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Sun L, Verhaegen ME, McGue J, Olivei AC, Dlugosz AA, Frankel TL, Harms PW. Development of a Multiplex Immunofluorescence Assay for Tumor Microenvironment Studies of Human and Murine Merkel Cell Carcinoma. J Transl Med 2024:102128. [PMID: 39182611 DOI: 10.1016/j.labinv.2024.102128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024] Open
Abstract
Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine carcinoma. Checkpoint inhibitor immunotherapy plays an essential role in management of advanced MCC; however, predictors of immunotherapy response remain poorly defined. Syngeneic mouse models suitable for testing novel immunotherapy and combination therapy approaches are likely to soon become available and will require assays for evaluating the tumor microenvironment (TME). Multiplex immunofluorescence (mIF) is a powerful approach to characterize the TME for understanding immunotherapy responses and immune surveillance. In this methods article, we provide detailed instructions on assay development for mIF, using as examples two new mIF panels for TME investigations of human and murine MCC tumors. Specifically, we demonstrate panels that allow simultaneous visualization of the Merkel cell master transcription factor SOX2 for tumor cell identification, alongside T-cells markers (CD3, CD8, and FOXP3), macrophage markers (F4/80 for mouse, CD163 for human), together with the checkpoint marker PD-L1 for human tumors, and the myeloid derived suppressor cell marker Arg1 for mouse tumors. We provide detailed protocols for investigators to incorporate these mIF panels into their investigations of human and murine MCC. We also provide fundamental guidance for mIF assay development that will be broadly useful for investigators who are considering modifying the panels presented here, or developing their own mIF panels.
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Affiliation(s)
- Lei Sun
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jake McGue
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alberto C Olivei
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrzej A Dlugosz
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, Ann Arbor, MI 48109, USA
| | - Timothy L Frankel
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul W Harms
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
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2
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Wiedenmann M, Barch M, Chang PS, Giltnane J, Risom T, Zijlstra A. An immunofluorescence-guided segmentation model in H&E images is enabled by tissue artifact correction by CycleGAN. Mod Pathol 2024:100591. [PMID: 39147031 DOI: 10.1016/j.modpat.2024.100591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/01/2024] [Indexed: 08/17/2024]
Abstract
Despite recent advances, the adoption of computer vision methods into clinical and commercial applications has been hampered by the limited availability of accurate ground truth tissue annotations required to train robust supervised models. Generating such ground truth can be accelerated by annotating tissue molecularly using immunofluorescence staining (IF) and mapping these annotations to a post-IF H&E (terminal H&E). Mapping the annotations between the IF and the terminal H&E increases both the scale and accuracy by which ground truth could be generated. However, discrepancies between terminal H&E and conventional H&E caused by IF tissue processing have limited this implementation. We sought to overcome this challenge and achieve compatibility between these parallel modalities using synthetic image generation, in which a cycle-consistent generative adversarial network (CycleGAN) was applied to transfer the appearance of conventional H&E such that it emulates the terminal H&E. These synthetic emulations allowed us to train a deep learning (DL) model for the segmentation of epithelium in the terminal H&E that could be validated against the IF staining of epithelial-based cytokeratins. The combination of this segmentation model with the CycleGAN stain transfer model enabled performative epithelium segmentation in conventional H&E images. The approach demonstrates that the training of accurate segmentation models for the breadth of conventional H&E data can be executed free of human-expert annotations by leveraging molecular annotation strategies such as IF, so long as the tissue impacts of the molecular annotation protocol are captured by generative models that can be deployed prior to the segmentation process.
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Affiliation(s)
- Marcel Wiedenmann
- Department of Computer and Information Science, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany.
| | - Mariya Barch
- Department of Research Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, 94080, CA, USA.
| | - Patrick S Chang
- Department of Research Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, 94080, CA, USA.
| | - Jennifer Giltnane
- Department of Research Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, 94080, CA, USA.
| | - Tyler Risom
- Department of Research Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, 94080, CA, USA.
| | - Andries Zijlstra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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3
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Wang UTT, Tian X, Liou YH, Lee SP, Hu HT, Lu CH, Lin PT, Cheng YJ, Chen P, Chen BC. Protein and lipid expansion microscopy with trypsin and tyramide signal amplification for 3D imaging. Sci Rep 2023; 13:21922. [PMID: 38081848 PMCID: PMC10713663 DOI: 10.1038/s41598-023-48959-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Expansion microscopy, whereby the relative positions of biomolecules are physically increased via hydrogel expansion, can be used to reveal ultrafine structures of cells under a conventional microscope. Despite its utility for achieving super-resolution imaging, expansion microscopy suffers a major drawback, namely reduced fluorescence signals caused by excessive proteolysis and swelling effects. This caveat results in a lower photon budget and disfavors fluorescence imaging over a large field of view that can cover an entire expanded cell, especially in 3D. In addition, the complex procedures and specialized reagents of expansion microscopy hinder its popularization. Here, we modify expansion microscopy by deploying trypsin digestion to reduce protein loss and tyramide signal amplification to enhance fluorescence signal for point-scanning-based imaging. We name our new methodology TT-ExM to indicate dual trypsin and tyramide treatments. TT-ExM may be applied for both antibody and lipid staining. TT-ExM displayed enhanced protein retention for endoplasmic reticulum and mitochondrial markers in COS-7 cell cultures. Importantly, TT-ExM-based lipid staining clearly revealed the complex 3D membrane structures in entire expanded cells. Through combined lipid and DNA staining, our TT-ExM methodology highlighted mitochondria by revealing their DNA and membrane structures in cytoplasm, as well as the lipid-rich structures formed via phase separation in nuclei at interphase. We also observed lipid-rich chromosome matrices in the mitotic cells. These high-quality 3D images demonstrate the practicality of TT-ExM. Thus, readily available reagents can be deployed in TT-ExM to significantly enhance fluorescence signals and generate high-quality and ultrafine-resolution images under confocal microscopy.
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Affiliation(s)
- Ueh-Ting Tim Wang
- Affiliated Senior High School of National Taiwan Normal University, Taipei, 106348, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Xuejiao Tian
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Tsing Hua University, Taipei, 11529, Taiwan
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yae-Huei Liou
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Sue-Ping Lee
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsiao-Tang Hu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Institute and Undergraduate Program of Electro-Optical Engineering, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Po-Ting Lin
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Ya-Jen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
- Neuroscience Program, NPAS, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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4
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Cohen R, Lee-Pullen T, Miller TJ, Meehan K, Fuller K, McCoy MJ. Optimising multiplex immunofluorescence staining for characterising the tumour immune micro-environment. Methods 2023; 219:48-57. [PMID: 37741563 DOI: 10.1016/j.ymeth.2023.09.004] [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] [Received: 06/05/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023] Open
Abstract
Exploring the tumour microenvironment provides insight into the unique interaction between the host and tumour. Ultimately, its study improves understanding of how an individual mounts and achieves an anti-tumour immune response. In the context of colorectal cancer, immune biomarkers within the tumour microenvironment outperform traditional histopathological staging in predicting disease recurrence. Multiplex immunofluorescence enables simultaneous assessment of multiple markers to provide a highly accurate classification of immune cells and their spatial characterisation relative to tumour tissue. Further, automated slide staining provides staining consistency and reduces labour costs. Image acquisition using a non-spectral scanner allows more researchers to utilise multiplexed immunofluorescence for translational research. Herein we describe the optimisation process of conducting automated staining using a five-colour, tyramide signal amplification-based multiplex immunofluorescence panel. Using antibodies against CD3, CD8, CD103 and cytokeratin, the panel characterises T cell populations within human colorectal adenocarcinoma tissue. We provide an overview of primary antibody titration and the development of tyramide signal amplification immunofluorescence monoplex assays. We detail the processes of antibody stripping and the role of exogenous horseradish peroxidase inhibition to facilitate multiplexing. An account of determining the staining sequence and fluorophore assignment is provided. We describe image acquisition using a standard fluorescence microscope slide scanner and the management of spectral crosstalk using this system. Finally, we briefly document the digital image analysis required to characterise cells and determine their spatial distribution within the colorectal tumour microenvironment.
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Affiliation(s)
- Ryan Cohen
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia; Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western, Australia.
| | - Tracey Lee-Pullen
- Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western, Australia; School of Medicine, The University of Western Australia, Perth, Western, Australia.
| | - Timothy J Miller
- Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western, Australia; School of Medicine, The University of Western Australia, Perth, Western, Australia.
| | - Katie Meehan
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia.
| | - Kathy Fuller
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia.
| | - Melanie J McCoy
- Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western, Australia; School of Medicine, The University of Western Australia, Perth, Western, Australia.
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5
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Harms PW, Frankel TL, Moutafi M, Rao A, Rimm DL, Taube JM, Thomas D, Chan MP, Pantanowitz L. Multiplex Immunohistochemistry and Immunofluorescence: A Practical Update for Pathologists. Mod Pathol 2023; 36:100197. [PMID: 37105494 DOI: 10.1016/j.modpat.2023.100197] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/07/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023]
Abstract
Our understanding of the biology and management of human disease has undergone a remarkable evolution in recent decades. Improved understanding of the roles of complex immune populations in the tumor microenvironment has advanced our knowledge of antitumor immunity, and immunotherapy has radically improved outcomes for many advanced cancers. Digital pathology has unlocked new possibilities for the assessment and discovery of the tumor microenvironment, such as quantitative and spatial image analysis. Despite these advances, tissue-based evaluations for diagnosis and prognosis continue to rely on traditional practices, such as hematoxylin and eosin staining, supplemented by the assessment of single biomarkers largely using chromogenic immunohistochemistry (IHC). Such approaches are poorly suited to complex quantitative analyses and the simultaneous evaluation of multiple biomarkers. Thus, multiplex staining techniques have significant potential to improve diagnostic practice and immuno-oncology research. The different approaches to achieve multiplexed IHC and immunofluorescence are described in this study. Alternatives to multiplex immunofluorescence/IHC include epitope-based tissue mass spectrometry and digital spatial profiling (DSP), which require specialized platforms not available to most clinical laboratories. Virtual multiplexing, which involves digitally coregistering singleplex IHC stains performed on serial sections, is another alternative to multiplex staining. Regardless of the approach, analysis of multiplexed stains sequentially or simultaneously will benefit from standardized protocols and digital pathology workflows. Although this is a complex and rapidly advancing field, multiplex staining is now technically feasible for most clinical laboratories and may soon be leveraged for routine diagnostic use. This review provides an update on the current state of the art for tissue multiplexing, including the capabilities and limitations of different techniques, with an emphasis on potential relevance to clinical diagnostic practice.
