | - Gregory Hamm
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences (CPSS), AstraZeneca, Cambridge, U.K
| | - John Swales
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences (CPSS), AstraZeneca, Cambridge, U.K
| | - Nicole Strittmatter
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences (CPSS), AstraZeneca, Cambridge, U.K
| | - Simon T Barry
- Bioscience, Discovery, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | | | - Josephine Bunch
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington TW11 0LW, U.K
| | - Richard Ja Goodwin
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences (CPSS), AstraZeneca, Cambridge, U.K
| | - Zoltan Takats
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, U.K
| |
Collapse
|
13
|
Liu L, Li Y, Zhang R, Li C, Xiong J, Wei Y. MIR205HG acts as a ceRNA to expedite cell proliferation and progression in lung squamous cell carcinoma via targeting miR-299-3p/MAP3K2 axis. BMC Pulm Med 2020; 20:163. [PMID: 32513149 PMCID: PMC7278044 DOI: 10.1186/s12890-020-1174-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 04/29/2020] [Indexed: 01/16/2023] Open
Abstract
INTRODUCTION Long noncoding RNAs (lncRNAs) have been associated with many types of cancers, but their molecular mechanisms in lung squamous cell carcinoma (LUSC) have not been fully studied. Therefore, the current study investigated the regulation role of microRNA-205 host gene (MIR205HG) in LUSC and recognized the target genes managed by this lncRNA. METHODS MIR205HG expression was assessed by the quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The effects of silenced MIR205HG on cell biological behaviors were detected by colony formation assay, transwell assay, flow cytometry analysis and western blot analysis. Luciferase reporter assay and RNA immunoprecipitation (RIP) assay were utilized to proof the binding relationship between miR-299-3p and MIR205HG/mitogen-activated protein kinase kinase kinase 2 (MAP 3 K2). RESULTS The expression levels of MIR205HG in LUSC tissues and cell lines were obviously up-regulated. Down-regulation of MIR205HG expression remarkably reduced cell proliferation, migration and epithelial-to-mesenchymal transition (EMT) progression, whereas promoted cell apoptosis. MIR205HG could bind with miR-299-3p and down-regulation of MIR205HG elevated miR-299-3p expression. MAP 3 K2 acted as the target gene of miR-299-3p and was up-regulated by MIR205HG overexpression. Overexpressing MAP 3 K2 could counteract the effects of down-regulating MIR205HG on LUSC progression to some degree. CONCLUSION MIR205HG acts as a competing endogenous RNA (ceRNA) to expedite cell proliferation and progression via targeting miR-299-3p in LUSC.
Collapse
Affiliation(s)
- Limin Liu
- Respiration Department, Tianyou Hospital Affiliated to Wuhan University of Science and Technology, No.9, Tujialing, Wuchang District, Wuhan, 430064, Hubei, China
| | - Yulei Li
- Respiration Department, Tianyou Hospital Affiliated to Wuhan University of Science and Technology, No.9, Tujialing, Wuchang District, Wuhan, 430064, Hubei, China
| | - Ruifang Zhang
- Respiration Department, Tianyou Hospital Affiliated to Wuhan University of Science and Technology, No.9, Tujialing, Wuchang District, Wuhan, 430064, Hubei, China
| | - Chun Li
- Respiration Department, Tianyou Hospital Affiliated to Wuhan University of Science and Technology, No.9, Tujialing, Wuchang District, Wuhan, 430064, Hubei, China
| | - Jing Xiong
- Respiration Department, Tianyou Hospital Affiliated to Wuhan University of Science and Technology, No.9, Tujialing, Wuchang District, Wuhan, 430064, Hubei, China
| | - Yuan Wei
- Three Wards of Outpatient Service, Wuhan Jin Yin Tan Hospital, No.1 Yintan Road, Dongxihu District, Wuhan, 433013, Hubei, China.
| |
Collapse
|
14
|
Kappeler BIG, Regitano LCA, Poleti MD, Cesar ASM, Moreira GCM, Gasparin G, Coutinho LL. MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness. BMC Mol Biol 2019; 20:1. [PMID: 30602381 PMCID: PMC6317189 DOI: 10.1186/s12867-018-0118-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/20/2018] [Indexed: 12/16/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs are involved in the regulation of many processes including cell proliferation, differentiation, neurogenesis, angiogenesis, and apoptosis. Beef tenderness is an organoleptic characteristic of great influence in the acceptance of meat by consumers. Previous studies have shown that collagen level, marbling, apoptosis and proteolysis are among the many factors that affect beef tenderness. Considering that miRNAs can modulate gene expression, this study was designed to identify differentially expressed miRNAs that could be modulating biological processes involved with beef tenderness. Results Deep sequence analysis of miRNA libraries from longissimus thoracis muscle allowed the identification of 42 novel and 308 known miRNAs. Among the known miRNAs, seven were specifically expressed in skeletal muscle. Differential expression analysis between animals with high (H) and low (L) estimated breeding values for shear force (EBVSF) revealed bta-mir-182 and bta-mir-183 are up-regulated (q value < 0.05) in animals with L EBVSF, and bta-mir-338 is up-regulated in animals with H EBVSF. The number of bovine predicted targets for bta-mir-182, bta-mir-183 and bta-mir-338 were 811, 281 and 222, respectively, which correspond to 1204 unique target genes. Among these, four of them, MEF2C, MAP3K2, MTDH and TNRC6B were common targets of the three differentially expressed miRNAs. The functional analysis identified important pathways related to tenderness such as apoptosis and the calpain–calpastatin system. Conclusion The results obtained indicate the importance of miRNAs in the regulatory mechanisms that influence muscle proteolysis and meat tenderness and contribute to our better understanding of the role of miRNAs in biological processes associated with beef tenderness. Electronic supplementary material The online version of this article (10.1186/s12867-018-0118-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Berna I G Kappeler
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Mirele D Poleti
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635-900, Brazil
| | - Aline S M Cesar
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Gabriel C M Moreira
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Gustavo Gasparin
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Luiz L Coutinho
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
| |
Collapse
|
15
|
Vaysse PM, Heeren RMA, Porta T, Balluff B. Mass spectrometry imaging for clinical research - latest developments, applications, and current limitations. Analyst 2018. [PMID: 28642940 DOI: 10.1039/c7an00565b] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry is being used in many clinical research areas ranging from toxicology to personalized medicine. Of all the mass spectrometry techniques, mass spectrometry imaging (MSI), in particular, has continuously grown towards clinical acceptance. Significant technological and methodological improvements have contributed to enhance the performance of MSI recently, pushing the limits of throughput, spatial resolution, and sensitivity. This has stimulated the spread of MSI usage across various biomedical research areas such as oncology, neurological disorders, cardiology, and rheumatology, just to name a few. After highlighting the latest major developments and applications touching all aspects of translational research (i.e. from early pre-clinical to clinical research), we will discuss the present challenges in translational research performed with MSI: data management and analysis, molecular coverage and identification capabilities, and finally, reproducibility across multiple research centers, which is the largest remaining obstacle in moving MSI towards clinical routine.
Collapse
Affiliation(s)
- Pierre-Maxence Vaysse
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Tiffany Porta
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| |
Collapse
|
16
|
Dilillo M, Heijs B, McDonnell LA. Mass spectrometry imaging: How will it affect clinical research in the future? Expert Rev Proteomics 2018; 15:709-716. [PMID: 30203995 DOI: 10.1080/14789450.2018.1521278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Mass spectrometry imaging (MSI) is a label free, multiplex imaging technology able to simultaneously record the distributions of 100's to 1000's of species, and which may be configured to study metabolites, lipids, glycans, peptides, and proteins simply by changing the tissue preparation protocol. Areas covered: The capability of MSI to complement established histopathological practice through the identification of biomarkers for differential diagnosis, patient prognosis, and response to therapy; the capability of MSI to annotate tissues on the basis of each pixel's mass spectral signature; the development of reproducible MSI through multicenter studies. Expert commentary: We discuss how MSI can be combined with microsampling/microdissection technologies in order to investigate, with more depth of coverage, the molecular changes uncovered by MSI.
