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Shafique A, Babaie M, Gonzalez R, Batten A, Sikdar S, Tizhoosh HR. Composite Biomarker Image for Advanced Visualization in Histopathology. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-4. [PMID: 38083181 DOI: 10.1109/embc40787.2023.10340335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Immunohistochemistry (IHC) biomarkers are essential tools for reliable cancer diagnosis and subtyping. It requires cross-staining comparison among Whole Slide Images (WSIs) of IHCs and hematoxylin and eosin (H&E) slides. Currently, pathologists examine the visually co-localized areas across IHC and H&E glass slides for a final diagnosis, which is a tedious and challenging task. Moreover, visually inspecting different IHC slides back and forth to analyze local co-expressions is inherently subjective and prone to error, even when carried out by experienced pathologists. Relying on digital pathology, we propose "Composite Biomarker Image" (CBI) in this work. CBI is a single image that can be composed using different filtered IHC biomarker images for better visualization. We present a CBI image produced in two steps by the proposed solution for better visualization and hence more efficient clinical workflow. In the first step, IHC biomarker images are aligned with the H&E images using one coordinate system and orientation. In the second step, the positive or negative IHC regions from each biomarker image (based on the pathologists' recommendation) are filtered and combined into one image using a fuzzy inference system. For evaluation, the resulting CBI images, from the proposed system, were evaluated qualitatively by the expert pathologists. The CBI concept helps the pathologists to identify the suspected target tissues more easily, which could be further assessed by examining the actual WSIs at the same suspected regions.
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Masuda S, Nakanishi Y. Application of Immunohistochemistry in Clinical Practices as a Standardized Assay for Breast Cancer. Acta Histochem Cytochem 2023; 56:1-8. [PMID: 36890849 PMCID: PMC9986307 DOI: 10.1267/ahc.22-00050] [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: 05/08/2022] [Accepted: 12/09/2022] [Indexed: 02/15/2023] Open
Abstract
Immunohistochemistry (IHC) has become an indispensable tool in the clinical practices for breast cancer; however, to achieve its standardization, numerous issues need to be overcome. In this review, we describe the development of IHC as an important clinical tool, and the challenges in standardizing IHC results for patients. We also present ideas for resolving the remaining issues and unmet needs, along with future directions.
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Affiliation(s)
- Shinobu Masuda
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine, Ohyaguchikami-cho 30-1, Itabashi-ku, Tokyo 173-8610, Japan
| | - Yoko Nakanishi
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine, Ohyaguchikami-cho 30-1, Itabashi-ku, Tokyo 173-8610, Japan
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3
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Cheng Y, Burrack RK, Li Q. Spatially Resolved and Highly Multiplexed Protein and RNA In Situ Detection by Combining CODEX With RNAscope In Situ Hybridization. J Histochem Cytochem 2022; 70:571-581. [PMID: 35848523 PMCID: PMC9393509 DOI: 10.1369/00221554221114174] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Highly multiplexed protein and RNA in situ detection on a single tissue section concurrently is highly desirable for both basic and applied biomedical research. CO-detection by inDEXing (CODEX) is a new and powerful platform to visualize up to 60 protein biomarkers in situ, and RNAscope in situ hybridization (RNAscope) is a novel RNA detection system with high sensitivity and unprecedent specificity at a single-cell level. Nevertheless, to our knowledge, the combination of CODEX and RNAscope remained unreported until this study. Here, we report a simple and reproducible combination of CODEX and RNAscope. We also determined the cross-reactivities of CODEX anti-human antibodies to rhesus macaques, a widely used animal model of human disease.
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Affiliation(s)
- Yilun Cheng
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska
| | - Rachel K. Burrack
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska
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4
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Casagrande N, Borghese C, Aldinucci D. Current and Emerging Approaches to Study Microenvironmental Interactions and Drug Activity in Classical Hodgkin Lymphoma. Cancers (Basel) 2022; 14:cancers14102427. [PMID: 35626032 PMCID: PMC9139207 DOI: 10.3390/cancers14102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary In classical Hodgkin Lymphoma (cHL), the tumor microenvironment (TME) plays an important role in tumor progression and treatment response, making its evaluation critical for determining prognosis, treatment strategies and predicting an increase in drug toxicity. Therefore, there is a need to utilize more complex systems to study the cHL-TME and its interplay with tumor cells. To evaluate new anticancer drugs and to find the mechanisms of drug resistance, this review summarizes emerging approaches for the analysis of the TME composition and to identify the state of the disease; the in vitro techniques used to determine the mechanisms involved in the building of an immunosuppressive and protective TME; new 3-dimensional (3D) models, the heterospheroids (HS), developed to mimic TME interactions. Here, we describe the present and likely future clinical applications indicated by the results of these studies and propose a classification for the in vitro culture methods used to study TME interactions in cHL. Abstract Classic Hodgkin lymphoma is characterized by a few tumor cells surrounded by a protective and immunosuppressive tumor microenvironment (TME) composed by a wide variety of noncancerous cells that are an active part of the disease. Therefore, new techniques to study the cHL-TME and new therapeutic strategies targeting specifically tumor cells, reactivating the antitumor immunity, counteracting the protective effects of the TME, were developed. Here, we describe new methods used to study the cell composition, the phenotype, and the spatial distribution of Hodgkin and Reed–Sternberg (HRS) cells and of noncancerous cells in tumor tissues. Moreover, we propose a classification, with increasing complexity, of the in vitro functional studies used to clarify the interactions leading not only to HRS cell survival, growth and drug resistance, but also to the immunosuppressive tumor education of monocytes, T lymphocytes and fibroblasts. This classification also includes new 3-dimensional (3D) models, obtained by cultivating HRS cells in extracellular matrix scaffolds or in sponge scaffolds, under non-adherent conditions with noncancerous cells to form heterospheroids (HS), implanted in developing chick eggs (ovo model). We report results obtained with these approaches and their applications in clinical setting.