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Affiliation(s)
- Paul W Harms
- Department of Pathology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Department of Dermatology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Rogel Cancer Center, Michigan Medicine/University of Michigan, Ann Arbor, Michigan.
| | - Timothy L Frankel
- Rogel Cancer Center, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Department of Surgery, Michigan Medicine/University of Michigan, Ann Arbor, Michigan
| | - Myrto Moutafi
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Department of Radiation Oncology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Janis M Taube
- Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center, and Johns Hopkins Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland; Department of Dermatology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center, and Johns Hopkins Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center, and Johns Hopkins Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland
| | - Dafydd Thomas
- Department of Pathology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Rogel Cancer Center, Michigan Medicine/University of Michigan, Ann Arbor, Michigan
| | - May P Chan
- Department of Pathology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Department of Dermatology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan
| | - Liron Pantanowitz
- Department of Pathology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan
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6
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Sheng W, Zhang C, Mohiuddin TM, Al-Rawe M, Zeppernick F, Falcone FH, Meinhold-Heerlein I, Hussain AF. Multiplex Immunofluorescence: A Powerful Tool in Cancer Immunotherapy. Int J Mol Sci 2023; 24:ijms24043086. [PMID: 36834500 PMCID: PMC9959383 DOI: 10.3390/ijms24043086] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Traditional immunohistochemistry (IHC) has already become an essential method of diagnosis and therapy in cancer management. However, this antibody-based technique is limited to detecting a single marker per tissue section. Since immunotherapy has revolutionized the antineoplastic therapy, developing new immunohistochemistry strategies to detect multiple markers simultaneously to better understand tumor environment and predict or assess response to immunotherapy is necessary and urgent. Multiplex immunohistochemistry (mIHC)/multiplex immunofluorescence (mIF), such as multiplex chromogenic IHC and multiplex fluorescent immunohistochemistry (mfIHC), is a new and emerging technology to label multiple biomarkers in a single pathological section. The mfIHC shows a higher performance in cancer immunotherapy. This review summarizes the technologies, which are applied for mfIHC, and discusses how they are employed for immunotherapy research.
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Affiliation(s)
- Wenjie Sheng
- Department of Gynecology and Obstetrics, Medical Faculty, Justus-Liebig-University Giessen, Klinikstr. 33, 35392 Giessen, Germany
| | - Chaoyu Zhang
- Department of Gynecology and Obstetrics, Medical Faculty, Justus-Liebig-University Giessen, Klinikstr. 33, 35392 Giessen, Germany
| | - T. M. Mohiuddin
- Department of Gynecology and Obstetrics, Medical Faculty, Justus-Liebig-University Giessen, Klinikstr. 33, 35392 Giessen, Germany
| | - Marwah Al-Rawe
- Department of Gynecology and Obstetrics, Medical Faculty, Justus-Liebig-University Giessen, Klinikstr. 33, 35392 Giessen, Germany
| | - Felix Zeppernick
- Department of Gynecology and Obstetrics, Medical Faculty, Justus-Liebig-University Giessen, Klinikstr. 33, 35392 Giessen, Germany
| | - Franco H. Falcone
- Institute for Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Ivo Meinhold-Heerlein
- Department of Gynecology and Obstetrics, Medical Faculty, Justus-Liebig-University Giessen, Klinikstr. 33, 35392 Giessen, Germany
| | - Ahmad Fawzi Hussain
- Department of Gynecology and Obstetrics, Medical Faculty, Justus-Liebig-University Giessen, Klinikstr. 33, 35392 Giessen, Germany
- Correspondence:
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7
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Fluorochromized tyramide-glucose oxidase as a multiplex fluorescent tyramide signal amplification system for histochemical analysis. Sci Rep 2022; 12:14807. [PMID: 36097273 PMCID: PMC9468149 DOI: 10.1038/s41598-022-19085-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/24/2022] [Indexed: 11/08/2022] Open
Abstract
Tyramide signal amplification (TSA) is a highly sensitive method for histochemical analysis. Previously, we reported a TSA system, biotinyl tyramine-glucose oxidase (BT-GO), for bright-filed imaging. Here, we develop fluorochromized tyramide-glucose oxidase (FT-GO) as a multiplex fluorescent TSA system. FT-GO involves peroxidase-catalyzed deposition of fluorochromized tyramide (FT) with hydrogen peroxide produced by enzymatic reaction between glucose and glucose oxidase. We showed that FT-GO enhanced immunofluorescence signals while maintaining low background signals. Compared with indirect immunofluorescence detections, FT-GO demonstrated a more widespread distribution of monoaminergic projection systems in mouse and marmoset brains. For multiplex labeling with FT-GO, we quenched antibody-conjugated peroxidase using sodium azide. We applied FT-GO to multiplex fluorescent in situ hybridization, and succeeded in labeling neocortical interneuron subtypes by coupling with immunofluorescence. FT-GO immunofluorescence further increased the detectability of an adeno-associated virus tracer. Given its simplicity and a staining with a high signal-to-noise ratio, FT-GO would provide a versatile platform for histochemical analysis.
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8
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Lengfeld J, Zhang H, Stoesz S, Murali R, Pass F, Greene MI, Goel PN, Grover P. Challenges in Detection of Serum Oncoprotein: Relevance to Breast Cancer Diagnostics. BREAST CANCER-TARGETS AND THERAPY 2021; 13:575-593. [PMID: 34703307 PMCID: PMC8524259 DOI: 10.2147/bctt.s331844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/02/2021] [Indexed: 11/23/2022]
Abstract
Breast cancer is a highly prevalent malignancy that shows improved outcomes with earlier diagnosis. Current screening and monitoring methods have improved survival rates, but the limitations of these approaches have led to the investigation of biomarker evaluation to improve early diagnosis and treatment monitoring. The enzyme-linked immunosorbent assay (ELISA) is a specific and robust technique ideally suited for the quantification of protein biomarkers from blood or its constituents. The continued clinical relevancy of this assay format will require overcoming specific technical challenges, including the ultra-sensitive detection of trace biomarkers and the circumventing of potential assay interference due to the expanding use of monoclonal antibody (mAb) therapeutics. Approaches to increasing the sensitivity of ELISA have been numerous and include employing more sensitive substrates, combining ELISA with the polymerase chain reaction (PCR), and incorporating nanoparticles as shuttles for detection antibodies and enzymes. These modifications have resulted in substantial boosts in the ability to detect extremely low levels of protein biomarkers, with some systems reliably detecting antigen at sub-femtomolar concentrations. Extensive utilization of mAb therapies in oncology has presented an additional contemporary challenge for ELISA, particularly when both therapeutic and assay antibodies target the same protein antigen. Resolution of issues such as epitope overlap and steric hindrance requires a rational approach to the design of diagnostic antibodies that takes advantage of modern antibody generation pipelines, epitope binning techniques and computational methods to strategically target biomarker epitopes. This review discusses technical strategies in ELISA implemented to date and their feasibility to address current constraints on sensitivity and problems with interference in the clinical setting. The impact of these recent advancements will depend upon their transformation from research laboratory protocols into facile, reliable detection systems that can ideally be replicated in point-of-care devices to maximize utilization and transform both the diagnostic and therapeutic monitoring landscape.
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Affiliation(s)
- Justin Lengfeld
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Hongtao Zhang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven Stoesz
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Research Division of Immunology; Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Franklin Pass
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Mark I Greene
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peeyush N Goel
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Payal Grover
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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9
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Manji GA, Van Tine BA, Lee SM, Raufi A, Pellicciotta I, Hirbe AC, Pradhan J, Chen A, Rabadan R, Schwartz GK. Phase 1 study of combination pexidartinib and sirolimus to target tumor associated macrophages in unresectable sarcoma and malignant peripheral nerve sheath tumors. Clin Cancer Res 2021; 27:5519-5527. [PMID: 34321280 DOI: 10.1158/1078-0432.ccr-21-1779] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/24/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE To evaluate the safety and tolerability in phase 1 first-in-human combination therapy with pexidartinib, an inhibitor of colony-stimulating factor-1 receptor, and sirolimus, an mTOR inhibitor, to target tumor associated macrophage (TAM) polarization in soft tissue sarcomas (STSs). EXPERIMENTAL DESIGN This multicenter phase 1 study used the time-to-event continual reassessment method (TITE-CRM) to study the combination of sirolimus, doses ranging from 2-6mg, with pexidartinib, doses ranging from 600-1000mg, both provided continuously on a 28 day cycle, in patients with advanced sarcoma. A total of 24 patients (eight MPNST, three tenosynovial giant cell tumor (TGCT), five leiomyosarcoma and eight with other sarcoma subtypes) were enrolled. The median age was 46 years, 56% were male, and 61% had >2 prior lines of therapy. RESULTS The recommended phase 2 dose (RP2D) was 2mg of sirolimus combined with 1000mg of pexidartinib daily. Of the 18 evaluable subjects, five experienced dose-limiting toxicities (2 elevated AST/ALT, 2 elevated sirolimus trough levels, and 1 grade 5 dehydration). Most common grade 2 or higher treatment related adverse events included anemia, fatigue, neutropenia, and lymphopenia. Clinical benefit was observed in 12 out of 18 (67%) evaluable subjects with 3 partial responses (all in TGCT) and 9 stable disease. Tissue staining indicated a decreased proportion of activated M2 macrophages within tumor samples with treatment. CONCLUSIONS Pexidartinib can be safely administered with sirolimus. These findings support further investigation of this combination to determine clinical efficacy. Clinicaltrials.gov identifier NCT02584647.