Collapse
Affiliation(s)
| | - Bram Heijs
- b Center for Proteomics and Metabolomics , Leiden University Medical Center , Leiden , The Netherlands
| | - Liam A McDonnell
- a Fondazione Pisana per la Scienza ONLUS , Pisa , Italy.,b Center for Proteomics and Metabolomics , Leiden University Medical Center , Leiden , The Netherlands
| |
Collapse
|
17
|
Huber K, Khamehgir-Silz P, Schramm T, Gorshkov V, Spengler B, Römpp A. Approaching cellular resolution and reliable identification in mass spectrometry imaging of tryptic peptides. Anal Bioanal Chem 2018; 410:5825-5837. [PMID: 30066193 PMCID: PMC6096711 DOI: 10.1007/s00216-018-1199-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/24/2018] [Accepted: 06/13/2018] [Indexed: 01/19/2023]
Abstract
On-tissue digestion has become the preferred method to identify proteins in mass spectrometry (MS) imaging. In this study, we report advances in data acquisition and protein identification for MS imaging after on-tissue digestion. Tryptic peptides in a coronal mouse brain section were measured at 50 μm pixel size and revealed detailed histological structures, e.g., the ependyma (consisting of one to two cell layers), which was confirmed by H&E staining. This demonstrates that MS imaging of tryptic peptides at or close to cellular resolution is within reach. We also describe a detailed identification workflow which resulted in the identification of 99 proteins (with 435 corresponding peptides), based on comparison with LC-MS/MS data and in silico digest. These results were obtained with stringent parameters, including high mass accuracy in imaging mode (RSME < 3 ppm) and at least two unique peptides per protein showing consistent spatial distribution. We identified almost 50% of proteins with at least four corresponding peptides. As there is no agreed approach for identification of proteins after on-tissue digestion yet, we discuss our workflow in detail and make the corresponding mass spectral data available as “open data” via ProteomeXchange (identifier PXD003172). With this, we would like to contribute to a more effective discussion and the development of new approaches for tryptic peptide identification in MS imaging. From an experimental point of view, we demonstrate the improvement due to the combination of high spatial resolution and high mass resolution/mass accuracy on a measurement at 25 μm pixel size in mouse cerebellum tissue. A whole body section of a mouse pub imaged at 50 μm pixel size (40 GB, 230,000 spectra) demonstrates the stability of our protocol. For this data set, we developed a workflow that is based on conversion to the common data format imzML and sequential application of freely available software tools. In combination, the presented results for spatial resolution, protein identification, and data processing constitute significant improvements for the field of on-tissue digestion. MS imaging of coronal mouse brain cerebellum with a pixel size of 25 μm: A Optical image, B myelin staining, C H&E staining, and D MS image overlay (RGB) of tryptic peptides m/z = 726.4045 ± 0.005, HGFLPR + H+ (red), m/z = 536.3173 ± 0.005, AKPAK + Na+ (green), and m/z = 994.5436 ± 0.005, WRQLIEK + Na+ (blue) ![]()
Collapse
Affiliation(s)
- Katharina Huber
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Pegah Khamehgir-Silz
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Thorsten Schramm
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Vladimir Gorshkov
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Andreas Römpp
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany. .,Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitaetsstrasse 30, 95440, Bayreuth, Germany.
| |
Collapse
|
18
|
Ahmad S, St Hilaire VR, Dandepally SR, Johnson GL, Williams AL, Scott JE. Discovery and characterization of an iminocoumarin scaffold as an inhibitor of MEKK2 (MAP3K2). Biochem Biophys Res Commun 2018; 496:205-211. [PMID: 29309787 DOI: 10.1016/j.bbrc.2018.01.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/04/2018] [Indexed: 12/24/2022]
Abstract
The kinase MEKK2 (MAP3K2) activates the MEK5/ERK5 cell signaling pathway and may play an important role in tumor growth and metastasis. Thus, MEKK2 may represent a novel kinase target for cancer. In order to identify inhibitors of MEKK2, we screened a library of compounds using a high throughput MEKK2 intrinsic ATPase enzyme assay. We identified two hits with validated structures and confirmed activity in the primary assay (IC50 values = 322 nM and 7.7 μM) and two orthogonal MEKK2 biochemical assays. Compound 1, the more potent hit, was the subject of further investigation. Limited structure-activity relationship (SAR) studies were performed on this iminocoumarin hit which resulted in ≥20-fold more potent analogs (e.g. 8 and 16 nM IC50). Two analogs had improved selectivity in a 50-member kinase profiling panel compared to the hit. These studies suggested that substitutions around the phenoxy ring of this scaffold can impart improved potency and selectivity for MEKK2. Analog Compound 1s (16 nM IC50) was further verified by external testing to inhibit MEKK2 and MEKK3 with similar potencies. Compound 1s displayed activity in cell-based assays in which it inhibited ERK5 pathway activation in cells and inhibited cell migration in a scratch assay. Thus, we have identified a scaffold that has promising potential to be developed into a highly selective and potent inhibitor of MEKK2. Information from these SAR studies provides specific guidance for the future design of MEKK2 inhibitor probes.
Collapse
Affiliation(s)
- Syed Ahmad
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, NC, USA
| | - Valentine R St Hilaire
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, NC, USA
| | - Srinivasa R Dandepally
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, NC, USA
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Alfred L Williams
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, NC, USA
| | - John E Scott
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, NC, USA.
| |
Collapse
|
19
|
Guran R, Vanickova L, Horak V, Krizkova S, Michalek P, Heger Z, Zitka O, Adam V. MALDI MSI of MeLiM melanoma: Searching for differences in protein profiles. PLoS One 2017; 12:e0189305. [PMID: 29220390 PMCID: PMC5722329 DOI: 10.1371/journal.pone.0189305] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/23/2017] [Indexed: 12/21/2022] Open
Abstract
Background Treatment of advanced cutaneous melanoma remains challenging, and new data on melanoma biology are required. The most widely accepted criteria for the prognostic evaluation of melanoma are histopathological and clinical parameters, and the identification of additional tumor markers is thus of paramount importance. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI), an important tool in cancer research, is useful for unraveling the molecular profile of melanoma. Methodology/Principal findings In this report, we used the melanoma-bearing Libechov minipig (MeLiM), a unique animal model that allows observation of the complete spontaneous regression of invasive cutaneous melanoma, to investigate i) the differences between melanoma and healthy skin protein profiles and ii) the proteins potentially involved in spontaneous regression. The MeLiM tissues were cryosected, histologically characterized, analyzed by MALDI MSI, and immunohistologically stained. Multivariate statistical analyses of the MALDI MSI data revealed ten relevant m/z ions, of which the expression levels varied significantly among the studied MeLiM tissues. These ion peaks were used to create mass ion images/maps and visualize the differences between tumor and healthy skin specimens, as well as among histologically characterized tissue regions. Conclusions/Significance Protein profiles comprising ten statistically significant mass ion peaks useful for differentiating cutaneous melanoma and healthy skin tissues were determined. Peaks at m/z 3044, 6011, 6140 and 10180 were overexpressed in melanoma compared with healthy skin tissue. More specifically, m/z 6140 was expressed at significantly (p < 0.05) higher levels in normally growing melanoma regions than in regions with early and late spontaneous regression. This study demonstrates the clinical utility of MALDI MSI for the analysis of tissue cryosections at a molecular level.
Collapse
Affiliation(s)
- Roman Guran
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Lucie Vanickova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
| | - Vratislav Horak
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, v.v.i., Libechov, Czech Republic
| | - Sona Krizkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Petr Michalek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
- * E-mail:
| |
Collapse
|
20
|
Kurreck A, Vandergrift LA, Fuss TL, Habbel P, Agar NYR, Cheng LL. Prostate cancer diagnosis and characterization with mass spectrometry imaging. Prostate Cancer Prostatic Dis 2017; 21:297-305. [PMID: 29209003 PMCID: PMC5988647 DOI: 10.1038/s41391-017-0011-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/15/2017] [Indexed: 02/06/2023]
Abstract
Background Prostate cancer (PCa), the most common cancer and second leading cause of cancer death in American men, presents the clinical challenge of distinguishing between indolent and aggressive tumors for proper treatment. PCa presents significant alterations in metabolic pathways that can potentially be measured using techniques like mass spectrometry (MS) or mass spectrometry imaging (MSI) and used to characterize PCa aggressiveness. MS quantifies metabolomic, proteomic, and lipidomic profiles of biological systems that can be further visualized for their spatial distributions through MSI. Methods PubMed was queried for all publications relating to MS and MSI in human prostate cancer from April 2007 to April 2017. With the goal of reviewing the utility of MSI in diagnosis and prognostication of human PCa, MSI articles that reported investigations of PCa-specific metabolites or metabolites indicating PCa aggressiveness were selected for inclusion. Articles were included that covered MS and MSI principles, limitations, and applications in PCa. Results We identified nine key studies on MSI in intact human prostate tissue specimens that determined metabolites which could either differentiate between benign and malignant prostate tissue or indicate prostate cancer aggressiveness. These MSI-detected biomarkers show promise in reliably identifying PCa and determining disease aggressiveness. Conclusions MSI represents an innovative technique with the ability to interrogate cancer biomarkers in relation to tissue pathologies and investigate tumor aggressiveness. We propose MSI as a powerful adjuvant histopathology imaging tool for prostate tissue evaluations, where clinical translation of this ex vivo technique could make possible the use of MSI for personalized medicine in diagnosis and prognosis of prostate cancer. Moreover, the knowledge provided from this technique can majorly contribute to the understanding of molecular pathogenesis of PCa and other malignant diseases.
