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Holterhus M, Altvater B, Kailayangiri S, Rossig C. The Cellular Tumor Immune Microenvironment of Childhood Solid Cancers: Informing More Effective Immunotherapies. Cancers (Basel) 2022; 14:cancers14092177. [PMID: 35565307 PMCID: PMC9105669 DOI: 10.3390/cancers14092177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 11/16/2022] Open
Abstract
Common pediatric solid cancers fail to respond to standard immuno-oncology agents relying on preexisting adaptive antitumor immune responses. The adoptive transfer of tumor-antigen specific T cells, such as CAR-gene modified T cells, is an attractive strategy, but its efficacy has been limited. Evidence is accumulating that local barriers in the tumor microenvironment prevent the infiltration of T cells and impede therapeutic immune responses. A thorough understanding of the components of the functional compartment of the tumor microenvironment and their interaction could inform effective combination therapies and novel engineered therapeutics, driving immunotherapy towards its full potential in pediatric patients. This review summarizes current knowledge on the cellular composition and significance of the tumor microenvironment in common extracranial solid cancers of childhood and adolescence, such as embryonal tumors and bone and soft tissue sarcomas, with a focus on myeloid cell populations that are often present in abundance in these tumors. Strategies to (co)target immunosuppressive myeloid cell populations with pharmacological anticancer agents and with selective antagonists are presented, as well as novel concepts aiming to employ myeloid cells to cooperate with antitumor T cell responses.
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Radtke AJ, Chu CJ, Yaniv Z, Yao L, Marr J, Beuschel RT, Ichise H, Gola A, Kabat J, Lowekamp B, Speranza E, Croteau J, Thakur N, Jonigk D, Davis JL, Hernandez JM, Germain RN. IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues. Nat Protoc 2022; 17:378-401. [PMID: 35022622 DOI: 10.1038/s41596-021-00644-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/05/2021] [Indexed: 01/02/2023]
Abstract
High-content imaging is needed to catalog the variety of cellular phenotypes and multicellular ecosystems present in metazoan tissues. We recently developed iterative bleaching extends multiplexity (IBEX), an iterative immunolabeling and chemical bleaching method that enables multiplexed imaging (>65 parameters) in diverse tissues, including human organs relevant for international consortia efforts. IBEX is compatible with >250 commercially available antibodies and 16 unique fluorophores, and can be easily adopted to different imaging platforms using slides and nonproprietary imaging chambers. The overall protocol consists of iterative cycles of antibody labeling, imaging and chemical bleaching that can be completed at relatively low cost in 2-5 d by biologists with basic laboratory skills. To support widespread adoption, we provide extensive details on tissue processing, curated lists of validated antibodies and tissue-specific panels for multiplex imaging. Furthermore, instructions are included on how to automate the method using competitively priced instruments and reagents. Finally, we present a software solution for image alignment that can be executed by individuals without programming experience using open-source software and freeware. In summary, IBEX is a noncommercial method that can be readily implemented by academic laboratories and scaled to achieve high-content mapping of diverse tissues in support of a Human Reference Atlas or other such applications.