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Affiliation(s)
- Gulam A Manji
- Medicine, Division of Hematology and Oncology, Columbia University
| | | | | | | | | | - Angela C Hirbe
- Division of Oncology, Washington University in St. Louis
| | - Jaya Pradhan
- Department of Medicine, Columbia University Irving Medical Center
| | - Andrew Chen
- Vagelos College of Physicians and Surgeons, Columbia University
| | - Raul Rabadan
- Department of Systems Biology, Columbia University Irving Medical Center
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10
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Dopie J, Sweredoski MJ, Moradian A, Belmont AS. Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins. J Cell Biol 2021; 219:151914. [PMID: 32609799 PMCID: PMC7480118 DOI: 10.1083/jcb.201910207] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/03/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
We present a simple ratio method to infer protein composition within cellular structures using proximity labeling approaches but compensating for the diffusion of free radicals. We used tyramide signal amplification (TSA) and label-free mass spectrometry (MS) to compare proteins in nuclear speckles versus centromeres. Our “TSA-MS ratio” approach successfully identified known nuclear speckle proteins. For example, 96% and 67% of proteins in the top 30 and 100 sorted proteins, respectively, are known nuclear speckle proteins, including proteins that we validated here as enriched in nuclear speckles. We show that MFAP1, among the top 20 in our list, forms droplets under certain circumstances and that MFAP1 expression levels modulate the size, stability, and dynamics of nuclear speckles. Localization of MFAP1 and its binding partner, PRPF38A, in droplet-like nuclear bodies precedes formation of nuclear speckles during telophase. Our results update older proteomic studies of nuclear speckles and should provide a useful reference dataset to guide future experimental dissection of nuclear speckle structure and function.
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Affiliation(s)
- Joseph Dopie
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Department of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, CA
| | - Annie Moradian
- Proteome Exploration Laboratory, Department of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, CA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
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11
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Kaneko R, Kawamura M, Kishimura A, Mori T, Katayama Y. Effect of a Chloroacetyl Modification on the Suppression of Dissociation of a Fluorescent Molecule from Cells for Antigen-Specific Cell Staining. ANAL SCI 2021; 37:529-532. [PMID: 33390414 DOI: 10.2116/analsci.20scn03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We previously developed a hydrolase-based fluorescence amplification method for antigen-specific cell labelling, in which fluorescent substrates stained cells by a non-covalent hydrophobic interaction. To improve the substrates retention in cells, we examined the effect of a chloroacetyl group modification on the substrate retention. We found that the chloroacetyl group suppressed the dissociation of the substrate after forming a covalent bond with intracellular proteins. However, the slow reaction speed of the chloroacetyl group allowed dissociation for cells in the early stage of the staining reaction.
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Affiliation(s)
- Ryosuke Kaneko
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University
| | | | - Akihiro Kishimura
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University.,Graduate School of System Life Science, Kyushu University.,Center for Future Chemistry, Kyushu University.,International Research Center for Molecular Systems, Kyushu University
| | - Takeshi Mori
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University.,Graduate School of System Life Science, Kyushu University.,Center for Future Chemistry, Kyushu University
| | - Yoshiki Katayama
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University.,Graduate School of System Life Science, Kyushu University.,Center for Future Chemistry, Kyushu University.,International Research Center for Molecular Systems, Kyushu University.,Center for Advanced Medical Innovation, Kyushu University.,Department of Biomedical Engineering, Chung Yuan Christian University
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12
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Piwosz K, Mukherjee I, Salcher MM, Grujčić V, Šimek K. CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology. Front Microbiol 2021; 12:640066. [PMID: 33746931 PMCID: PMC7970053 DOI: 10.3389/fmicb.2021.640066] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so to microbial eukaryotes. Application of this technique revealed that Paraphysomonas or Spumella-like chrysophytes, considered to be among the most prominent members of protistan communities in pelagic environments, are omnipresent but actually less abundant than expected, in contrast to little known groups such as heterotrophic cryptophyte lineages (e.g., CRY1), cercozoans, katablepharids, or the MAST lineages. Combination of CARD-FISH with tracer techniques and application of double CARD-FISH allow visualization of food vacuole contents of specific flagellate groups, thus considerably challenging our current, simplistic view that they are predominantly bacterivores. Experimental manipulations with natural communities revealed that larger flagellates are actually omnivores ingesting both prokaryotes and other protists. These new findings justify our proposition of an updated model of microbial food webs in pelagic environments, reflecting more authentically the complex trophic interactions and specific roles of flagellated protists, with inclusion of at least two additional trophic levels in the nanoplankton size fraction. Moreover, we provide a detailed CARD-FISH protocol for protists, exemplified on mixo- and heterotrophic nanoplanktonic flagellates, together with tips on probe design, a troubleshooting guide addressing most frequent obstacles, and an exhaustive list of published probes targeting protists.
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Affiliation(s)
- Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
- Centre ALGATECH, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Indranil Mukherjee
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
| | - Michaela M. Salcher
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
| | - Vesna Grujčić
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Karel Šimek
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
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13
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Reverse Phase Protein Arrays. Methods Mol Biol 2021; 2237:103-122. [PMID: 33237412 DOI: 10.1007/978-1-0716-1064-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Reverse phase protein arrays (RPPA) are used to quantify proteins and protein posttranslational modifications in cellular lysates and body fluids. RPPA technology is suitable for biomarker discovery, protein pathway profiling, functional phenotype analysis, and drug discovery mechanism of action. The principles of RPPA technology are (a) immobilizing protein-containing specimens on a coated slide in discrete spots, (b) antibody recognition of proteins, (c) amplification chemistries to detect the protein-antibody complex, and (d) quantifying spot intensity. Construction of a RPPA begins with the robotic liquid transfer of protein-containing specimens from microtiter plates onto nitrocellulose-coated slides. The robotic arrayer deposits each sample as discrete spots in an array format. Specimens, controls, and calibrators are printed on each array, thus providing a complete calibrated assay on a single slide. Each RPPA slide is subsequently probed with catalyzed signal amplification chemistries and a single primary antibody, a secondary antibody, and either fluorescent or colorimetric dyes. The focus of this chapter is to describe RPPA detection and imaging using a colorimetric (diaminobenzidine (DAB)) detection strategy.
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14
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Abstract
FISH has gained an irreplaceable place in microbiology because of its ability to detect and locate a microorganism, or a group of organisms, within complex samples. However, FISH role has evolved drastically in the last few decades and its value has been boosted by several advances in signal intensity, imaging acquisitions, automation, method robustness, and, thus, versatility. This has resulted in a range of FISH variants that gave researchers the ability to access a variety of other valuable information such as complex population composition, metabolic activity, gene detection/quantification, or subcellular location of genetic elements. In this chapter, we will review the more relevant FISH variants, their intended use, and how they address particular challenges of classical FISH.
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Affiliation(s)
- Nuno M Guimarães
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.
| | - Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
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15
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Bhaumik S, Boyer J, Banerjee C, Clark S, Sebastiao N, Vela E, Towne P. Fluorescent multiplexing of 3D spheroids: Analysis of biomarkers using automated immunohistochemistry staining platform and multispectral imaging. J Cell Biochem 2020; 121:4974-4990. [PMID: 32692912 PMCID: PMC7689845 DOI: 10.1002/jcb.29827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/24/2020] [Accepted: 06/23/2020] [Indexed: 11/25/2022]
Abstract
In preclinical cancer studies, three-dimensional (3D) cell spheroids and aggregates are preferred over monolayer cell cultures due to their architectural and functional similarity to solid tumors. We performed a proof-of-concept study to generate physiologically relevant and predictive preclinical models using non-small cell lung adenocarcinoma, and colon and colorectal adenocarcinoma cell line-derived 3D spheroids and aggregates. Distinct panels were designed to determine the expression profiles of frequently studied biomarkers of the two cancer subtypes. The lung adenocarcinoma panel included ALK, EGFR, TTF-1, and CK7 biomarkers, and the colon and colorectal adenocarcinoma panel included BRAF V600E, MSH2, MSH6, and CK20. Recent advances in immunofluorescence (IF) multiplexing and imaging technology enable simultaneous detection and quantification of multiple biomarkers on a single slide. In this study, we performed IF staining of multiple biomarkers per section on formalin-fixed paraffin-embedded 3D spheroids and aggregates. We optimized protocol parameters for automated IF and demonstrated staining concordance with automated chromogenic immunohistochemistry performed with validated protocols. Next, post-acquisition spectral unmixing of the captured fluorescent signals were utilized to delineate four differently stained biomarkers within a single multiplex IF image, followed by automated quantification of the expressed markers. This workflow has the potential to be adapted to preclinical high-throughput screening and drug efficacy studies utilizing 3D spheroids from cancer cell lines and patient-derived organoids. The process allows for cost, time, and resource savings through concurrent staining of several biomarkers on a single slide, the ability to study the interactions of multiple expressed proteins within a single region of interest, and enable quantitative assessment of biomarkers in cancer cells.
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16
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Buescher M, Oberhofer G, Garcia-Perez NC, Bucher G. A Protocol for Double Fluorescent In Situ Hybridization and Immunohistochemistry for the Study of Embryonic Brain Development in Tribolium castaneum. Methods Mol Biol 2020; 2047:219-232. [PMID: 31552657 DOI: 10.1007/978-1-4939-9732-9_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The red flour beetle, Tribolium castaneum, is an emerging model system well suited to the study of embryonic brain development and evolution (see Chapters 11 and 13 ). Brain genesis is driven by specific gene products whose expression underlies a tight spatiotemporal control. Therefore, the analysis of gene expression in time and space provides valuable insights into the molecular mechanisms that govern brain development. Since Tribolium-specific antibodies are scarce, fluorescent RNA in situ hybridization is the method of choice to determine the dynamics of individual gene expression. We have modified common RNA in situ protocols to facilitate the concomitant detection of two gene-specific expression patterns (double fluorescent RNA in situ). In addition, we describe a procedure which combines fluorescent single RNA in situ and immunostaining with gene-specific antibodies. Conventional in situ using RNA probes that are complementary to mature mRNAs often produce diffuse signals. We demonstrate that RNA in situ probes complementary to intronic gene sequences facilitate single cell resolution because the fluorescent signal is restricted to the nucleus. We believe our protocols can be adapted easily to suit the analysis of brain development in other insect species.