Collapse
Affiliation(s)
- Annika Kurreck
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Hematology and Oncology, Charité Medical University of Berlin, Berlin, Germany
| | - Lindsey A Vandergrift
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Taylor L Fuss
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Piet Habbel
- Department of Hematology and Oncology, Charité Medical University of Berlin, Berlin, Germany
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Leo L Cheng
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
21
|
Lou S, Balluff B, de Graaff MA, Cleven AHG, Briaire-de Bruijn I, Bovée JVMG, McDonnell LA. High-grade sarcoma diagnosis and prognosis: Biomarker discovery by mass spectrometry imaging. Proteomics 2017; 16:1802-13. [PMID: 27174013 DOI: 10.1002/pmic.201500514] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 05/04/2016] [Accepted: 05/09/2016] [Indexed: 12/24/2022]
Abstract
The combination of high heterogeneity, both intratumoral and intertumoral, with their rarity has made diagnosis, prognosis of high-grade sarcomas difficult. There is an urgent need for more objective molecular biomarkers, to differentiate between the many different subtypes, and to also provide new treatment targets. Mass spectrometry imaging (MSI) has amply demonstrated its ability to identify potential new markers for patient diagnosis, survival, metastasis and response to therapy in cancer research. In this study, we investigated the ability of MALDI-MSI of proteins to distinguish between high-grade osteosarcoma (OS), leiomyosarcoma (LMS), myxofibrosarcoma (MFS) and undifferentiated pleomorphic sarcoma (UPS) (Ntotal = 53). We also investigated if there are individual proteins or protein signatures that are statistically associated with patient survival. Twenty diagnostic protein signals were found characteristic for specific tumors (p ≤ 0.05), amongst them acyl-CoA-binding protein (m/z 11 162), macrophage migration inhibitory factor (m/z 12 350), thioredoxin (m/z 11 608) and galectin-1 (m/z 14 633) were assigned. Another nine protein signals were found to be associated with overall survival (p ≤ 0.05), including proteasome activator complex subunit 1 (m/z 9753), indicative for non-OS patients with poor survival; and two histone H4 variants (m/z 11 314 and 11 355), indicative of poor survival for LMS patients.
Collapse
Affiliation(s)
- Sha Lou
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Benjamin Balluff
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.,Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, The Netherlands
| | - Marieke A de Graaff
- Department of Pathology, Leiden University, Medical Center, Leiden, The Netherlands
| | - Arjen H G Cleven
- Department of Pathology, Leiden University, Medical Center, Leiden, The Netherlands
| | | | - Judith V M G Bovée
- Department of Pathology, Leiden University, Medical Center, Leiden, The Netherlands
| | - Liam A McDonnell
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Pathology, Leiden University, Medical Center, Leiden, The Netherlands.,Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| |
Collapse
|
22
|
Yuan Y, Xie X, Jiang Y, Wei Z, Wang P, Chen F, Li X, Sun C, Zhao H, Zeng X, Jiang L, Zhou Y, Dan H, Feng M, Liu R, Wang Z, Chen Q. LRP6 is identified as a potential prognostic marker for oral squamous cell carcinoma via MALDI-IMS. Cell Death Dis 2017; 8:e3035. [PMID: 28880263 PMCID: PMC5636978 DOI: 10.1038/cddis.2017.433] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 06/07/2017] [Accepted: 06/12/2017] [Indexed: 02/05/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is a leading cause of cancer-related deaths worldwide, with 500 000 new cases each year. However, the mechanisms underlying OSCC development are relatively unknown. In this study, matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS)-based proteomic strategy was used to profile the differentially expressed peptides/proteins between OSCC tissues and their adjacent noncancerous tissues. Sixty-seven unique peptide peaks and five distinct proteins were identified with changed expression levels. Among them, LRP6 expression was found to be upregulated in OSCC tissues, and correlated with a cluster of clinicopathologic parameters, including smoking, drinking, tumor differentiation status, lymph node metastasis and survival time. Notably, knockdown of LRP6 inhibited the proliferation ability of OSCC cells. Furthermore, we demonstrated that the expression of LRP6 in OSCC cells is positively correlated with its downstream oncogene, FGF8. The present study suggests that LRP6 could be a potential biomarker for OSCC patients, and might further assist in the therapeutic decisions in OSCC treatment.
Collapse
Affiliation(s)
- Yao Yuan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaoyan Xie
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yuchen Jiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zihao Wei
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Peiqi Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Fangman Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xinyi Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chongkui Sun
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Hang Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Zeng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lu Jiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yu Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Hongxia Dan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mingye Feng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Rui Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhiyong Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
23
|
Prentice BM, Caprioli RM, Vuiblet V. Label-free molecular imaging of the kidney. Kidney Int 2017; 92:580-598. [PMID: 28750926 PMCID: PMC6193761 DOI: 10.1016/j.kint.2017.03.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 12/25/2022]
Abstract
In this review, we will highlight technologies that enable scientists to study the molecular characteristics of tissues and/or cells without the need for antibodies or other labeling techniques. Specifically, we will focus on matrix-assisted laser desorption/ionization imaging mass spectrometry, infrared spectroscopy, and Raman spectroscopy.
Collapse
Affiliation(s)
- Boone M Prentice
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Departments of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee, USA; Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA.
| | - Vincent Vuiblet
- Biophotonic Laboratory, UMR CNRS 7369 URCA, Reims, France; Nephropathology, Department of Biopathology Laboratory, CHU de Reims, Reims, France; Nephrology and Renal Transplantation department, CHU de Reims, Reims, France.
| |
Collapse
|
24
|
Global Proteomics-based Identification and Validation of Thymosin Beta-4 X-Linked as a Prognostic Marker for Head and Neck Squamous Cell Carcinoma. Sci Rep 2017; 7:9031. [PMID: 28831179 PMCID: PMC5567379 DOI: 10.1038/s41598-017-09539-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/26/2017] [Indexed: 12/14/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) represents a major health concern worldwide. We applied the matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) to analyze paired normal (N) and tumor (T) samples from head and neck squamous cell carcinoma as well as liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis in HNSCC cell lines to identify tumor-associated biomarkers. Our results showed a number of proteins found to be over-expressed in HNSCC. We identified thymosin beta-4 X-linked (TMSB4X) is one of the most significant candidate biomarkers. Higher TMSB4X expression in the tumor was found by N/T-paired HNSCC samples at both RNA and protein level. Overexpression of TMSB4X was found significantly associated with poor prognosis of overall survival (OS, P = 0.006) and recurrence-free survival (RFS, P = 0.013) in HNSCC patients. Silencing of TMSB4X expression in HNSCC cell line reduced the proliferation and invasion ability in vitro, as well as inhibited the cervical lymph node metastasis in vivo. Altogether, our global proteomics analysis identified that TMSB4X is a newly discovered biomarker in HNSCC whose functions resulted in enhanced proliferation and metastasis in vitro and in vivo. TMSB4X may be a potential therapeutic target for treating HNSCC patients.