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Affiliation(s)
- Andrea J Radtke
- Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Colin J Chu
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ziv Yaniv
- Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Li Yao
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - James Marr
- Leica Microsystems Inc., Wetzlar, Germany
| | - Rebecca T Beuschel
- Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hiroshi Ichise
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anita Gola
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Howard Hughes Medical Institute, Robin Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Juraj Kabat
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bradley Lowekamp
- Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emily Speranza
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Innate Immunity and Pathogenesis Section, Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Joshua Croteau
- Department of Business Development, BioLegend, Inc, San Diego, CA, USA
| | - Nishant Thakur
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Jeremy L Davis
- Surgical Oncology Program, Metastasis Biology Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan M Hernandez
- Surgical Oncology Program, Metastasis Biology Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ronald N Germain
- Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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Keratinocytes Regulate the Threshold of Inflammation by Inhibiting T Cell Effector Functions. Cells 2021; 10:cells10071606. [PMID: 34206914 PMCID: PMC8306889 DOI: 10.3390/cells10071606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Whilst the importance of keratinocytes as a first-line defense has been widely investigated, little is known about their interactions with non-resident immune cells. In this study, the impact of human keratinocytes on T cell effector functions was analyzed in an antigen-specific in vitro model of allergic contact dermatitis (ACD) to nickel sulfate. Keratinocytes partially inhibited T cell proliferation and cytokine production. This effect was dependent on the keratinocyte/T cell ratio and was partially reversible by increasing the number of autologous dendritic cells. The inhibition of T cell proliferation by keratinocytes was independent of the T cell subtype and antigen presentation by different professional antigen-presenting cells. Autologous and heterologous keratinocytes showed comparable effects, while the fixation of keratinocytes with paraformaldehyde abrogated the immunosuppressive effect. The separation of keratinocytes and T cells by a transwell chamber, as well as a cell-free keratinocyte supernatant, inhibited T cell effector functions to the same amount as directly co-cultured keratinocytes, thus proving that soluble factor/s account for the observed suppressive effects. In conclusion, keratinocytes critically control the threshold of inflammatory processes in the skin by inhibiting T cell proliferation and cytokine production.
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Duplancic R, Kero D. Novel approach for quantification of multiple immunofluorescent signals using histograms and 2D plot profiling of whole-section panoramic images. Sci Rep 2021; 11:8619. [PMID: 33883639 PMCID: PMC8060297 DOI: 10.1038/s41598-021-88101-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 04/08/2021] [Indexed: 12/27/2022] Open
Abstract
We describe a novel approach for quantification and colocalization of immunofluorescence (IF) signals of multiple markers on high-resolution panoramic images of serial histological sections utilizing standard staining techniques and readily available software for image processing and analysis. Human gingiva samples stained with primary antibodies against the common leukocyte antigen CD45 and factors related to heparan sulfate glycosaminoglycans (HS GAG) were used. Expression domains and spatial gradients of IF signals were quantified by histograms and 2D plot profiles, respectively. The importance of histomorphometric profiling of tissue samples and IF signal thresholding is elaborated. This approach to quantification of IF staining utilizes pixel (px) counts and comparison of px grey value (GV) or luminance. No cell counting is applied either to determine the cellular content of a given histological section nor the number of cells positive to the primary antibody of interest. There is no selection of multiple Regions-Of-Interest (ROIs) since the entire histological section is quantified. Although the standard IF staining protocol is applied, the data output enables colocalization of multiple markers (up to 30) from a given histological sample. This can serve as an alternative for colocalization of IF staining of multiple primary antibodies based on repeating cycles of staining of the same histological section since those techniques require non standard staining protocols and sophisticated equipment that can be out of reach for small laboratories in academic settings. Combined with the data from ontological bases, this approach to quantification of IF enables creation of in silico virtual disease models.
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Affiliation(s)
- Roko Duplancic
- Study Program of Dental Medicine, School of Medicine, University of Split, Soltanska 2, 21000, Split, Croatia
| | - Darko Kero
- Study Program of Dental Medicine, School of Medicine, University of Split, Soltanska 2, 21000, Split, Croatia. .,Department of Anatomy, Histology and Embryology, Laboratory for Early Human Development, School of Medicine, University of Split, Soltanska 2, 21000, Split, Croatia.
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Harizanova J, Fermin Y, Malik-Sheriff RS, Wieczorek J, Ickstadt K, Grecco HE, Zamir E. Highly Multiplexed Imaging Uncovers Changes in Compositional Noise within Assembling Focal Adhesions. PLoS One 2016; 11:e0160591. [PMID: 27519053 PMCID: PMC4982658 DOI: 10.1371/journal.pone.0160591] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 07/21/2016] [Indexed: 12/25/2022] Open
Abstract
Integrin adhesome proteins bind each other in alternative manners, forming within the cell diverse cell-matrix adhesion sites with distinct properties. An intriguing question is how such modular assembly of adhesion sites is achieved correctly solely by self-organization of their components. Here we address this question using high-throughput multiplexed imaging of eight proteins and two phosphorylation sites in a large number of single focal adhesions. We found that during the assembly of focal adhesions the variances of protein densities decrease while the correlations between them increase, suggesting reduction in the noise levels within these structures. These changes correlate independently with the area and internal density of focal adhesions, but not with their age or shape. Artificial neural network analysis indicates that a joint consideration of multiple components improves the predictability of paxillin and zyxin levels in internally dense focal adhesions. This suggests that paxillin and zyxin densities in focal adhesions are fine-tuned by integrating the levels of multiple other components, thus averaging-out stochastic fluctuations. Based on these results we propose that increase in internal protein densities facilitates noise suppression in focal adhesions, while noise suppression enables their stable growth and further density increase—hence forming a feedback loop giving rise to a quality-controlled assembly.