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Affiliation(s)
- Marita Buescher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Georg Oberhofer
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Natalia Carolina Garcia-Perez
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany.
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17
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Yaghoobi V, Martinez-Morilla S, Liu Y, Charette L, Rimm DL, Harigopal M. Advances in quantitative immunohistochemistry and their contribution to breast cancer. Expert Rev Mol Diagn 2020; 20:509-522. [PMID: 32178550 DOI: 10.1080/14737159.2020.1743178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Automated image analysis provides an objective, quantitative, and reproducible method of measurement of biomarkers. Image quantification is particularly well suited for the analysis of tissue microarrays which has played a major pivotal role in the rapid assessment of molecular biomarkers. Data acquired from grinding up bulk tissue samples miss spatial information regarding cellular localization; therefore, methods that allow for spatial cell phenotyping at high resolution have proven to be valuable in many biomarker discovery assays. Here, we focus our attention on breast cancer as an example of a tumor type that has benefited from quantitative biomarker studies using tissue microarray format.Areas covered: The history of immunofluorescence and immunohistochemistry and the current status of these techniques, including multiplexing technologies (spectral and non-spectral) and image analysis software will be addressed. Finally, we will turn our attention to studies that have provided proof-of-principle evidence that have been impacted from the use of these techniques.Expert opinion: Assessment of prognostic and predictive biomarkers on tissue sections and TMA using Quantitative immunohistochemistry is an important advancement in the investigation of biologic markers. The challenges in standardization of quantitative technologies for accurate assessment are required for adoption into routine clinical practice.
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Affiliation(s)
- Vesal Yaghoobi
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | - Yuting Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Lori Charette
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Malini Harigopal
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
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18
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Procedural Requirements and Recommendations for Multiplex Immunofluorescence Tyramide Signal Amplification Assays to Support Translational Oncology Studies. Cancers (Basel) 2020; 12:cancers12020255. [PMID: 31972974 PMCID: PMC7072187 DOI: 10.3390/cancers12020255] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 12/22/2022] Open
Abstract
In the development of a multiplex immunofluorescence (IF) platform and the optimization and validation of new multiplex IF panels using a tyramide signal amplification system, several technical requirements are important for high-quality staining, analysis, and results. The aim of this review is to discuss the basic requirements for performing multiplex IF tyramide signal amplification (TSA) in formalin-fixed, paraffin-embedded cancer tissues to support translational oncology research. Our laboratory has stained approximately 4000 formalin-fixed, paraffin-embedded tumor samples using the multiplex IF TSA system for immune profiling of several labeled biomarkers in a single slide to elucidate cancer biology at a protein level and identify therapeutic targets and biomarkers. By analyzing several proteins in thousands of cells on a single slide, this technique provides a systems-level view of various processes in various tumor tissues. Although this technology shows high flexibility in cancer studies, it presents several challenges when applied to study different histology cancers. Our experience shows that adequate antibody validation, staining optimization, analysis strategies, and data generation are important steps for generating quality results. Tissue management, fixation procedures, storage, and cutting can also affect the results of the assay and must be standardized. Overall, this method is reliable for supporting translational research given a precise, step-by-step approach.
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19
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Abstract
Multiplexed imaging platforms to simultaneously detect multiple epitopes in the same tissue section emerged in the last years as very powerful tools to study tumor immune contexture. These revolutionary technologies are providing a deep methodology for tumor evaluation in formalin-fixed and paraffin-embedded (FFPE) to improve the understanding of tumor microenvironment, new targets for treatment, prognostic and predictive biomarkers, and translational studies. Multiplexed imaging platforms allow for the identification of several antigens simultaneously from a single tissue section, core needle biopsies, and tissue microarrays. In recent years, multiplexed imaging has improved the abilities to characterize the different types of cell populations in malignant and non-malignant tissues, and their spatial distribution in relationship to clinical outcomes. Multiplexed technologies associated with digital image analysis software offer a high-quality throughput assay to study cancer specimens at multiple time points before, during and after treatment. The aim of this chapter is to provide a review of multiplexed imaging covering its fundamentals, advantages, disadvantages, and material and methods for staining applied to FFPE tumor tissues and focusing on the use of multiplex immunofluorescence with tyramine signal amplification staining for immune profiling and translational research.
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20
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Vasaturo A, Galon J. Multiplexed immunohistochemistry for immune cell phenotyping, quantification and spatial distribution in situ. Methods Enzymol 2019; 635:51-66. [PMID: 32122553 DOI: 10.1016/bs.mie.2019.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is increasingly recognized that a deep characterization of the immune microenvironment is required for the identification of prognostic and predictive immune biomarkers. Recent advances in the field of tissue imaging resulted in the development of fluorescence multiplex IHC technologies enabling quantitative assessment of immune phenotypes and functional orientation of immune cells in a way similar to flow cytometry, while simultaneously providing tissue context and spatial distribution. Multiplex immunofluorescent technology to FFPE tumor tissue is applied to characterize immune infiltration and PD-L1 expression. A panel consists of five protein markers: CD8, CD68, PD-L1, CK, and SOX10. The assay workflow is fast, optimized and compatible with existing instrumentation. The resulting images can be analyzed with routinely used software for digital pathology enabling the quantification of dynamic range of expression, co-localization and co-expression of markers in the whole tissue. In this chapter, we provide the protocol for the use of the UltiMapper™ I/O PD-L1 multiplex assay, from the bench to the image analysis, as well as an overview of the current multiplex image analysis solutions. Such deep profiling could guide the development of strategies to better select immune checkpoint molecules and a better stratification of patients who will potentially benefit from immunotherapies.
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Affiliation(s)
| | - Jérôme Galon
- INSERM, Laboratory of Integrative Cancer Immunology, Équipe Labellisée Ligue Contre le Cancer, Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Paris, France; Centre de Recherche des Cordeliers, Paris, France
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21
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Protein Chemical Labeling Using Biomimetic Radical Chemistry. Molecules 2019; 24:molecules24213980. [PMID: 31684188 PMCID: PMC6864698 DOI: 10.3390/molecules24213980] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 01/17/2023] Open
Abstract
Chemical labeling of proteins with synthetic low-molecular-weight probes is an important technique in chemical biology. To achieve this, it is necessary to use chemical reactions that proceed rapidly under physiological conditions (i.e., aqueous solvent, pH, low concentration, and low temperature) so that protein denaturation does not occur. The radical reaction satisfies such demands of protein labeling, and protein labeling using the biomimetic radical reaction has recently attracted attention. The biomimetic radical reaction enables selective labeling of the C-terminus, tyrosine, and tryptophan, which is difficult to achieve with conventional electrophilic protein labeling. In addition, as the radical reaction proceeds selectively in close proximity to the catalyst, it can be applied to the analysis of protein–protein interactions. In this review, recent trends in protein labeling using biomimetic radical reactions are discussed.
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22
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Sato S, Tsushima M, Nakamura H. Utilization of Single Electron Transfer Reaction in Protein Chemical Labeling. J SYN ORG CHEM JPN 2019. [DOI: 10.5059/yukigoseikyokaishi.77.463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shinichi Sato
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
| | | | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
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23
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State-of-the-Art of Profiling Immune Contexture in the Era of Multiplexed Staining and Digital Analysis to Study Paraffin Tumor Tissues. Cancers (Basel) 2019; 11:cancers11020247. [PMID: 30791580 PMCID: PMC6406364 DOI: 10.3390/cancers11020247] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 02/07/2023] Open
Abstract
Multiplexed platforms for multiple epitope detection have emerged in the last years as very powerful tools to study tumor tissues. These revolutionary technologies provide important visual techniques for tumor examination in formalin-fixed paraffin-embedded specimens to improve the understanding of the tumor microenvironment, promote new treatment discoveries, aid in cancer prevention, as well as allowing translational studies to be carried out. The aim of this review is to highlight the more recent methodologies that use multiplexed staining to study simultaneous protein identification in formalin-fixed paraffin-embedded tumor tissues for immune profiling, clinical research, and potential translational analysis. New multiplexed methodologies, which permit the identification of several proteins at the same time in one single tissue section, have been developed in recent years with the ability to study different cell populations, cells by cells, and their spatial distribution in different tumor specimens including whole sections, core needle biopsies, and tissue microarrays. Multiplexed technologies associated with image analysis software can be performed with a high-quality throughput assay to study cancer specimens and are important tools for new discoveries. The different multiplexed technologies described in this review have shown their utility in the study of cancer tissues and their advantages for translational research studies and application in cancer prevention and treatments.
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24
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Fu C, Jin S, Shi W, Oh J, Cao H, Jung YM. Catalyzed Deposition of Signal Reporter for Highly Sensitive Surface-Enhanced Raman Spectroscopy Immunoassay Based on Tyramine Signal Amplification Strategy. Anal Chem 2018; 90:13159-13162. [DOI: 10.1021/acs.analchem.8b02419] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Cuicui Fu
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, P. R. China
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon 24341, Korea
| | - Sila Jin
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon 24341, Korea
| | - Wenbing Shi
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, P. R. China
| | - Joohee Oh
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon 24341, Korea
| | - Haiyan Cao
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, P. R. China
| | - Young Mee Jung
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon 24341, Korea
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25
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Petitprez F, Sun CM, Lacroix L, Sautès-Fridman C, de Reyniès A, Fridman WH. Quantitative Analyses of the Tumor Microenvironment Composition and Orientation in the Era of Precision Medicine. Front Oncol 2018; 8:390. [PMID: 30319963 PMCID: PMC6167550 DOI: 10.3389/fonc.2018.00390] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/30/2018] [Indexed: 11/20/2022] Open
Abstract
Tumors are formed by aggregates of cells of various origins including malignant, stromal and immune cells. The number of therapies targeting the microenvironment is increasing as the tumor microenvironment is more and more recognized as playing an essential role in tumor control. In the era of precision medicine, it is essential to precisely estimate the composition, organization and functionality of the individual patient tumor microenvironment and to find ways to therapeutically modulate it. To quantify the cell populations present in the tumor microenvironment, many tools are now available and the most recent approaches will be reviewed herein. We provide an overview of experimental and computational methodologies used to quantify tumor-associated cellular populations, including immunohistochemistry, flow and mass cytometry, bulk and single-cell transcriptomic approaches. We illustrate their respective contribution to characterize the microenvironment. We also discuss how these methods allow to guide therapeutic choices, in relation to the predictive value of some characteristics of the microenvironment.