Collapse
|
25
|
Su DW, Nieva J. Biophysical technologies for understanding circulating tumor cell biology and metastasis. Transl Lung Cancer Res 2017; 6:473-485. [PMID: 28904890 DOI: 10.21037/tlcr.2017.05.08] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An understanding of cancer evolution in lung cancer with its associated resistance to therapy can only be achieved with repeated sampling and analysis of the cancer. Given the high risks and costs associated with repeat physical biopsy, alternative technologies must be applied. Several modalities exist for analysis and re-analysis of cancer biology. Among them are the CellSearch platform, the CTC chip, and the high-definition CTC platform. While the former is primarily able to provide prognosticating information in the form of CTC enumeration, the latter two have the advantage of serving as a platform to study tumor biology. Techniques for analysis of single cell genomics, as well as protein expression on a single cell basis provide scientists with the capacity to understand cancer cell populations as a collection of individual cells, rather than as an average of all cells. A multimodal combination of circulating tumor DNAs (ctDNAs), CTCs, proteomics, and CTC-derived xenografts (CDXs) to create computational models useful in diagnosis, prognostication, and predictiveness to treatment is likely the future of tailoring individualized cancer care.
Collapse
Affiliation(s)
- Derrick W Su
- Norris Cancer Center, University of Southern California, Los Angeles, USA
| | - Jorge Nieva
- Norris Cancer Center, University of Southern California, Los Angeles, USA
| |
Collapse
|
26
|
Belov ME, Ellis SR, Dilillo M, Paine MRL, Danielson WF, Anderson GA, de Graaf EL, Eijkel GB, Heeren RMA, McDonnell LA. Design and Performance of a Novel Interface for Combined Matrix-Assisted Laser Desorption Ionization at Elevated Pressure and Electrospray Ionization with Orbitrap Mass Spectrometry. Anal Chem 2017; 89:7493-7501. [DOI: 10.1021/acs.analchem.7b01168] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Shane R. Ellis
- M4I,
The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229 ER Maastricht, The Netherlands
| | | | - Martin R. L. Paine
- M4I,
The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229 ER Maastricht, The Netherlands
| | | | | | | | - Gert B. Eijkel
- M4I,
The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ron M. A. Heeren
- M4I,
The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229 ER Maastricht, The Netherlands
| | | |
Collapse
|
27
|
MALDI imaging: beyond classic diagnosis. BOLETIN MEDICO DEL HOSPITAL INFANTIL DE MEXICO 2017; 74:212-218. [PMID: 29382489 DOI: 10.1016/j.bmhimx.2017.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/21/2017] [Accepted: 03/28/2017] [Indexed: 02/04/2023] Open
Abstract
Mass spectrometry has been the focus of technology development and application for imaging for several decades. Imaging mass spectrometry using matrix-assisted laser desorption ionization is a new and effective tool for molecular studies of complex biological samples such as tissue sections. As histological features remain intact throughout the analysis of a section, distribution maps of multiple analytes can be correlated with histological and clinical features. Spatial molecular arrangements can be assessed without the need for target-specific reagents, allowing the discovery of diagnostic and prognostic markers of different cancer types and enabling the determination of effective therapies.
Collapse
|
28
|
Esteve C, Jones EA, Kell DB, Boutin H, McDonnell LA. Mass spectrometry imaging shows major derangements in neurogranin and in purine metabolism in the triple-knockout 3×Tg Alzheimer mouse model. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:747-754. [PMID: 28411106 DOI: 10.1016/j.bbapap.2017.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 04/04/2017] [Accepted: 04/07/2017] [Indexed: 01/06/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) can simultaneously measure hundreds of biomolecules directly from tissue. Using different sample preparation strategies, proteins and metabolites have been profiled to study the molecular changes in a 3×Tg mouse model of Alzheimer's disease. In comparison with wild-type (WT) control mice MALDI-MSI revealed Alzheimer's disease-specific protein profiles, highlighting dramatic reductions of a protein with m/z 7560, which was assigned to neurogranin and validated by immunohistochemistry. The analysis also revealed substantial metabolite changes, especially in metabolites related to the purine metabolic pathway, with a shift towards an increase in hypoxanthine/xanthine/uric acid in the 3×Tg AD mice accompanied by a decrease in AMP and adenine. Interestingly these changes were also associated with a decrease in ascorbic acid, consistent with oxidative stress. Furthermore, the metabolite N-arachidonyl taurine was increased in the diseased mouse brain sections, being highly abundant in the hippocampus. Overall, we describe an interesting shift towards pro-inflammatory molecules (uric acid) in the purinergic pathway associated with a decrease in anti-oxidant level (ascorbic acid). Together, these observations fit well with the increased oxidative stress and neuroinflammation commonly observed in AD. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
Collapse
Affiliation(s)
- Clara Esteve
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Emrys A Jones
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Douglas B Kell
- School of Chemistry, The University of Manchester, Manchester, Lancs M13 9PL, UK; Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, Lancs, UK
| | - Hervé Boutin
- Faculty of Medicine and Human Sciences, The University of Manchester, Manchester, UK; Wolfson Molecular Imaging Center, The University of Manchester, Manchester, UK
| | - Liam A McDonnell
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands; Fondazione Pisana per la Scienza ONLUS, Pisa, Italy.
| |
Collapse
|
29
|
Hinsch A, Buchholz M, Odinga S, Borkowski C, Koop C, Izbicki JR, Wurlitzer M, Krech T, Wilczak W, Steurer S, Jacobsen F, Burandt EC, Stahl P, Simon R, Sauter G, Schlüter H. MALDI imaging mass spectrometry reveals multiple clinically relevant masses in colorectal cancer using large-scale tissue microarrays. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:165-173. [PMID: 28117928 DOI: 10.1002/jms.3916] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/13/2017] [Accepted: 01/19/2017] [Indexed: 06/06/2023]
Abstract
For identification of clinically relevant masses to predict status, grade, relapse and prognosis of colorectal cancer, we applied Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) to a tissue micro array containing formalin-fixed and paraffin-embedded tissue samples from 349 patients. Analysis of our MALDI-IMS data revealed 27 different m/z signals associated with epithelial structures. Comparison of these signals showed significant association with status, grade and Ki-67 labeling index. Fifteen out of 27 IMS signals revealed a significant association with survival. For seven signals (m/z 654, 776, 788, 904, 944, 975 and 1013) the absence and for eight signals (m/z 643, 678, 836, 886, 898, 1095, 1459 and 1477) the presence were associated with decreased life expectancy, including five masses (m/z 788, 836, 904, 944 and 1013) that provided prognostic information independently from the established prognosticators pT and pN. Combination of these five masses resulted in a three-step classifier that provided prognostic information superior to univariate analysis. In addition, a total of 19 masses were associated with tumor stage, grade, metastasis and cell proliferation. Our data demonstrate the suitability of combining IMS and large-scale tissue micro arrays to simultaneously identify and validate clinically useful molecular marker. Copyright © 2017 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- A Hinsch
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - M Buchholz
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - S Odinga
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - C Borkowski
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - C Koop
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - J R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - M Wurlitzer
- Dept. of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - T Krech
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - W Wilczak
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - S Steurer
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - F Jacobsen
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - E-C Burandt
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - P Stahl
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - R Simon
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - G Sauter
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - H Schlüter
- Dept. of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| |
Collapse
|
30
|
Panderi I, Yakirevich E, Papagerakis S, Noble L, Lombardo K, Pantazatos D. Differentiating tumor heterogeneity in formalin-fixed paraffin-embedded (FFPE) prostate adenocarcinoma tissues using principal component analysis of matrix-assisted laser desorption/ionization imaging mass spectral data. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:160-170. [PMID: 27791282 DOI: 10.1002/rcm.7776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/25/2016] [Accepted: 10/24/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE Many patients with adenocarcinoma of the prostate present with advanced and metastatic cancer at the time of diagnosis. There is an urgent need to detect biomarkers that will improve the diagnosis and prognosis of this disease. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) is playing a key role in cancer research and it can be useful to unravel the molecular profile of prostate cancer biopsies. METHODS MALDI imaging data sets are highly complex and their interpretation requires the use of multivariate statistical methods. In this study, MALDI-IMS technology, sequential principal component analysis (PCA) and two-dimensional (2-D) peak distribution tests were employed to investigate tumor heterogeneity in formalin-fixed paraffin-embedded (FFPE) prostate cancer biopsies. RESULTS Multivariate statistics revealed a number of mass ion peaks obtained from different tumor regions that were distinguishable from the adjacent normal regions within a given specimen. These ion peaks have been used to generate ion images and visualize the difference between tumor and normal regions. Mass peaks at m/z 3370, 3441, 3447 and 3707 exhibited stronger ion signals in the tumor regions. CONCLUSIONS This study reports statistically significant mass ion peaks unique to tumor regions in adenocarcinoma of the prostate and adds to the clinical utility of MALDI-IMS for analysis of FFPE tissue at a molecular level that supersedes all other standard histopathologic techniques for diagnostic purposes used in the current clinical practice. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Irene Panderi