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Affiliation(s)
- Jana Harizanova
- Department of Systemic Cell Biology, Max Planck Institute of Molecular, Physiology, Dortmund, Germany
| | - Yessica Fermin
- Faculty of Statistics, TU Dortmund University, Dortmund, Germany
| | - Rahuman S. Malik-Sheriff
- Department of Systemic Cell Biology, Max Planck Institute of Molecular, Physiology, Dortmund, Germany
| | - Jakob Wieczorek
- Faculty of Statistics, TU Dortmund University, Dortmund, Germany
| | - Katja Ickstadt
- Faculty of Statistics, TU Dortmund University, Dortmund, Germany
| | - Hernán E. Grecco
- Department of Systemic Cell Biology, Max Planck Institute of Molecular, Physiology, Dortmund, Germany
- * E-mail: (HEG); (EZ)
| | - Eli Zamir
- Department of Systemic Cell Biology, Max Planck Institute of Molecular, Physiology, Dortmund, Germany
- * E-mail: (HEG); (EZ)
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Wittke S, Baxmann S, Fahlenkamp D, Kiessig ST. Tumor heterogeneity as a rationale for a multi-epitope approach in an autologous renal cell cancer tumor vaccine. Onco Targets Ther 2016; 9:523-37. [PMID: 26889089 PMCID: PMC4743638 DOI: 10.2147/ott.s92182] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
PURPOSE An autologous tumor vaccine already used successfully in the immune therapy of renal cell carcinoma was investigated in detail. The evaluation of potential tumor markers should allow for the assessment of potency according to pharmaceutical regulations. METHODS A panel of 36 tumor-associated antigens and cellular marker proteins was characterized in a total of 133 tumor cell lysates by methods such as ELISA, Western blots, and topological proteomics. The induction of tumor-associated antigen-specific antibodies was demonstrated by immunization in mice. RESULTS Tumor heterogeneity was demonstrated: none of the tumor-associated antigens investigated were detectable in each tumor lysate. In parallel, the coincidental presence of potential danger signals was shown for HSP-60 and HSP-70. The presence of both antigen and danger signal allowed a successful induction of an immune response in a murine model. CONCLUSION The verified tumor heterogeneity indicates the need for a multi-epitope approach for the successful immunotherapy in renal cell carcinoma.
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Affiliation(s)
- Stefan Wittke
- University of Applied Sciences Bremerhaven, Faculty of Biotechnology Bremerhaven, Bochum, Germany
| | | | - Dirk Fahlenkamp
- Department of Urology, Zeisigwald Bethanien Hospital, Chemnitz, Germany
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7
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Large molecular systems landscape uncovers T cell trapping in human skin cancer. Sci Rep 2016; 6:19012. [PMID: 26757895 PMCID: PMC4725819 DOI: 10.1038/srep19012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 12/02/2015] [Indexed: 12/13/2022] Open
Abstract
Immune surveillance of tumour cells is an important function of CD8 T lymphocytes, which has failed in cancer for reasons still unknown in many respect but mainly related to cellular processes in the tumour microenvironment. Applying imaging cycler microscopy to analyse the immune contexture in a human skin cancer we could identify and map 7,000 distinct cell surface-associated multi-protein assemblies. The resulting combinatorial geometry-based high-functional resolution led to discovery of a mechanism of T cell trapping in the epidermis, which involves SPIKE, a network of suprabasal keratinocyte projections piercing and interconnecting CD8 T cells. It appears initiated by clusters of infrabasal T and dendritic cells connected via cell projections across a fractured basal lamina to suprabasal keratinocytes and T lymphocytes.