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Affiliation(s)
- Florent Petitprez
- INSERM, UMR_S 1138, Cordeliers Research Center, Team Cancer, Immune Control and Escape, Paris, France.,University Paris Descartes Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France.,Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Cheng-Ming Sun
- INSERM, UMR_S 1138, Cordeliers Research Center, Team Cancer, Immune Control and Escape, Paris, France.,University Paris Descartes Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - Laetitia Lacroix
- INSERM, UMR_S 1138, Cordeliers Research Center, Team Cancer, Immune Control and Escape, Paris, France.,University Paris Descartes Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - Catherine Sautès-Fridman
- INSERM, UMR_S 1138, Cordeliers Research Center, Team Cancer, Immune Control and Escape, Paris, France.,University Paris Descartes Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Wolf H Fridman
- INSERM, UMR_S 1138, Cordeliers Research Center, Team Cancer, Immune Control and Escape, Paris, France.,University Paris Descartes Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
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26
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Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel B, Ma J, Belmont AS. Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. J Cell Biol 2018; 217:4025-4048. [PMID: 30154186 PMCID: PMC6219710 DOI: 10.1083/jcb.201807108] [Citation(s) in RCA: 227] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 08/05/2018] [Accepted: 08/07/2018] [Indexed: 02/03/2023] Open
Abstract
Chen et al. present TSA-Seq, a new mapping method that measures cytological distances relative to spatially distinct nuclear subcompartments. From novel nuclear organization maps of human cells, they identify transcription hot zones of high gene density that are near nuclear speckles and enriched in highly expressed genes, housekeeping genes, and genes with low transcriptional pausing. While nuclear compartmentalization is an essential feature of three-dimensional genome organization, no genomic method exists for measuring chromosome distances to defined nuclear structures. In this study, we describe TSA-Seq, a new mapping method capable of providing a “cytological ruler” for estimating mean chromosomal distances from nuclear speckles genome-wide and for predicting several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results in K562 cells reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple spatially separated nuclear domains including two types of transcription “hot zones.” Transcription hot zones protruding furthest into the nuclear interior and positioning deterministically very close to nuclear speckles have higher numbers of total genes, the most highly expressed genes, housekeeping genes, genes with low transcriptional pausing, and super-enhancers. Our results demonstrate the capability of TSA-Seq for genome-wide mapping of nuclear structure and suggest a new model for spatial organization of transcription and gene expression.
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Affiliation(s)
- Yu Chen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Yang Zhang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL.,Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA
| | - Yuchuan Wang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA
| | - Liguo Zhang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Eva K Brinkman
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Robert Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL .,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL
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27
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Chadwick ML, Lane A, Thomas D, Smith AR, White AR, Davidson D, Feng Y, Boscolo E, Zheng Y, Adams DM, Gupta A, Veillette A, Chow LML. Combined mTOR and MEK inhibition is an effective therapy in a novel mouse model for angiosarcoma. Oncotarget 2018; 9:24750-24765. [PMID: 29872503 PMCID: PMC5973867 DOI: 10.18632/oncotarget.25345] [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: 03/09/2018] [Accepted: 04/21/2018] [Indexed: 02/03/2023] Open
Abstract
Angiosarcoma is an aggressive malignancy of vascular origin that occurs de novo or in the context of previous cancer therapy. Despite multi-modal aggressive treatment including surgical resection, chemotherapy, and radiation, five-year overall survival remains poor at 35%. Due to its rarity, little is known about its molecular pathology and clinical trials have been extremely difficult to conduct. Development of animal models for rare diseases like angiosarcoma is critical to improve our understanding of tumorigenesis and to test novel treatment regimens. A genetically engineered mouse model for angiosarcoma was generated by conditional deletion of Trp53, Pten, and Ptpn12 in endothelial cells. Tumors arising from these mice recapitulate the histology and molecular pathology of the human disease including hyperactivation of the PI3K/mTOR and MAPK signaling pathways. Treatment of tumor-bearing mice with mTOR or MEK inhibitors effectively inactivated signaling and resulted in reduced proliferation and elevated apoptosis leading to tumor regression. The effect of treatment on tumor growth was transient and proliferation was restored after a period of dormancy. However, combined inhibition of mTOR and MEK resulted in profound tumor regression which was sustained for the duration of treatment. These results suggest that angiosarcoma may be effectively treated by this drug combination.
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Affiliation(s)
- Michelle L Chadwick
- Department of Cancer and Cell Biology, University of Cincinnati, Cincinnati, OH, USA.,Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Adam Lane
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Dana Thomas
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Amanda R Smith
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Angela R White
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Yuxin Feng
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elisa Boscolo
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yi Zheng
- Department of Cancer and Cell Biology, University of Cincinnati, Cincinnati, OH, USA.,Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Denise M Adams
- Vascular Anomalies Center, Boston Children's Hospital, Boston, MA, USA
| | - Anita Gupta
- Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - André Veillette
- Institut de Recherches Cliniques de Montréal, Montréal, Canada
| | - Lionel M L Chow
- Department of Cancer and Cell Biology, University of Cincinnati, Cincinnati, OH, USA.,Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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28
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Yeon S, Bell F, Shultz M, Lawrence G, Harpole M, Espina V. Dual-Color, Multiplex Analysis of Protein Microarrays for Precision Medicine. Methods Mol Biol 2018; 1550:149-170. [PMID: 28188529 DOI: 10.1007/978-1-4939-6747-6_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Generating molecular information in a clinically relevant time frame is the first hurdle to truly integrating precision medicine in health care. Reverse phase protein microarrays are being utilized in clinical trials for quantifying posttranslationally modified signal transduction proteins and cellular signaling pathways, allowing direct comparison of the activation state of proteins from multiple specimens, or individual patient specimens, within the same array. This technology provides diagnostic and therapeutic information critical to precision medicine. To enhance accessibility of this technology, two hurdles must be overcome: data normalization and data acquisition. Herein we describe an unamplified, dual-color signal detection methodology for reverse phase protein microarrays that allows multiplex, within spot data normalization, reduces data acquisition time, simplifies automated spot detection, and provides a stable signal output. This method utilizes Quantum Nanocrystal fluorophore labels (Qdot) substituted for organic fluorophores coupled with an imager (ArrayCAM) that captures images of the microarray rather than sequentially scanning the array. Streamlining and standardizing the data analysis steps with ArrayCAM high-resolution, dual mode chromogenic/fluorescent array imaging overcomes the data acquisition hurdle. The spot location and analysis algorithm provides certain parameter settings that can be tailored to the particular microarray type (fluorescent vs. colorimetric), resulting in greater than 99 % spot location sensitivity. The described method demonstrates equivalent sensitivity for a non-amplified Qdot immunoassay when using automated vs. manual immunostaining procedures.
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Affiliation(s)
- Solomon Yeon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Life Science Lab Building, MS1A9, Manassas, VA, 20110, USA
| | | | | | - Grace Lawrence
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Life Science Lab Building, MS1A9, Manassas, VA, 20110, USA
| | - Michael Harpole
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Life Science Lab Building, MS1A9, Manassas, VA, 20110, USA
| | - Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Life Science Lab Building, MS1A9, Manassas, VA, 20110, USA.
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29
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Baldelli E, Calvert V, Hodge A, VanMeter A, Petricoin EF, Pierobon M. Reverse Phase Protein Microarrays. Methods Mol Biol 2018; 1606:149-169. [PMID: 28502000 DOI: 10.1007/978-1-4939-6990-6_11] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While genes and RNA encode information about cellular status, proteins are considered the engine of the cellular machine, as they are the effective elements that drive all cellular functions including proliferation, migration, differentiation, and apoptosis. Consequently, investigations of the cellular protein network are considered a fundamental tool for understanding cellular functions.Alteration of the cellular homeostasis driven by elaborate intra- and extracellular interactions has become one of the most studied fields in the era of personalized medicine and targeted therapy. Increasing interest has been focused on developing and improving proteomic technologies that are suitable for analysis of clinical samples. In this context, reverse-phase protein microarrays (RPPA) is a sensitive, quantitative, high-throughput immunoassay for protein analyses of tissue samples, cells, and body fluids.RPPA is well suited for broad proteomic profiling and is capable of capturing protein activation as well as biochemical reactions such as phosphorylation, glycosylation, ubiquitination, protein cleavage, and conformational alterations across hundreds of samples using a limited amount of biological material. For these reasons, RPPA represents a valid tool for protein analyses and generates data that help elucidate the functional signaling architecture through protein-protein interaction and protein activation mapping for the identification of critical nodes for individualized or combinatorial targeted therapy.
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Affiliation(s)
- Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Valerie Calvert
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Alex Hodge
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Amy VanMeter
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA.
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30
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Gartrell RD, Marks DK, Hart TD, Li G, Davari DR, Wu A, Blake Z, Lu Y, Askin KN, Monod A, Esancy CL, Stack EC, Jia DT, Armenta PM, Fu Y, Izaki D, Taback B, Rabadan R, Kaufman HL, Drake CG, Horst BA, Saenger YM. Quantitative Analysis of Immune Infiltrates in Primary Melanoma. Cancer Immunol Res 2018; 6:481-493. [PMID: 29467127 DOI: 10.1158/2326-6066.cir-17-0360] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 11/06/2017] [Accepted: 02/15/2018] [Indexed: 01/08/2023]
Abstract
Novel methods to analyze the tumor microenvironment (TME) are urgently needed to stratify melanoma patients for adjuvant immunotherapy. Tumor-infiltrating lymphocyte (TIL) analysis, by conventional pathologic methods, is predictive but is insufficiently precise for clinical application. Quantitative multiplex immunofluorescence (qmIF) allows for evaluation of the TME using multiparameter phenotyping, tissue segmentation, and quantitative spatial analysis (qSA). Given that CD3+CD8+ cytotoxic lymphocytes (CTLs) promote antitumor immunity, whereas CD68+ macrophages impair immunity, we hypothesized that quantification and spatial analysis of macrophages and CTLs would correlate with clinical outcome. We applied qmIF to 104 primary stage II to III melanoma tumors and found that CTLs were closer in proximity to activated (CD68+HLA-DR+) macrophages than nonactivated (CD68+HLA-DR-) macrophages (P < 0.0001). CTLs were further in proximity from proliferating SOX10+ melanoma cells than nonproliferating ones (P < 0.0001). In 64 patients with known cause of death, we found that high CTL and low macrophage density in the stroma (P = 0.0038 and P = 0.0006, respectively) correlated with disease-specific survival (DSS), but the correlation was less significant for CTL and macrophage density in the tumor (P = 0.0147 and P = 0.0426, respectively). DSS correlation was strongest for stromal HLA-DR+ CTLs (P = 0.0005). CTL distance to HLA-DR- macrophages associated with poor DSS (P = 0.0016), whereas distance to Ki67- tumor cells associated inversely with DSS (P = 0.0006). A low CTL/macrophage ratio in the stroma conferred a hazard ratio (HR) of 3.719 for death from melanoma and correlated with shortened overall survival (OS) in the complete 104 patient cohort by Cox analysis (P = 0.009) and merits further development as a biomarker for clinical application. Cancer Immunol Res; 6(4); 481-93. ©2018 AACR.