- Brown University, Warren Alpert Medical School, COBRE Center for Cancer Research, Rhode Island Hospital, Providence, RI, USA
- National and Kapodistrian University of Athens, Department of Pharmacy, Division of Pharmaceutical Chemistry, Laboratory of Pharmaceutical Analysis, Athens, Greece
| | - Evgeny Yakirevich
- Brown University, Warren Alpert Medical School, Department of Pathology, Rhode Island Hospital, Providence, RI, USA
| | - Silvana Papagerakis
- University of Michigan Comprehensive Cancer Center, School of Medicine, Department of Periodontics and Oral Medicine, Division of Oral Pathology/Medicine/Radiology, Ann Arbor, MI, USA
| | - Lelia Noble
- Brown University, Warren Alpert Medical School, COBRE Center for Cancer Research, Rhode Island Hospital, Providence, RI, USA
| | - Kara Lombardo
- Brown University, Warren Alpert Medical School, Department of Pathology, Rhode Island Hospital, Providence, RI, USA
| | - Dionysios Pantazatos
- Brown University, Warren Alpert Medical School, COBRE Center for Cancer Research, Rhode Island Hospital, Providence, RI, USA
- Weill Cornell Medical College, Division of Infectious Diseases, Transplantation-Oncology Infectious Disease Program, New York, NY, USA
| |
Collapse
|
31
|
Ucal Y, Durer ZA, Atak H, Kadioglu E, Sahin B, Coskun A, Baykal AT, Ozpinar A. Clinical applications of MALDI imaging technologies in cancer and neurodegenerative diseases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:795-816. [PMID: 28087424 DOI: 10.1016/j.bbapap.2017.01.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 12/08/2016] [Accepted: 01/06/2017] [Indexed: 12/25/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) enables localization of analytes of interest along with histology. More specifically, MALDI-IMS identifies the distributions of proteins, peptides, small molecules, lipids, and drugs and their metabolites in tissues, with high spatial resolution. This unique capacity to directly analyze tissue samples without the need for lengthy sample preparation reduces technical variability and renders MALDI-IMS ideal for the identification of potential diagnostic and prognostic biomarkers and disease gradation. MALDI-IMS has evolved rapidly over the last decade and has been successfully used in both medical and basic research by scientists worldwide. In this review, we explore the clinical applications of MALDI-IMS, focusing on the major cancer types and neurodegenerative diseases. In particular, we re-emphasize the diagnostic potential of IMS and the challenges that must be confronted when conducting MALDI-IMS in clinical settings. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
Collapse
Affiliation(s)
- Yasemin Ucal
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Zeynep Aslıhan Durer
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Hakan Atak
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Elif Kadioglu
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Betul Sahin
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Abdurrahman Coskun
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Ahmet Tarık Baykal
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Aysel Ozpinar
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey.
| |
Collapse
|
32
|
Arentz G, Mittal P, Zhang C, Ho YY, Briggs M, Winderbaum L, Hoffmann MK, Hoffmann P. Applications of Mass Spectrometry Imaging to Cancer. Adv Cancer Res 2017; 134:27-66. [PMID: 28110654 DOI: 10.1016/bs.acr.2016.11.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pathologists play an essential role in the diagnosis and prognosis of benign and cancerous tumors. Clinicians provide tissue samples, for example, from a biopsy, which are then processed and thin sections are placed onto glass slides, followed by staining of the tissue with visible dyes. Upon processing and microscopic examination, a pathology report is provided, which relies on the pathologist's interpretation of the phenotypical presentation of the tissue. Targeted analysis of single proteins provide further insight and together with clinical data these results influence clinical decision making. Recent developments in mass spectrometry facilitate the collection of molecular information about such tissue specimens. These relatively new techniques generate label-free mass spectra across tissue sections providing nonbiased, nontargeted molecular information. At each pixel with spatial coordinates (x/y) a mass spectrum is acquired. The acquired mass spectrums can be visualized as intensity maps displaying the distribution of single m/z values of interest. Based on the sample preparation, proteins, peptides, lipids, small molecules, or glycans can be analyzed. The generated intensity maps/images allow new insights into tumor tissues. The technique has the ability to detect and characterize tumor cells and their environment in a spatial context and combined with histological staining, can be used to aid pathologists and clinicians in the diagnosis and management of cancer. Moreover, such data may help classify patients to aid therapy decisions and predict outcomes. The novel complementary mass spectrometry-based methods described in this chapter will contribute to the transformation of pathology services around the world.
Collapse
Affiliation(s)
- G Arentz
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - P Mittal
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - C Zhang
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - Y-Y Ho
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - M Briggs
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia; ARC Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, SA, Australia
| | - L Winderbaum
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - M K Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - P Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia.
| |
Collapse
|
33
|
Staunton L, Tonry C, Lis R, Espina V, Liotta L, Inzitari R, Bowden M, Fabre A, O'Leary J, Finn SP, Loda M, Pennington SR. Pathology-Driven Comprehensive Proteomic Profiling of the Prostate Cancer Tumor Microenvironment. Mol Cancer Res 2017; 15:281-293. [PMID: 28057717 DOI: 10.1158/1541-7786.mcr-16-0358] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/11/2016] [Accepted: 12/13/2016] [Indexed: 11/16/2022]
Abstract
Prostate cancer is the second most common cancer in men worldwide. Gleason grading is an important predictor of prostate cancer outcomes and is influential in determining patient treatment options. Clinical decisions based on a Gleason score of 7 are difficult as the prognosis for individuals diagnosed with Gleason 4+3 cancer is much worse than for those diagnosed with Gleason 3+4 cancer. Laser capture microdissection (LCM) is a highly precise method to isolate specific cell populations or discrete microregions from tissues. This report undertook a detailed molecular characterization of the tumor microenvironment in prostate cancer to define the proteome in the epithelial and stromal regions from tumor foci of Gleason grades 3 and 4. Tissue regions of interest were isolated from several Gleason 3+3 and Gleason 4+4 tumors using telepathology to leverage specialized pathology expertise to support LCM. Over 2,000 proteins were identified following liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of all regions of interest. Statistical analysis revealed significant differences in protein expression (>100 proteins) between Gleason 3 and Gleason 4 regions-in both stromal and epithelial compartments. A subset of these proteins has had prior strong association with prostate cancer, thereby providing evidence for the authenticity of the approach. Finally, validation of these proteins by immunohistochemistry has been obtained using an independent cohort of prostate cancer tumor specimens.Implications: This unbiased strategy provides a strong foundation for the development of biomarker protein panels with significant diagnostic and prognostic potential. Mol Cancer Res; 15(3); 281-93. ©2017 AACR.
Collapse
Affiliation(s)
- Lisa Staunton
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Claire Tonry
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Rosina Lis
- Center for Molecular Oncologic Pathology, Harvard Medical School, Boston, Massachusetts
| | - Virginia Espina
- Center for Applied Proteomics, George Mason University, Fairfax, Virginia
| | - Lance Liotta
- Center for Applied Proteomics, George Mason University, Fairfax, Virginia
| | - Rosanna Inzitari
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Michaela Bowden
- Center for Molecular Oncologic Pathology, Harvard Medical School, Boston, Massachusetts
| | - Aurelie Fabre
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,Department of Histopathology, St Vincent's University Hospital, Dublin, Ireland
| | - John O'Leary
- Department of Histopathology, St. James's Hospital, Dublin, Ireland
| | - Stephen P Finn
- Department of Histopathology, St. James's Hospital, Dublin, Ireland
| | - Massimo Loda
- Center for Molecular Oncologic Pathology, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
| |
Collapse
|
34
|
Nazari M, Muddiman DC. Polarity switching mass spectrometry imaging of healthy and cancerous hen ovarian tissue sections by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI). Analyst 2017; 141:595-605. [PMID: 26402586 DOI: 10.1039/c5an01513h] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry imaging (MSI) is a rapidly evolving field for monitoring the spatial distribution and abundance of analytes in biological tissue sections. It allows for direct and simultaneous analysis of hundreds of different compounds in a label-free manner. In order to obtain a comprehensive metabolite and lipid data, a polarity switching MSI method using infrared matrix assisted laser desorption electrospray ionization (IR-MALDESI) was developed and optimized where the electrospray polarity was alternated from one voxel to the next. Healthy and cancerous ovarian hen tissue sections were analyzed using this method. Distribution and relative abundance of different metabolites and lipids within each tissue section were discerned, and differences between the two were revealed. Additionally, the utility of using mass spectrometry concepts such as spectral accuracy and sulfur counting for confident identification of analytes in an untargeted method are discussed.