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8
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Schubert W. Advances in toponomics drug discovery: Imaging cycler microscopy correctly predicts a therapy method of amyotrophic lateral sclerosis. Cytometry A 2015; 87:696-703. [PMID: 25869332 PMCID: PMC4676937 DOI: 10.1002/cyto.a.22671] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An imaging cycler microscope (ICM) is a fully automated (epi)fluorescence microscope which overcomes the spectral resolution limit resulting in parameter- and dimension-unlimited fluorescence imaging. This enables the spatial resolution of large molecular systems with their emergent topological properties (toponome) in morphologically intact cells and tissues displaying thousands of multi protein assemblies at a time. The resulting combinatorial geometry of these systems has been shown to be key for in-vivo/in-situ detection of lead proteins controlling protein network topology and (dys)function: If lead proteins are blocked or downregulated the corresponding disease protein network disassembles. Here, correct therapeutic predictions are exemplified for ALS. ICM drug target studies have discovered an 18-dimensional cell surface molecular system in ALS-PBMC with a lead drug target protein, whose therapeutic downregulation is now reported to show statistically significant effect with stop of disease progression in one third of the ALS patients. Together, this clinical and the earlier experimental validations of the ICM approach indicate that ICM readily discovers in vivo robustness nodes of disease with lead proteins controlling them. Breaking in vivo robustness nodes using drugs against their lead proteins is likely to overcome current high drug attrition rates. © 2015 The Author. Published by Wiley Periodicals, Inc, on behalf of ISAC.
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Affiliation(s)
- Walter Schubert
- Department of Medicine, Molecular Pattern Recognition Research Group, Otto Von Guericke University, Magdeburg, Germany
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Schubert W. Systematic, spatial imaging of large multimolecular assemblies and the emerging principles of supramolecular order in biological systems. J Mol Recognit 2014; 27:3-18. [PMID: 24375580 PMCID: PMC4283051 DOI: 10.1002/jmr.2326] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 01/27/2023]
Abstract
Understanding biological systems at the level of their relational (emergent) molecular properties in functional protein networks relies on imaging methods, able to spatially resolve a tissue or a cell as a giant, non-random, topologically defined collection of interacting supermolecules executing myriads of subcellular mechanisms. Here, the development and findings of parameter-unlimited functional super-resolution microscopy are described-a technology based on the fluorescence imaging cycler (IC) principle capable of co-mapping thousands of distinct biomolecular assemblies at high spatial resolution and differentiation (<40 nm distances). It is shown that the subcellular and transcellular features of such supermolecules can be described at the compositional and constitutional levels; that the spatial connection, relational stoichiometry, and topology of supermolecules generate hitherto unrecognized functional self-segmentation of biological tissues; that hierarchical features, common to thousands of simultaneously imaged supermolecules, can be identified; and how the resulting supramolecular order relates to spatial coding of cellular functionalities in biological systems. A large body of observations with IC molecular systems microscopy collected over 20 years have disclosed principles governed by a law of supramolecular segregation of cellular functionalities. This pervades phenomena, such as exceptional orderliness, functional selectivity, combinatorial and spatial periodicity, and hierarchical organization of large molecular systems, across all species investigated so far. This insight is based on the high degree of specificity, selectivity, and sensitivity of molecular recognition processes for fluorescence imaging beyond the spectral resolution limit, using probe libraries controlled by ICs.