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Affiliation(s)
- Robyn D Gartrell
- Departments of Pediatrics, Pediatric Hematology/Oncology and Medicine, Hematology/Oncology, Columbia University Medical Center/New York Presbyterian, New York, New York
| | - Douglas K Marks
- Department of Medicine, Division of Hematology/Oncology, Columbia University Medical Center/New York Presbyterian, New York, New York
| | - Thomas D Hart
- Columbia University, Columbia College, New York, New York
| | - Gen Li
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York
| | | | - Alan Wu
- Mailman School of Public Health, Columbia University, New York, New York
| | - Zoë Blake
- Department of Medicine, Division of Hematology/Oncology, Columbia University Medical Center/New York Presbyterian, New York, New York
| | - Yan Lu
- Department of Medicine, Division of Hematology/Oncology, Columbia University Medical Center/New York Presbyterian, New York, New York
| | | | - Anthea Monod
- Department of Systems Biology, Columbia University, New York, New York
| | - Camden L Esancy
- Department of Medicine, Division of Hematology/Oncology, Columbia University Medical Center/New York Presbyterian, New York, New York
| | | | - Dan Tong Jia
- Columbia University, College of Physician and Surgeons, New York, New York
| | - Paul M Armenta
- Columbia University, College of Physician and Surgeons, New York, New York
| | - Yichun Fu
- Columbia University, College of Physician and Surgeons, New York, New York
| | - Daisuke Izaki
- Columbia University, Columbia College, New York, New York
| | - Bret Taback
- Department of Surgery, Columbia University Medical Center/New York Presbyterian, New York, New York
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, New York
| | - Howard L Kaufman
- Department of Surgery, Rutgers Cancer Institute, New York, New York
| | - Charles G Drake
- Department of Medicine, Division of Hematology/Oncology, Columbia University Medical Center/New York Presbyterian, New York, New York
| | - Basil A Horst
- Department of Dermatopathology, Columbia University Medical Center, New York, New York
| | - Yvonne M Saenger
- Department of Medicine, Division of Hematology/Oncology, Columbia University Medical Center/New York Presbyterian, New York, New York.
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Abstract
Researchers in behavioral neuroscience have long sought imaging techniques that can identify and distinguish neural ensembles that are activated by sequentially applied stimuli at single-cell resolution across the whole brain. Taking advantage of the different kinetics of immediate-early genes' mRNA and protein expression, we addressed this problem by developing tyramide-amplified immunohistochemistry-fluorescence in situ hybridization (TAI-FISH), a dual-epoch neural-activity-dependent labeling protocol. Here we describe the step-by-step procedures for TAI-FISH on brain sections from mice that were sequentially stimulated by morphine (appetitive first stimulus) and foot shock (aversive second stimulus). We exemplify our approach by FISH-labeling the neural ensembles that were activated by the second stimulus for the mRNA expression of c-fos, a well-established marker of neural activation. We labeled neuronal ensembles activated by the first stimulus using fluorescence immunohistochemistry (IHC) for the c-fos protein. To further improve the temporal separation of the c-fos mRNA and protein signals, we provide instructions on how to enhance the protein signals using tyramide signal amplification (TSA). Compared with other dual-epoch labeling techniques, TAI-FISH provides better temporal separation of the activated neural ensembles and is better suited to investigation of whole-brain responses. TAI-FISH has been used to investigate neural activation patterns in response to appetitive and aversive stimuli, and we expect it to be more broadly utilized for visualizing brain responses to other types of stimuli, such as sensory stimuli or psychiatric drugs. From first stimulation to image analysis, TAI-FISH takes ∼9 d to complete.
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32
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Chen T, Hong R, Magda D, Bieniarz C, Morrison L, Miller LW. Time Gated Luminescence Imaging of Immunolabeled Human Tissues. Anal Chem 2017; 89:12713-12719. [PMID: 29115129 DOI: 10.1021/acs.analchem.7b02734] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multiplexed immunofluorescence imaging of formalin-fixed, paraffin-embedded tissues is a powerful tool for investigating proteomic profiles and diagnosing disease. However, conventional immunofluorescence with organic dyes is limited in the number of colors that can be simultaneously visualized, is made less sensitive by tissue autofluorescence background, and is usually incompatible with commonly used hematoxylin and eosin staining. Herein, we demonstrate the comparative advantages of using time-gated luminescence microscopy in combination with an emissive Tb(III) complex, Lumi4-Tb, for tissue imaging in terms of sensitivity, multiplexing potential, and compatibility with common immunohistochemistry protocols. We show that time-gated detection of millisecond-scale Tb(III) emission increases signal-to-noise ratio relative to conventional steady-state detection of organic dye fluorescence and permits visualization of low-abundance tissue markers such as Bcl-6 or MSH-6. In addition, temporal separation of long- and short-lifetime (∼nanosecond) signals adds a second dimension for multiplexing and also permits detection of intermolecular Tb(III)-to-dye Förster resonance energy transfer. Furthermore, we demonstrate that the Lumi4-Tb complex is compatible with tyramide signal amplification and, unlike conventional organic dyes, can be reliably used on tissue stained with hematoxylin and eosin. Our results indicate that time-gated luminescence microscopy using Tb(III) labels can provide a sensitive and robust method to perform multiplexed immunofluorescence on archived or clinical tissue specimens.
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Affiliation(s)
- Ting Chen
- Department of Chemistry, University of Illinois at Chicago , 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Rui Hong
- Ventana Medical Systems , 1910 E Innovation Park Drive, Tucson, Arizona 85755, United States
| | - Darren Magda
- Lumiphore, Inc. , 600 Bancroft Way, Suite B, Berkeley, California 94710, United States
| | - Christopher Bieniarz
- Ventana Medical Systems , 1910 E Innovation Park Drive, Tucson, Arizona 85755, United States
| | - Larry Morrison
- Ventana Medical Systems , 1910 E Innovation Park Drive, Tucson, Arizona 85755, United States
| | - Lawrence W Miller
- Department of Chemistry, University of Illinois at Chicago , 845 West Taylor Street, Chicago, Illinois 60607, United States
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33
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Fozooni T, Ravan H, Sasan H. Signal Amplification Technologies for the Detection of Nucleic Acids: from Cell-Free Analysis to Live-Cell Imaging. Appl Biochem Biotechnol 2017; 183:1224-1253. [DOI: 10.1007/s12010-017-2494-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/24/2017] [Indexed: 12/15/2022]
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34
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Li Y, Wu J, Zhang C, Chen Y, Wang Y, Xie M. Manganese dioxide nanoparticle-based colorimetric immunoassay for the detection of alpha-fetoprotein. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2303-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Covalently deposited dyes: a new chromogen paradigm that facilitates analysis of multiple biomarkers in situ. J Transl Med 2017; 97:104-113. [PMID: 27869794 DOI: 10.1038/labinvest.2016.115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/06/2016] [Accepted: 10/03/2016] [Indexed: 01/10/2023] Open
Abstract
Multiplexed analysis of multiple biomarkers in a tissue sample requires use of reporter dyes with specific spectral properties that enable discrimination of signals. Conventional chromogens with broad absorbance spectra, widely used in immunohistochemistry (IHC), offer limited utility for multiplexed detection. Many dyes with narrow absorbance spectra, eg rhodamines, fluoresceins, and cyanines, potentially useful for multiplexed detection are well-characterized; however, generation of a chromogenic reagent useful for IHC analysis has not been demonstrated. Studies reported herein demonstrate utility of tyramine-chemistry for synthesis of a wide variety of new chromogenic dye conjugates useful for multiplexed in situ analysis using conventional light microscopes. The dyes, useful individually or in blends to generate new colors, provide signal sensitivity and dynamic range similar to conventional DAB chromogen, while enabling analysis of co-localized biomarkers. It is anticipated that this new paradigm will enable generation of a wide variety of new chromogens, useful for both research and clinical biomarker analysis that will benefit clinicians and patients.