Collapse
Affiliation(s)
- Milad Nazari
- W. M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.
| | - David C Muddiman
- W. M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.
| |
Collapse
|
35
|
Abstract
One of the big clinical challenges in the treatment of cancer is the different behavior of cancer patients under guideline therapy. An important determinant for this phenomenon has been identified as inter- and intratumor heterogeneity. While intertumor heterogeneity refers to the differences in cancer characteristics between patients, intratumor heterogeneity refers to the clonal and nongenetic molecular diversity within a patient. The deciphering of intratumor heterogeneity is recognized as key to the development of novel therapeutics or treatment regimens. The investigation of intratumor heterogeneity is challenging since it requires an untargeted molecular analysis technique that accounts for the spatial and temporal dynamics of the tumor. So far, next-generation sequencing has contributed most to the understanding of clonal evolution within a cancer patient. However, it falls short in accounting for the spatial dimension. Mass spectrometry imaging (MSI) is a powerful tool for the untargeted but spatially resolved molecular analysis of biological tissues such as solid tumors. As it provides multidimensional datasets by the parallel acquisition of hundreds of mass channels, multivariate data analysis methods can be applied for the automated annotation of tissues. Moreover, it integrates the histology of the sample, which enables studying the molecular information in a histopathological context. This chapter will illustrate how MSI in combination with statistical methods and histology has been used for the description and discovery of intratumor heterogeneity in different cancers. This will give evidence that MSI constitutes a unique tool for the investigation of intratumor heterogeneity, and could hence become a key technology in cancer research.
Collapse
|
36
|
Computational Methods for Mass Spectrometry Imaging: Challenges, Progress, and Opportunities. HEALTH INFORMATION SCIENCE 2017. [DOI: 10.1007/978-3-319-44981-4_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
37
|
Huang KT, Ludy S, Calligaris D, Dunn IF, Laws E, Santagata S, Agar NYR. Rapid Mass Spectrometry Imaging to Assess the Biochemical Profile of Pituitary Tissue for Potential Intraoperative Usage. Adv Cancer Res 2016; 134:257-282. [PMID: 28110653 DOI: 10.1016/bs.acr.2016.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pituitary adenomas are relatively common intracranial neoplasms that are frequently treated with surgical resection. Rapid visualization of pituitary tissue remains a challenge as current techniques either produce little to no information on hormone-secreting function or are too slow to practically aid in intraoperative or even perioperative decision-making. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) represents a powerful method by which molecular maps of tissue samples can be created, yielding a two-dimensional representation of the expression patterns of small molecules and proteins from biologic samples. In this chapter, we review the use of MALDI MSI, its application to the characterization of the pituitary gland, and its potential applications for guiding the management of pituitary adenomas.
Collapse
Affiliation(s)
- K T Huang
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - S Ludy
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - D Calligaris
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - I F Dunn
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - E Laws
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - S Santagata
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - N Y R Agar
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States.
| |
Collapse
|
38
|
Wang X, Han J, Hardie DB, Yang J, Pan J, Borchers CH. Metabolomic profiling of prostate cancer by matrix assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry imaging using Matrix Coating Assisted by an Electric Field (MCAEF). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:755-767. [PMID: 28017863 DOI: 10.1016/j.bbapap.2016.12.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 12/15/2022]
Abstract
In this work, we combined the use of two MALDI matrices (quercetin and 9-aminoacridine), a recently developed new matrix coating technique - matrix coating assisted by an electric field (MCAEF), and matrix-assisted laser desorption/ionization - Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) to detect and image endogenous compounds in the cancerous and non-cancerous regions of three human prostate cancer (stage II) tissue specimens. After three rounds of imaging data acquisitions (i.e., quercetin for positive and negative ion detection and 9-aminoacridine for negative ion detection), and metabolite identification, a total of 1091 metabolites including 1032 lipids and 59 other metabolites were routinely detected and successfully localized. Of these compounds, 250 and 217 were only detected in either the cancerous or the non-cancerous regions respectively, although we cannot rule out the presence of these metabolites at concentrations below the detection limit. In addition, 152 of the other 624 metabolites showed differential distributions (p<0.05, t-test) between the two regions of the tissues. Further studies on a larger number of clinical specimens will need to be carried out to confirm this large number of apparently cancer-related metabolites. The successful determination of the spatial locations and abundances of these endogenous biomolecules indicated significant metabolism abnormalities - e.g., increased energy charge and under-expression of neutral acyl glycerides, in the prostate cancer samples. To our knowledge, this work has resulted in MALDI-MS imaging of the largest group of metabolites in prostate cancer thus far and demonstrated the importance of using complementary matrices for comprehensive metabolomic imaging by MALDI-MS. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
Collapse
Affiliation(s)
- Xiaodong Wang
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Jun Han
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Jingxi Pan
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada; Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada.
| |
Collapse
|
39
|
Boskamp T, Lachmund D, Oetjen J, Cordero Hernandez Y, Trede D, Maass P, Casadonte R, Kriegsmann J, Warth A, Dienemann H, Weichert W, Kriegsmann M. A new classification method for MALDI imaging mass spectrometry data acquired on formalin-fixed paraffin-embedded tissue samples. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:916-926. [PMID: 27836618 DOI: 10.1016/j.bbapap.2016.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 12/28/2022]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) shows a high potential for applications in histopathological diagnosis, and in particular for supporting tumor typing and subtyping. The development of such applications requires the extraction of spectral fingerprints that are relevant for the given tissue and the identification of biomarkers associated with these spectral patterns. We propose a novel data analysis method based on the extraction of characteristic spectral patterns (CSPs) that allow automated generation of classification models for spectral data. Formalin-fixed paraffin embedded (FFPE) tissue samples from N=445 patients assembled on 12 tissue microarrays were analyzed. The method was applied to discriminate primary lung and pancreatic cancer, as well as adenocarcinoma and squamous cell carcinoma of the lung. A classification accuracy of 100% and 82.8%, resp., could be achieved on core level, assessed by cross-validation. The method outperformed the more conventional classification method based on the extraction of individual m/z values in the first application, while achieving a comparable accuracy in the second. LC-MS/MS peptide identification demonstrated that the spectral features present in selected CSPs correspond to peptides relevant for the respective classification. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
Collapse
Affiliation(s)
- Tobias Boskamp
- Center for Industrial Mathematics, University of Bremen, Bremen, Germany; SCiLS GmbH, Bremen, Germany.
| | - Delf Lachmund
- Center for Industrial Mathematics, University of Bremen, Bremen, Germany
| | - Janina Oetjen
- MALDI Imaging Lab, University of Bremen, Bremen, Germany
| | | | | | - Peter Maass
- Center for Industrial Mathematics, University of Bremen, Bremen, Germany; MALDI Imaging Lab, University of Bremen, Bremen, Germany; SCiLS GmbH, Bremen, Germany
| | | | - Jörg Kriegsmann
- Proteopath GmbH, Trier, Germany; Center for Histology, Cytology and Molecular Diagnostic, Trier, Germany
| | - Arne Warth
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hendrik Dienemann
- Thoraxklinik Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Mark Kriegsmann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
40
|
Yoshimura Y, Goto-Inoue N, Moriyama T, Zaima N. Significant advancement of mass spectrometry imaging for food chemistry. Food Chem 2016; 210:200-11. [DOI: 10.1016/j.foodchem.2016.04.096] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 02/17/2016] [Accepted: 04/20/2016] [Indexed: 11/30/2022]
|
41
|
Schwamborn K, Kriegsmann M, Weichert W. MALDI imaging mass spectrometry - From bench to bedside. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:776-783. [PMID: 27810414 DOI: 10.1016/j.bbapap.2016.10.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/24/2016] [Accepted: 10/28/2016] [Indexed: 10/20/2022]
Abstract
Today, pathologists face many challenges in defining the precise morphomolecular diagnosis and in guiding clinicians to the optimal patients' treatment. To achieve this goal, increasingly, classical histomorphological methods have to be supplemented by high throughput molecular assays. Since MALDI imaging mass spectrometry (IMS) enables the assessment of spatial molecular arrangements in tissue sections, it goes far beyond microscopy in providing hundreds of different molecular images from a single scan without the need of target-specific reagents. Thus, this technology has the potential to uncover new markers for diagnostic purposes or markers that correlate with disease severity as well as prognosis and therapeutic response. Additionally, in the future MALDI IMS based classifiers measured with this technology in real time in the diagnostic setting might be applicable in the routine diagnostic setting. In this review, recently published studies that show the usefulness, advantages, and applicability of MALDI IMS in different fields of pathology (diagnosis, prognosis and treatment response) are highlighted. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
Collapse
Affiliation(s)
- Kristina Schwamborn
- Institute of Pathology, Technische Universität München (TUM), Munich, Germany.