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Affiliation(s)
- Walter Schubert
- Molecular pattern recognition research group, O-v-G-university MagdeburgGermany
- International faculty, Max-Planck (CAS-MPG) partner institute for computational biologyShanghai, China
- Human toponome project, TNLMunich, Germany
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Domanova O, Borbe S, Mühlfeld S, Becker M, Kubitz R, Häussinger D, Berlage T. Toponomics method for the automated quantification of membrane protein translocation. BMC Bioinformatics 2011; 12:370. [PMID: 21929784 PMCID: PMC3230911 DOI: 10.1186/1471-2105-12-370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 09/19/2011] [Indexed: 01/30/2023] Open
Abstract
Background Intra-cellular and inter-cellular protein translocation can be observed by microscopic imaging of tissue sections prepared immunohistochemically. A manual densitometric analysis is time-consuming, subjective and error-prone. An automated quantification is faster, more reproducible, and should yield results comparable to manual evaluation. The automated method presented here was developed on rat liver tissue sections to study the translocation of bile salt transport proteins in hepatocytes. For validation, the cholestatic liver state was compared to the normal biological state. Results An automated quantification method was developed to analyze the translocation of membrane proteins and evaluated in comparison to an established manual method. Firstly, regions of interest (membrane fragments) are identified in confocal microscopy images. Further, densitometric intensity profiles are extracted orthogonally to membrane fragments, following the direction from the plasma membrane to cytoplasm. Finally, several different quantitative descriptors were derived from the densitometric profiles and were compared regarding their statistical significance with respect to the transport protein distribution. Stable performance, robustness and reproducibility were tested using several independent experimental datasets. A fully automated workflow for the information extraction and statistical evaluation has been developed and produces robust results. Conclusions New descriptors for the intensity distribution profiles were found to be more discriminative, i.e. more significant, than those used in previous research publications for the translocation quantification. The slow manual calculation can be substituted by the fast and unbiased automated method.
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Affiliation(s)
- Olga Domanova
- Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven, Sankt Augustin, Germany.
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Berndt U, Philipsen L, Bartsch S, Hu Y, Röcken C, Bertram W, Hämmerle M, Rösch T, Sturm A. Comparative Multi-Epitope-Ligand-Cartography reveals essential immunological alterations in Barrett's metaplasia and esophageal adenocarcinoma. Mol Cancer 2010; 9:177. [PMID: 20604962 PMCID: PMC2909181 DOI: 10.1186/1476-4598-9-177] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2010] [Accepted: 07/06/2010] [Indexed: 12/21/2022] Open
Abstract
Background Barrett's esophagus (BE) is caused by gastroesophageal reflux with consecutive mucosal inflammation, predisposing patients to the development of esophageal adenocarcinoma (EAC). We investigated changes in T cell-related mucosal combinatorial molecular protein patterns in both diseases using the novel Multi-Epitope-Ligand-Cartography, a unique robotic whole-cell imaging technology that simultaneously visualizes dozens of proteins in structurally intact tissues and correlates cellular localization of proteins with function. Results Biopsies were taken during endoscopy from BE, EAC, and normal control tissue, and proteomic microscopy was performed on 32 different epitopes. When the significance level was set to p < 0.0005 and the search depth to five antibody combinations, controls and BE can be differentiated by 63, controls and EAC by 3222, and BE from EAC by 1521 distinct protein combinations. For example, the number of activated apoptotic naïve and memory T cells was significantly increased only in BE, whereas the number of activated apoptotic helper and regulatory T cells was significantly elevated in BE and EAC. In contrast, the number of activated apoptotic cytotoxic T cells was significantly elevated only in EAC. Confirming different pathways in BE and EAC, the number of T lymphocytes with p53 expression and downregulation of bcl2 expression (CD3+p53+Bcl2-NfkB-) was significantly increased in EAC compared to BE and controls. Interestingly, the number of precursor T cells (CD7+) was significantly elevated only in EAC. These cells lack Bax and caspase-8, suggesting impaired apoptosis in the early stages of T cell differentiation. Conclusion Proteomic analysis showed for the first time that proteins, which are critically involved in the mucosal immune system of the esophagus, are distinctly expressed in BE and EAC, whereas others are comparably altered in both diseases, suggesting that many pathogenic events might be shared by both diseases. Topological proteomic analysis, therefore, helps us to understand the different pathogenic events in the underlying disease pathways.
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Affiliation(s)
- Uta Berndt
- Department of Medicine, Division of Gastroenterology and Hepatology, Charité-Campus Virchow Clinic, Universitätsmedizin Berlin, Germany.