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36
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Toki MI, Carvajal-Hausdorf DE, Altan M, McLaughlin J, Henick B, Schalper KA, Syrigos KN, Rimm DL. EGFR-GRB2 Protein Colocalization Is a Prognostic Factor Unrelated to Overall EGFR Expression or EGFR Mutation in Lung Adenocarcinoma. J Thorac Oncol 2016; 11:1901-1911. [PMID: 27449805 DOI: 10.1016/j.jtho.2016.06.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/16/2016] [Accepted: 06/27/2016] [Indexed: 10/21/2022]
Abstract
INTRODUCTION EGFR is a therapeutic target in NSCLC for EGFR-mutant patients. Proximity ligation assay (PLA) is a method to detect functional signaling associated protein complexes. Growth factor receptor bound protein 2 (GRB2) is an adaptor protein that binds to the phosphorylated residues of active EGFR. Interaction of EGFR and GRB2 correlates with active EGFR signaling and leads to activation of the MAPK/ERK pathway. METHODS A PLA developed to detect EGFR-GRB2 interaction was measured by quantitative immunofluorescence using Automated Quantitative Analysis technology. EGFR pathway activation was assessed in patients with NSCLC with different mutation status along with overall EGFR expression. Additionally, the PLA to detect EGFR-GRB2 interaction was evaluated as a prognostic marker in two cohorts of patients with lung adenocarcinoma. RESULTS The PLA to detect EGFR-GRB2 interaction was unrelated to overall EGFR expression or mutation in a series of patients with NSCLC with known mutation status. EGFR-mutant (p = 0.04) and EGFR/KRAS wild-type tumors (p = 0.0049) had significantly higher EGFR pathway activation compared with KRAS-mutant cases, with no significant difference shown between mutation sites. In two series of patients with lung adenocarcinoma, the PLA to detect EGFR-GRB2 interaction was independently associated with longer survival (hazard ratio = 0.46, 95% confidence interval: 0.2-0.78, p = 0.0085 and hazard ratio = 0.48, 95% confidence interval: 0.2-0.85, p = 0.017). Total EGFR protein expression alone was not correlated with outcome. CONCLUSIONS EGFR colocalization with GRB2 as assessed by PLA is not correlated with EGFR expression levels or mutation status, defining a patient group that may show EGFR pathway activation, as illustrated by its prognostic value. Future studies may determine whether this group is more likely to respond to EGFR-targeted therapies.
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Affiliation(s)
- Maria I Toki
- Department of Pathology, Yale University Medical School, New Haven, Connecticut
| | | | - Mehmet Altan
- Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut
| | - Joseph McLaughlin
- Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut
| | - Brian Henick
- Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut
| | - Kurt A Schalper
- Department of Pathology, Yale University Medical School, New Haven, Connecticut; Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut
| | - Konstantinos N Syrigos
- Third Department of Medicine, University of Athens, School of Medicine, Sotiria General Hospital, Athens, Greece
| | - David L Rimm
- Department of Pathology, Yale University Medical School, New Haven, Connecticut; Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut.
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37
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Akama K, Shirai K, Suzuki S. Droplet-Free Digital Enzyme-Linked Immunosorbent Assay Based on a Tyramide Signal Amplification System. Anal Chem 2016; 88:7123-9. [DOI: 10.1021/acs.analchem.6b01148] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kenji Akama
- Sysmex Corporation, 4-4-4 Takatsukadai, Nishi-ku, Kobe 651-2271, Japan
| | - Kentaro Shirai
- Sysmex Corporation, 4-4-4 Takatsukadai, Nishi-ku, Kobe 651-2271, Japan
| | - Seigo Suzuki
- Sysmex Corporation, 4-4-4 Takatsukadai, Nishi-ku, Kobe 651-2271, Japan
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38
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Lin TE, Bondarenko A, Lesch A, Pick H, Cortés-Salazar F, Girault HH. Untersuchung der Tyrosinase-Expression in nicht-metastatischen und metastatischen Melanomgeweben durch elektrochemische Rastersondenmikroskopie. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tzu-En Lin
- Laboratoire d'Electrochimie Physique et Analytique; École Polytechnique Fédérale de Lausanne, EPFL Valais Wallis; CH-1951 Sion Schweiz
| | - Alexandra Bondarenko
- Laboratoire d'Electrochimie Physique et Analytique; École Polytechnique Fédérale de Lausanne, EPFL Valais Wallis; CH-1951 Sion Schweiz
| | - Andreas Lesch
- Laboratoire d'Electrochimie Physique et Analytique; École Polytechnique Fédérale de Lausanne, EPFL Valais Wallis; CH-1951 Sion Schweiz
| | - Horst Pick
- Laboratory of Physical Chemistry of Polymers and Membranes; École Polytechnique Fédérale de Lausanne; CH-1015 Lausanne Schweiz
| | - Fernando Cortés-Salazar
- Laboratoire d'Electrochimie Physique et Analytique; École Polytechnique Fédérale de Lausanne, EPFL Valais Wallis; CH-1951 Sion Schweiz
| | - Hubert H. Girault
- Laboratoire d'Electrochimie Physique et Analytique; École Polytechnique Fédérale de Lausanne, EPFL Valais Wallis; CH-1951 Sion Schweiz
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39
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Lin TE, Bondarenko A, Lesch A, Pick H, Cortés-Salazar F, Girault HH. Monitoring Tyrosinase Expression in Non-metastatic and Metastatic Melanoma Tissues by Scanning Electrochemical Microscopy. Angew Chem Int Ed Engl 2016; 55:3813-6. [DOI: 10.1002/anie.201509397] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/02/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Tzu-En Lin
- Laboratoire d'Electrochimie Physique et Analytique; École Polytechnique Fédérale de Lausanne, EPFL Valais Wallis; CH-1951 Sion Switzerland
| | - Alexandra Bondarenko
- Laboratoire d'Electrochimie Physique et Analytique; École Polytechnique Fédérale de Lausanne, EPFL Valais Wallis; CH-1951 Sion Switzerland
| | - Andreas Lesch
- Laboratoire d'Electrochimie Physique et Analytique; École Polytechnique Fédérale de Lausanne, EPFL Valais Wallis; CH-1951 Sion Switzerland
| | - Horst Pick
- Laboratory of Physical Chemistry of Polymers and Membranes; École Polytechnique Fédérale de Lausanne; CH-1015 Lausanne Switzerland
| | - Fernando Cortés-Salazar
- Laboratoire d'Electrochimie Physique et Analytique; École Polytechnique Fédérale de Lausanne, EPFL Valais Wallis; CH-1951 Sion Switzerland
| | - Hubert H. Girault
- Laboratoire d'Electrochimie Physique et Analytique; École Polytechnique Fédérale de Lausanne, EPFL Valais Wallis; CH-1951 Sion Switzerland
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40
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Polaske NW, Kelly BD, Ashworth-Sharpe J, Bieniarz C. Quinone Methide Signal Amplification: Covalent Reporter Labeling of Cancer Epitopes using Alkaline Phosphatase Substrates. Bioconjug Chem 2016; 27:660-6. [DOI: 10.1021/acs.bioconjchem.5b00652] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nathan W. Polaske
- Ventana Medical Systems, Inc., 1910 East Innovation
Park Drive, Tucson, Arizona 85755, United States
| | - Brian D. Kelly
- Ventana Medical Systems, Inc., 1910 East Innovation
Park Drive, Tucson, Arizona 85755, United States
| | - Julia Ashworth-Sharpe
- Ventana Medical Systems, Inc., 1910 East Innovation
Park Drive, Tucson, Arizona 85755, United States
| | - Christopher Bieniarz
- Ventana Medical Systems, Inc., 1910 East Innovation
Park Drive, Tucson, Arizona 85755, United States
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41
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Herzig GPD, Aydin M, Dunigan S, Shah P, Jeong KC, Park SH, Ricke SC, Ahn S. Magnetic Bead-Based Immunoassay Coupled with Tyramide Signal Amplification for Detection of S
almonella
in Foods. J Food Saf 2016. [DOI: 10.1111/jfs.12255] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Gene P. D. Herzig
- Department of Biological Sciences; Arkansas State University; Jonesboro AR
| | - Muhsin Aydin
- Molecular Biosciences Program; Arkansas State University; Jonesboro AR
| | - Samantha Dunigan
- Department of Biological Sciences; Arkansas State University; Jonesboro AR
| | - Parth Shah
- Cell Biology and Neuroscience Department; Rutgers University; New Brunswick NJ
| | - Kwang Cheol Jeong
- Emerging Pathogens Institute and Department of Animal Sciences; Institute of Food and Agricultural Sciences, University of Florida; Gainesville FL
| | - Si Hong Park
- Center for Food Safety, Department of Food Science; University of Arkansas; Fayetteville AR
| | - Steven C. Ricke
- Center for Food Safety, Department of Food Science; University of Arkansas; Fayetteville AR
| | - Soohyoun Ahn
- Food Science and Human Nutrition Department; Institute of Food and Agricultural Sciences, University of Florida; Gainesville FL
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42
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Abstract
Reverse phase protein array (RPPA) technology evolved from the advent of miniaturized immunoassays and gene microarray technology. Reverse phase protein arrays provide either a low throughput or high throughput methodology for quantifying proteins and their post-translationally modified forms in both cellular and non-cellular samples. As the demand for patient tailored therapies increases so does the need for precise and sensitive technology to accurately profile the molecular circuitry driving an individual patient's disease. RPPAs are currently utilized in clinical trials for profiling and comparing the functional state of protein signaling pathways, either temporally within tumors, between patients, or within the same patients before/after treatment. RPPAs are generally employed for quantifying large numbers of samples on one array, under identical experimental conditions. However, the goal of personalized cancer medicine is to design therapies based on the molecular portrait of a patient's tumor, which in turn result in more efficacious treatments with less toxicity. Therefore, RPPAs are also being validated for low throughput assays of individual patient samples. This review explores RPPA technology in the cancer research field, concentrating on its role as a fundamental tool for deciphering protein signaling networks and its emerging role in personalized medicine.
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Kirov IV, Van Laere K, Khrustaleva LI. High resolution physical mapping of single gene fragments on pachytene chromosome 4 and 7 of Rosa. BMC Genet 2015; 16:74. [PMID: 26134672 PMCID: PMC4488978 DOI: 10.1186/s12863-015-0233-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rosaceae is a family containing many economically important fruit and ornamental species. Although fluorescence in situ hybridization (FISH)-based physical mapping of plant genomes is a valuable tool for map-based cloning, comparative genomics and evolutionary studies, no studies using high resolution physical mapping have been performed in this family. Previously we proved that physical mapping of single-copy genes as small as 1.1 kb is possible on mitotic metaphase chromosomes of Rosa wichurana using Tyramide-FISH. In this study we aimed to further improve the physical map of Rosa wichurana by applying high resolution FISH to pachytene chromosomes. RESULTS Using high resolution Tyramide-FISH and multicolor Tyramide-FISH, 7 genes (1.7-3 kb) were successfully mapped on pachytene chromosomes 4 and 7 of Rosa wichurana. Additionally, by using multicolor Tyramide-FISH three closely located genes were simultaneously visualized on chromosome 7. A detailed map of heterochromatine/euchromatine patterns of chromosome 4 and 7 was developed with indication of the physical position of these 7 genes. Comparison of the gene order between Rosa wichurana and Fragaria vesca revealed a poor collinearity for chromosome 7, but a perfect collinearity for chromosome 4. CONCLUSIONS High resolution physical mapping of short probes on pachytene chromosomes of Rosa wichurana was successfully performed for the first time. Application of Tyramide-FISH on pachytene chromosomes allowed the mapping resolution to be increased up to 20 times compared to mitotic metaphase chromosomes. High resolution Tyramide-FISH and multicolor Tyramide-FISH might become useful tools for further physical mapping of single-copy genes and for the integration of physical and genetic maps of Rosa wichurana and other members of the Rosaceae.