| | - Mark Kriegsmann
- University of Heidelberg, Department of Pathology, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technische Universität München (TUM), Munich, Germany
| |
Collapse
|
42
|
An approach to optimize sample preparation for MALDI imaging MS of FFPE sections using fractional factorial design of experiments. Anal Bioanal Chem 2016; 408:6729-40. [DOI: 10.1007/s00216-016-9793-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/01/2016] [Accepted: 07/12/2016] [Indexed: 12/29/2022]
|
43
|
Huang T, She K, Peng G, Wang W, Huang J, Li J, Wang Z, He J. MicroRNA-186 suppresses cell proliferation and metastasis through targeting MAP3K2 in non-small cell lung cancer. Int J Oncol 2016; 49:1437-44. [PMID: 27498924 DOI: 10.3892/ijo.2016.3637] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/22/2016] [Indexed: 11/05/2022] Open
Abstract
MicroRNAs are a class of small endogenous non-coding RNAs that play crucial roles in the initiation and progression of human cancers. miR-186 was found decreased in various human malignancies and function as a tumor suppressor. However, the regulating mechanism of miR-186 in growth and metastasis of human non-small cell lung cancer (NSCLC) is still poorly understood. We investigated the role of miR-186 in the growth and metastasis of human NSCLC. In the present study, we found that miR-186 was significantly decreased in lung cancer tissues and cells. Furthermore, overexpression of miR-186 suppressed lung cancer cell proliferation, migration and invasion, and induced cell apoptosis. Moreover, we found that confirmed mitogen-activated protein kinase kinase kinase 2 (MAP3K2) protein was increased in lung cancer tissues and confirmed that MAP3K2 is a target gene of miR-186. In addition, knockdown of MAP3K2 by RNA interference inhibited lung cancer cell proliferation, migration and invasion, and promoted cell apoptosis in vitro. Furthermore, we observed tthat the overexpression of MAP3K2 partially reversed the inhibitory effect of miR-186 on the proliferation and metastasis of A549 and HCC827 cell lines. Taken together, our data indicated that miR-186 regulates lung cancer growth and metastasis through suppressing MAP3K2 expression, at least partly. Therefore, miR-186-MAP3K2 may represent a new and useful potential clinical treatment and diagnosis target for NSCLC.
Collapse
Affiliation(s)
- Tonghai Huang
- Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Kelin She
- Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Guilin Peng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, P.R. China
| | - Wei Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, P.R. China
| | - Jun Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, P.R. China
| | - Jingpei Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, P.R. China
| | - Zheng Wang
- Department of Thoracic Surgery, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Jianxing He
- Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| |
Collapse
|
44
|
Kurabe N, Igarashi H, Ohnishi I, Tajima S, Inoue Y, Takahashi Y, Setou M, Sugimura H. Visualization of sphingolipids and phospholipids in the fundic gland mucosa of human stomach using imaging mass spectrometry. World J Gastrointest Pathophysiol 2016; 7:235-241. [PMID: 27190696 PMCID: PMC4867403 DOI: 10.4291/wjgp.v7.i2.235] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/21/2016] [Accepted: 03/02/2016] [Indexed: 02/06/2023] Open
Abstract
AIM: To analyze the lipid distribution in gastric mucosae.
METHODS: Imaging mass spectrometry (MS) is a useful tool to survey the distribution of biomolecules in surgical specimens. Here we used the imaging MS apparatus named iMScope to identify the dominant molecules present in the human gastric mucosa near the fundic glands. Five gastric specimens were subjected to iMScope analysis. These specimens were also analyzed by immunohistochemistry using MUC5AC, H(+)-K(+)-ATPaseβ Claudin18 antibodies.
RESULTS: Three major molecules with m/z 725.5, 780.5, and 782.5 detected in the gastric mucosa were identified as sphingomyelin (SM) (d18:1/16:0), phosphatidylcholine (PC) (16:0/18:2), and PC (16:0/18:1), respectively, through MS/MS analyses. Using immunohistological staining, SM (d18:1/16:0) signals were mainly co-localized with the foveolar epithelium marker MUC5AC. In contrast, PC (16:0/18:2) signals were observed in the region testing positive for the fundic gland marker H(+)-K(+)-ATPaseβ. PC (16:0/18:1) signals were uniformly distributed throughout the mucosa.
CONCLUSION: Our basic data will contribute to the studies of lipid species in physical and pathological conditions of the human stomach.
Collapse
|
45
|
Potential of MALDI imaging for the toxicological evaluation of environmental pollutants. J Proteomics 2016; 144:133-9. [PMID: 27178109 DOI: 10.1016/j.jprot.2016.05.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/13/2016] [Accepted: 05/08/2016] [Indexed: 01/02/2023]
Abstract
Risk assessment related to the exposure of humans to chemicals released into the environment is a major concern of our modern societies. In this context, toxicology plays a crucial role to characterize the effects of this exposure on health and identify the targets of these molecules. MALDI imaging mass spectrometry (IMS) is an enabling technology for biodistribution studies of chemicals. Although the majority of published studies are presented in a pharmacological context, the concepts discussed in this review can be applied to the toxicological evaluation of chemicals released into the environment. The major asset of IMS is the simultaneous localization and identification of a parent molecule and its metabolites without labeling and without any prior knowledge. Quantification methods developed in IMS are presented with application to an environmental pollutant. IMS is effective in the localization of chemicals and endogenous species. This opens unique perspectives for the discovery of molecular alterations in metabolites and protein biomarkers that could help for a better understanding of toxicity mechanisms. Distribution studies of agrochemicals in plants by IMS can contribute to a better understanding of their mode of action and to a more effective use of these chemicals, avoiding the current concern of environmental damage.