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Pierre S, Scholich K. Toponomics: studying protein-protein interactions and protein networks in intact tissue. MOLECULAR BIOSYSTEMS 2010; 6:641-7. [PMID: 20237641 DOI: 10.1039/b910653g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The function of a protein is determined on several levels including the genome, transcriptome, proteome, and the recently introduced toponome. The toponome describes the topology of all proteins, protein complexes and protein networks which constitute and influence the microenvironment of a given protein. It has long been known that cellular function or dysfunction of proteins strongly depends on their microenvironment and even small changes in protein arrangements can dramatically alter their activity/function. Thus, deciphering the topology of the multi-dimensional networks which control normal and disease-related pathways will give a better understanding of the mechanisms underlying disease development. While various powerful proteomic tools allow simultaneous quantification of proteins, only a limited number of techniques are available to visualize protein networks in intact cells and tissues. This review discusses a novel approach to map and decipher functional molecular networks of proteins in intact cells or tissues. Multi-epitope-ligand-cartography (MELC) is an imaging technology that identifies and quantifies protein networks at the subcellular level of morphologically-intact specimens. This immunohistochemistry-based method allows serial visualization and biomathematical analysis of up to 100 cellular components using fluorescence-labelled tags. The resulting toponome maps, simultaneously ranging from the subcellular to the supracellular scale, have the potential to provide the basis for a mathematical description of the dynamic topology of protein networks, and will complement current proteomic data to enhance the understanding of physiological and pathophysiological cell functions.
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Affiliation(s)
- Sandra Pierre
- Institut für Klinische Pharmakologie, Klinikum der Johann Wolfgang Goethe-Universität, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
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Jüch M, Smalla KH, Kähne T, Lubec G, Tischmeyer W, Gundelfinger ED, Engelmann M. Congenital lack of nNOS impairs long-term social recognition memory and alters the olfactory bulb proteome. Neurobiol Learn Mem 2009; 92:469-84. [DOI: 10.1016/j.nlm.2009.06.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 05/19/2009] [Accepted: 06/10/2009] [Indexed: 12/21/2022]
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Wang Y, Chiu JF, He QY. Genomics and Proteomics in Drug Design and Discovery. Pharmacology 2009. [DOI: 10.1016/b978-0-12-369521-5.00020-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
One hundred and fifty years after Virchow introduced his fundamental concept of cellular pathology, we now have tools that allow us to unravel the mechanisms of single living cells on a previously unprecedented level of detail. By exploring the molecular cellular phenotype, multiparametric cytometry not only detects specific cellular functions in general but also offers insights into the interaction of single subunits of proteins (e.g., growth factor receptors). Several quantitative and objective techniques allow analysis of single-cell preparations as well as tissue sections to obtain data on different cellular parameters. This opens the way to quantitative and objective histology, which in the future may be possible even without blood or the need to make an incision. To use this huge amount of data for treatment decisions in an individual patient, novel bioinformatic concepts are needed in order to predict the individual course of a disease. The concept of cytomics centers on the cell as the integral unit of all life and explores diseases starting from the cell and going to subcellular units (top-down analysis).
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16
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Berndt U, Philipsen L, Bartsch S, Wiedenmann B, Baumgart DC, Hämmerle M, Sturm A. Systematic high-content proteomic analysis reveals substantial immunologic changes in colorectal cancer. Cancer Res 2008; 68:880-8. [PMID: 18245490 DOI: 10.1158/0008-5472.can-07-2923] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The immune system is a significant determinant of epithelial tumorigenesis, but its role in colorectal cancer pathogenesis is not well understood. The function of the immune system depends upon the integrity of the protein network environment, and thus, we performed MELC immunofluorescence microscopy focusing on the lamina propria. By analyzing structurally intact tissues from colorectal cancer, ulcerative colitis, and healthy colonic mucosa, we used this unique and novel highly multiplexed robotic-imaging technology, which allows visualizing dozens of proteins simultaneously, and explored the toponome in colorectal cancer mucosa for the first time. We identified 1,930 motifs that distinguish control from colorectal cancer tissue. In colorectal cancer, the number of activated T cells is increased, explained by a lack of bax, caspase-3, and caspase-8. Whereas CD4(+)CD25(+) T cells are decreased and are, other than in ulcerative colitis, not activated, cytotoxic T cells are significantly increased in colorectal cancer. Furthermore, the number of activated human lymphocyte antigen (HLA)-DR(+) T-cells is increased in colorectal cancer, pointing to an altered antigen presentation. In colorectal cancer, CD3(+)CD29(+) expression and assembly of the LFA-1 and LFA-3 receptor are differentially changed, indicating a distinct regulation of T-cell adhesion in colorectal cancer. We also identified increased numbers of natural killer and CD44(+) cells in the colorectal cancer mucosa and nuclear factor-kappaB as regulator of apoptosis in these cell populations. High-content proteomic analysis showed that colorectal cancer induces a tremendous modification of protein expression profiles in the lamina propria. Thus, topological proteomic analysis may help to unravel the role of the adaptive immune system in colorectal cancer and aid the development of new antitumor immunotherapy approaches.