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Affiliation(s)
- Ilya V Kirov
- Department of Genetics, Biotechnology, Plant Breeding and Seed Science, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str.49, 127550, Moscow, Russia. .,Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Listvennichnaya Alleya 5, 127550, Moscow, Russia. .,Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090, Melle, Belgium.
| | - Katrijn Van Laere
- Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090, Melle, Belgium.
| | - Ludmila I Khrustaleva
- Department of Genetics, Biotechnology, Plant Breeding and Seed Science, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str.49, 127550, Moscow, Russia. .,Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Listvennichnaya Alleya 5, 127550, Moscow, Russia.
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Herrity AN, Petruska JC, Stirling DP, Rau KK, Hubscher CH. The effect of spinal cord injury on the neurochemical properties of vagal sensory neurons. Am J Physiol Regul Integr Comp Physiol 2015; 308:R1021-33. [PMID: 25855310 DOI: 10.1152/ajpregu.00445.2014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 04/01/2015] [Indexed: 12/29/2022]
Abstract
The vagus nerve is composed primarily of nonmyelinated sensory neurons whose cell bodies are located in the nodose ganglion (NG). The vagus has widespread projections that supply most visceral organs, including the bladder. Because of its nonspinal route, the vagus nerve itself is not directly damaged from spinal cord injury (SCI). Because most viscera, including bladder, are dually innervated by spinal and vagal sensory neurons, an impact of SCI on the sensory component of vagal circuitry may contribute to post-SCI visceral pathologies. To determine whether SCI, in male Wistar rats, might impact neurochemical characteristics of NG neurons, immunohistochemical assessments were performed for P2X3 receptor expression, isolectin B4 (IB4) binding, and substance P expression, three known injury-responsive markers in sensory neuronal subpopulations. In addition to examining the overall population of NG neurons, those innervating the urinary bladder also were assessed separately. All three of the molecular markers were represented in the NG from noninjured animals, with the majority of the neurons binding IB4. In the chronically injured rats, there was a significant increase in the number of NG neurons expressing P2X3 and a significant decrease in the number binding IB4 compared with noninjured animals, a finding that held true also for the bladder-innervating population. Overall, these results indicate that vagal afferents, including those innervating the bladder, display neurochemical plasticity post-SCI that may have implications for visceral homeostatic mechanisms and nociceptive signaling.
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Affiliation(s)
- April N Herrity
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, Kentucky; Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky
| | - Jeffrey C Petruska
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, Kentucky; Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky; Department of Neurological Surgery, University of Louisville, Louisville, Kentucky
| | - David P Stirling
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky; Department of Neurological Surgery, University of Louisville, Louisville, Kentucky; Department of Microbiology & Immunology, University of Louisville School of Medicine, Louisville, Kentucky; and
| | - Kristofer K Rau
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, Kentucky; Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky; Department of Anesthesiology, University of Louisville, Louisville, Kentucky
| | - Charles H Hubscher
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, Kentucky; Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky;
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Abstract
Enzyme-linked signal amplification is a key technique used to enhance the immunohistochemical detection of protein, mRNA, and other molecular species. Tyramide signal amplification (TSA) is based on a catalytic reporter deposit in close vicinity to the epitope of interest. The advantages of this technique are its simplicity, enhanced sensitivity, high specificity, and compatibility with modern multi-label fluorescent microscopy. Here, we describe the use of a TSA kit to increase the signal of enhanced green fluorescent protein (eGFP) expressed under the control of Slc17a6 regulatory elements in the brain of a transgenic mouse. The labeling procedure consists of 6 basic steps: (1) tissue preparation, (2) blocking of nonspecific epitopes, (3) binding with primary antibody, (4) binding with horseradish peroxidase-conjugated secondary antibody, (5) reacting with fluorescent tyramide substrate, and (6) imaging of the signal. The procedures described herein detail these steps and provide additional guidance and background to assist novice users.
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Stack EC, Wang C, Roman KA, Hoyt CC. Multiplexed immunohistochemistry, imaging, and quantitation: a review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis. Methods 2014; 70:46-58. [PMID: 25242720 DOI: 10.1016/j.ymeth.2014.08.016] [Citation(s) in RCA: 507] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 08/12/2014] [Accepted: 08/29/2014] [Indexed: 12/16/2022] Open
Abstract
Tissue sections offer the opportunity to understand a patient's condition, to make better prognostic evaluations and to select optimum treatments, as evidenced by the place pathology holds today in clinical practice. Yet, there is a wealth of information locked up in a tissue section that is only partially accessed, due mainly to the limitations of tools and methods. Often tissues are assessed primarily based on visual analysis of one or two proteins, or 2-3 DNA or RNA molecules. Even while analysis is still based on visual perception, image analysis is starting to address the variability of human perception. This is in contrast to measuring characteristics that are substantially out of reach of human perception, such as parameters revealed through co-expression, spatial relationships, heterogeneity, and low abundance molecules. What is not routinely accessed is the information revealed through simultaneous detection of multiple markers, the spatial relationships among cells and tissue in disease, and the heterogeneity now understood to be critical to developing effective therapeutic strategies. Our purpose here is to review and assess methods for multiplexed, quantitative, image analysis based approaches, using new multicolor immunohistochemistry methods, automated multispectral slide imaging, and advanced trainable pattern recognition software. A key aspect of our approach is presenting imagery in a workflow that engages the pathologist to utilize the strengths of human perception and judgment, while significantly expanding the range of metrics collectable from tissue sections and also provide a level of consistency and precision needed to support the complexities of personalized medicine.
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Chung CY, Cook CE, Lin GW, Huang TY, Chang CC. Reliable protocols for whole-mount fluorescent in situ hybridization (FISH) in the pea aphid Acyrthosiphon pisum: a comprehensive survey and analysis. INSECT SCIENCE 2014; 21:265-277. [PMID: 24850784 DOI: 10.1111/1744-7917.12086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/18/2013] [Indexed: 06/03/2023]
Abstract
RNA in situ hybridization (ISH), including chromogenic ISH (CISH) and fluorescent ISH (FISH), has become a powerful tool for revealing the spatial distribution of gene transcripts in model organisms. Previously, we developed a robust protocol for whole-mount RNA CISH in the pea aphid Acyrthosiphon pisum, an emerging insect genomic model. In order to improve the resolving capacity of gene detection, we comprehensively surveyed current protocols of whole-mount RNA-FISH and developed protocols that allow, using confocal microscopy, clearer visualization of target messenger RNAs (mRNAs) - including those subcellularly localized and those with spatially overlapping expression. We find that Fast dye-based substrate fluorescence (SF), tyramide signal amplification (TSA), and TSA Plus all enable identifying gene expression thanks to multiplex amplification of fluorescent signals. By contrast, methods of direct fluorescence (DF) do not allow visualizing signals. Detection of a single gene target was achieved with SF and TSA Plus for most mRNAs, whereas TSA only allowed visualization of abundant transcripts such as Apvas1 and Appiwi2 in the germ cells. For detection of multiple gene targets using double FISH, we recommend: (i) TSA/TSA, rather than TSA Plus/TSA Plus for colocalized mRNAs abundantly expressed in germ cells, as proteinase K treatment can be omitted; and (ii) SF/TSA Plus for other gene targets such as Apen1 and Apen2 as inactivation of enzyme conjugates is not required. SF/SF is not ideal for double FISH experiments due to signal blurring. Based on these new conditions for RNA-FISH, we have obtained a better understanding of germline specification and embryonic segmentation in the pea aphid. We anticipate that the RNA-FISH protocols for the pea aphid may also be used for other aphids and possibly other insect species, thus expanding the range of species from which useful insights into development and evolution may be obtained.
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Affiliation(s)
- Chen-yo Chung
- Laboratory for Genetics and Development, Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
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Lohse J, Petersen KH, Woller NC, Pedersen HC, Skladtchikova G, Jørgensen RM. Improved Catalyzed Reporter Deposition, iCARD. Bioconjug Chem 2014; 25:1036-42. [DOI: 10.1021/bc400311g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jesper Lohse
- Dako A/S, Produktionsvej 42, 2600 Glostrup, Denmark
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Zhou J, Tang J, Chen G, Tang D. Layer-by-layer multienzyme assembly for highly sensitive electrochemical immunoassay based on tyramine signal amplification strategy. Biosens Bioelectron 2014; 54:323-8. [DOI: 10.1016/j.bios.2013.11.032] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/05/2013] [Accepted: 11/08/2013] [Indexed: 10/26/2022]
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Maaß A, Heiseler T, Maaß F, Fritz J, Hofmeyer T, Glotzbach B, Becker S, Kolmar H. A general strategy for antibody library screening via conversion of transient target binding into permanent reporter deposition. Protein Eng Des Sel 2014; 27:41-7. [PMID: 24402333 DOI: 10.1093/protein/gzt060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report here a generally applicable method for the selective covalent attachment of a reporter molecule to a replicating entity that allows one to obtain specific binders from a single round of library screening. We show that selective biotinylation of phage particles displaying a binder to any given target can be achieved by application of a coupled enzyme reaction on the surface of the target-binding phage particles that includes a peroxidase, an oxidase and a catalase. Due to the covalent linkage of biotin together with the tight and stable interaction of biotin with streptavidin, very stringent wash conditions for removal of nonspecific binders can be applied. The method termed (3)CARD (triple catalytic reporter deposition) was successfully applied to single-round screening of a phage display library of camelid single-domain antibodies against three different target proteins.
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Affiliation(s)
- Alexander Maaß
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
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