Collapse
|
46
|
Wang X, Han J, Hardie DB, Yang J, Borchers CH. The use of matrix coating assisted by an electric field (MCAEF) to enhance mass spectrometric imaging of human prostate cancer biomarkers. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:86-95. [PMID: 26757076 DOI: 10.1002/jms.3728] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
In this work, we combined a newly developed matrix coating technique - matrix coating assisted by an electric field (MCAEF) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to enhance the imaging of peptides and proteins in tissue specimens of human prostate cancer. MCAEF increased the signal-to-noise ratios of the detected proteins by a factor of 2 to 5, and 232 signals were detected within the m/z 3500-37500 mass range on a time-of-flight mass spectrometer and with the sinapinic acid MALDI matrix. Among these species, three proteins (S100-A9, S100-A10, and S100-A12) were only observed in the cancerous cell region and 14 proteins, including a fragment of mitogen-activated protein kinase/extracellular signal-regulated kinase kinase kinase 2, a fragment of cAMP-regulated phosphoprotein 19, 3 apolipoproteins (C-I, A-I, and A-II), 2 S100 proteins (A6 and A8), β-microseminoprotein, tumor protein D52, α-1-acid glycoprotein 1, heat shock protein β-1, prostate-specific antigen, and 2 unidentified large peptides at m/z 5002.2 and 6704.2, showed significantly differential distributions at the p < 0.05 (t-test) level between the cancerous and the noncancerous regions of the tissue. Among these 17 species, the distributions of apolipoprotein C-I, S100-A6, and S100-A8 were verified by immunohistological staining. In summary, this study resulted in the imaging of the largest group of proteins in prostate cancer tissues by MALDI-MS reported thus far, and is the first to show a correlation between S100 proteins and prostate cancer in a MS imaging study. The successful imaging of the three proteins only found in the cancerous tissues, as well as those showing differential expressions demonstrated the potential of MCAEF-MALDI/MS for the in situ detection of potential cancer biomarkers. Copyright © 2015 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Xiaodong Wang
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Jun Han
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada
| |
Collapse
|
47
|
Harn YC, Powers MJ, Shank EA, Jojic V. Deconvolving molecular signatures of interactions between microbial colonies. Bioinformatics 2015; 31:i142-50. [PMID: 26072476 PMCID: PMC4765860 DOI: 10.1093/bioinformatics/btv251] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Motivation: The interactions between microbial colonies through chemical signaling are not well understood. A microbial colony can use different molecules to inhibit or accelerate the growth of other colonies. A better understanding of the molecules involved in these interactions could lead to advancements in health and medicine. Imaging mass spectrometry (IMS) applied to co-cultured microbial communities aims to capture the spatial characteristics of the colonies’ molecular fingerprints. These data are high-dimensional and require computational analysis methods to interpret. Results: Here, we present a dictionary learning method that deconvolves spectra of different molecules from IMS data. We call this method MOLecular Dictionary Learning (MOLDL). Unlike standard dictionary learning methods which assume Gaussian-distributed data, our method uses the Poisson distribution to capture the count nature of the mass spectrometry data. Also, our method incorporates universally applicable information on common ion types of molecules in MALDI mass spectrometry. This greatly reduces model parameterization and increases deconvolution accuracy by eliminating spurious solutions. Moreover, our method leverages the spatial nature of IMS data by assuming that nearby locations share similar abundances, thus avoiding overfitting to noise. Tests on simulated datasets show that this method has good performance in recovering molecule dictionaries. We also tested our method on real data measured on a microbial community composed of two species. We confirmed through follow-up validation experiments that our method recovered true and complete signatures of molecules. These results indicate that our method can discover molecules in IMS data reliably, and hence can help advance the study of interaction of microbial colonies. Availability and implementation: The code used in this paper is available at: https://github.com/frizfealer/IMS_project. Contact:vjojic@cs.unc.edu Supplementary information:Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Y-C Harn
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - M J Powers
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - E A Shank
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - V Jojic
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
48
|
Goto T, Terada N, Inoue T, Kobayashi T, Nakayama K, Okada Y, Yoshikawa T, Miyazaki Y, Uegaki M, Utsunomiya N, Makino Y, Sumiyoshi S, Yamasaki T, Kamba T, Ogawa O. Decreased expression of lysophosphatidylcholine (16:0/OH) in high resolution imaging mass spectrometry independently predicts biochemical recurrence after surgical treatment for prostate cancer. Prostate 2015; 75:1821-30. [PMID: 26332786 DOI: 10.1002/pros.23088] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 08/18/2015] [Indexed: 12/31/2022]
Abstract
BACKGROUND Human prostate cancers are highly heterogeneous, indicating a need for various novel biomarkers to predict their prognosis. Lipid metabolism affects numerous cellular processes, including cell growth, proliferation, differentiation, and motility. Direct profiling of lipids in tissue using high-resolution matrix-assisted laser desorption/ionization imaging mass spectrometry (HR-MALDI-IMS) may provide molecular details that supplement tissue morphology. METHODS Prostate tissue samples were obtained from 31 patients, with localized prostate cancer who underwent radical prostatectomy. The samples were assessed by HR-MALDI-IMS in positive mode, with the molecules identified by tandem mass spectrometry (MS/MS). The effect of identified molecules on prostate specific antigen recurrence free survival after radical prostatectomy was determined by Cox regression analysis and by the Kaplan-Meier method. RESULTS Thirteen molecules were found to be highly expressed in prostate tissue, with five being significantly lower in cancer tissue than in benign epithelium. MS/MS showed that these molecules were [lysophosphatidylcholine (LPC)(16:0/OH)+H](+), [LPC(16:0/OH)+Na](+), [LPC(16:0/OH)+K](+), [LPC(16:0/OH)+matrix+H](+), and [sphingomyelin (SM)(d18:1/16:0)+H](+). Reduced expression of LPC(16:0/OH) in cancer tissue was an independent predictor of biochemical recurrence after radical prostatectomy. CONCLUSIONS HR-MALDI-IMS showed that the expression of LPC(16:0/OH) and SM(d18:1/16:0) was lower in prostate cancer than in benign prostate epithelium. These differences in expression of phospholipids may predict prostate cancer aggressiveness, and provide new insights into lipid metabolism in prostate cancer.
Collapse
Affiliation(s)
- Takayuki Goto
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Naoki Terada
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takahiro Inoue
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Kobayashi
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenji Nakayama
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshiyuki Okada
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Yoshikawa
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yu Miyazaki
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masayuki Uegaki
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Noriaki Utsunomiya
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuki Makino
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinji Sumiyoshi
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Toshinari Yamasaki
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomomi Kamba
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Ogawa
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| |
Collapse
|
49
|
Ahmad S, Johnson GL, Scott JE. Identification of ponatinib and other known kinase inhibitors with potent MEKK2 inhibitory activity. Biochem Biophys Res Commun 2015; 463:888-93. [PMID: 26056008 DOI: 10.1016/j.bbrc.2015.06.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/04/2015] [Indexed: 12/11/2022]
Abstract
The kinase MEKK2 (MAP3K2) may play an important role in tumor growth and metastasis for several cancer types. Thus, targeting MEKK2 may represent a novel strategy for developing more effective therapies for cancer. In order to identify small molecules with MEKK2 inhibitory activity, we screened a collection of known kinase inhibitors using a high throughput MEKK2 intrinsic ATPase enzyme assay and confirmed activity of the most potent hits with this primary assay. We also confirmed activities of these known kinase inhibitors with an MEKK2 transphosphorylation slot blot assay using MKK6 as a substrate. We observed a good correlation in potencies between the two orthogonal MEKK2 kinase activity assay formats for this set of inhibitors. We report that ponatinib, AT9283, AZD7762, JNJ-7706621, PP121 and hesperadin had potent MEKK2 enzyme inhibitory activities ranging from 4.7 to 60 nM IC50. Ponatinib is an FDA-approved drug that potently inhibited MEKK2 enzyme activity with IC50 values of 10-16 nM. AT9283 is currently in clinical trials and produced MEKK2 IC50 values of 4.7-18 nM. This set of known kinase inhibitors represents some of the most potent in vitro MEKK2 inhibitors reported to date and may be useful as research tools. Although these compounds are not selective for MEKK2, the structures of these compounds give insight into pharmacophores that potently inhibit MEKK2 and could be used as initial leads to design highly selective inhibitors of MEKK2.
Collapse
Affiliation(s)
- Syed Ahmad
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, NC, USA
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - John E Scott
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, NC, USA.
| |
Collapse
|
50
|
Drake RR, Jones EE, Powers TW, Nyalwidhe JO. Altered glycosylation in prostate cancer. Adv Cancer Res 2015; 126:345-82. [PMID: 25727153 DOI: 10.1016/bs.acr.2014.12.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Prostate cancer is annually the most common newly diagnosed cancer in men. The prostate functions as a major secretory gland for the production of glycoproteins critical to sperm activation and reproduction. Prostate-specific antigen (PSA), produced by the prostate, is one of the most commonly assayed glycoproteins in blood, serving as a biomarker for early detection and progression of prostate cancer. The single site of N-glycosylation on PSA has been the target of multiple glycan characterization studies. In this review, the extensive number of studies that have characterized the changes in O-linked and N-linked glycosylations associated with prostate cancer development and progression will be summarized. This includes analysis of the glycosylation of PSA, and other prostate glycoproteins, in tissues, clinical biofluids, and cell line models. Other studies are summarized in the context of understanding the complexities of these glycan changes in order to address the many confounding questions associated with prostate cancer, as well as efforts to improve prostate cancer biomarker assays using targeted glycomic-based strategies.
Collapse
Affiliation(s)
- Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA.
| | - E Ellen Jones
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Thomas W Powers
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Julius O Nyalwidhe
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia, USA
| |
Collapse
|