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Affiliation(s)
- Uta Berndt
- Department of Medicine, Division of Gastroenterology and Hepatology, Charité-Campus Virchow Klinikum, Universitätsmedizin Berlin, Berlin, Germany
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Tárnok A, Bocsi J, Brockhoff G. Cytomics - importance of multimodal analysis of cell function and proliferation in oncology. Cell Prolif 2007; 39:495-505. [PMID: 17109634 PMCID: PMC6496464 DOI: 10.1111/j.1365-2184.2006.00407.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cancer is a highly complex and heterogeneous disease involving a succession of genetic changes (frequently caused or accompanied by exogenous trauma), and resulting in a molecular phenotype that in turn results in a malignant specification. The development of malignancy has been described as a multistep process involving self-sufficiency in growth signals, insensitivity to antigrowth signals, evasion of apoptosis, limitless replicative potential, sustained angiogenesis, and finally tissue invasion and metastasis. The quantitative analysis of networking molecules within the cells might be applied to understand native-state tissue signalling biology, complex drug actions and dysfunctional signalling in transformed cells, that is, in cancer cells. High-content and high-throughput single-cell analysis can lead to systems biology and cytomics. The application of cytomics in cancer research and diagnostics is very broad, ranging from the better understanding of the tumour cell biology to the identification of residual tumour cells after treatment, to drug discovery. The ultimate goal is to pinpoint in detail these processes on the molecular, cellular and tissue level. A comprehensive knowledge of these will require tissue analysis, which is multiplex and functional; thus, vast amounts of data are being collected from current genomic and proteomic platforms for integration and interpretation as well as for new varieties of updated cytomics technology. This overview will briefly highlight the most important aspects of this continuously developing field.
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Affiliation(s)
- A Tárnok
- Department of Paediatric Cardiology, Cardiac Centre Leipzig GmbH, University of Leipzig, Leipzig, Germany.
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18
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Thiel A, Thiesen HJ. [Research strategies towards a holistic characterization of rheumatoid arthritis--a systems biology approach]. Z Rheumatol 2005; 64:408-15. [PMID: 16184349 DOI: 10.1007/s00393-005-0770-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Accepted: 07/28/2005] [Indexed: 10/25/2022]
Abstract
Genome-wide screening methods used in functional genomics (genome, transcriptome, proteome and metabolom analysis) have increasingly been conducted in integrative research platforms to enable a comprehensive holistic characterization of multifactorial polygenic diseases. First results of this research strategy demonstrate that extended data sets are compiled whose quality is ensured by the application of standard operating procedures (SOPs) and the integration of specific laboratory information management systems (LIMS). Experimental data derived from this technology and methodology platform are obtained by applying standardized sampling procedures followed by comprehensive experimental validation and bioinformatic comparisons with the world knowledge publicly available. This research strategy should finally lead to a holistic understanding of the pathogenesis presented in rheumatoid arthritis by identifying disease-associated regulatory networks (pathways) and assigning them to cell populations involved in the disease mechanisms. In addition, it has to be investigated to what extent genetic as well as epigenetic factors direct disease initiation and progression in potential conjunction with environmental impacts (infections, smoking, etc.).
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Affiliation(s)
- A Thiel
- Deutsches Rheumaforschungszentrum, Berlin, Germany
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