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McGinnis LM, Ibarra-Lopez V, Rost S, Ziai J. Clinical and research applications of multiplexed immunohistochemistry and in situ hybridization. J Pathol 2021; 254:405-417. [PMID: 33723864 DOI: 10.1002/path.5663] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 12/28/2022]
Abstract
Over the past decade, invention and adoption of novel multiplexing technologies for tissues have made increasing impacts in basic and translational research and, to a lesser degree, clinical medicine. Platforms capable of highly multiplexed immunohistochemistry or in situ RNA measurements promise evaluation of protein or RNA targets at levels of plex and sensitivity logs above traditional methods - all with preservation of spatial context. These methods promise objective biomarker quantification, markedly increased sensitivity, and single-cell resolution. Increasingly, development of novel technologies is enabling multi-omic interrogations with spatial correlation of RNA and protein expression profiles in the same sample. Such sophisticated methods will provide unprecedented insights into tissue biology, biomarker science, and, ultimately, patient health. However, this sophistication comes at significant cost, requiring extensive time, practical knowledge, and resources to implement. This review will describe the technical features, advantages, and limitations of currently available multiplexed immunohistochemistry and spatial transcriptomic platforms. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Lisa M McGinnis
- Department of Research Pathology, Genentech, Inc, South San Francisco, CA, USA
| | | | - Sandra Rost
- Department of Research Pathology, Genentech, Inc, South San Francisco, CA, USA
| | - James Ziai
- Department of Research Pathology, Genentech, Inc, South San Francisco, CA, USA
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6
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Sood A, Sui Y, McDonough E, Santamaría-Pang A, Al-Kofahi Y, Pang Z, Jahrling PB, Kuhn JH, Ginty F. Comparison of Multiplexed Immunofluorescence Imaging to Chromogenic Immunohistochemistry of Skin Biomarkers in Response to Monkeypox Virus Infection. Viruses 2020; 12:E787. [PMID: 32717786 PMCID: PMC7472296 DOI: 10.3390/v12080787] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 12/17/2022] Open
Abstract
Over the last 15 years, advances in immunofluorescence-imaging based cycling methods, antibody conjugation methods, and automated image processing have facilitated the development of a high-resolution, multiplexed tissue immunofluorescence (MxIF) method with single cell-level quantitation termed Cell DIVETM. Originally developed for fixed oncology samples, here it was evaluated in highly fixed (up to 30 days), archived monkeypox virus-induced inflammatory skin lesions from a retrospective study in 11 rhesus monkeys to determine whether MxIF was comparable to manual H-scoring of chromogenic stains. Six protein markers related to immune and cellular response (CD68, CD3, Hsp70, Hsp90, ERK1/2, ERK1/2 pT202_pY204) were manually quantified (H-scores) by a pathologist from chromogenic IHC double stains on serial sections and compared to MxIF automated single cell quantification of the same markers that were multiplexed on a single tissue section. Overall, there was directional consistency between the H-score and the MxIF results for all markers except phosphorylated ERK1/2 (ERK1/2 pT202_pY204), which showed a decrease in the lesion compared to the adjacent non-lesioned skin by MxIF vs an increase via H-score. Improvements to automated segmentation using machine learning and adding additional cell markers for cell viability are future options for improvement. This method could be useful in infectious disease research as it conserves tissue, provides marker colocalization data on thousands of cells, allowing further cell level data mining as well as a reduction in user bias.
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Affiliation(s)
- Anup Sood
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| | - Yunxia Sui
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| | - Elizabeth McDonough
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| | - Alberto Santamaría-Pang
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| | - Yousef Al-Kofahi
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| | - Zhengyu Pang
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| | - Peter B. Jahrling
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Frederick, MD 21702, USA;
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Frederick, MD 21702, USA;
| | - Fiona Ginty
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
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Does the Use of the "Proseek ® Multiplex Oncology I Panel" on Peritoneal Fluid Allow a Better Insight in the Pathophysiology of Endometriosis, and in Particular Deep-Infiltrating Endometriosis? J Clin Med 2020; 9:jcm9062009. [PMID: 32604857 PMCID: PMC7355450 DOI: 10.3390/jcm9062009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 02/06/2023] Open
Abstract
Endometriosis appears to share certain cancer-related processes, such as cell attachment, invasion, proliferation and neovascularization, some of which can also be found in other healthy tissues. In order to better understand the altered milieu of the peritoneal cavity, while acknowledging the reported similarities between endometriosis and neoplastic processes, we applied a multiplex oncology panel to search for specific biomarker signatures in the peritoneal fluid of women with endometriosis, women with deep-infiltrating endometriosis (DIE), as well as controls. In total, 84 patients were included in our study, 53 women with endometriosis and 31 controls. Ninety-two proteins were measured in prospectively collected peritoneal fluid (PF) samples, using the "Proseek® Multiplex Oncology I Panel". We first compared patients with endometriosis versus controls, and in a second step, DIE versus endometriosis patients without DIE. Out of the 92 analyzed proteins, few showed significant differences between the groups. In patients with endometriosis, ICOS ligand, Endothelial growth factor, E-selectin, Receptor tyrosine-protein kinase erbB-2, Interleukin-6 receptor alpha, Vascular endothelial growth factor receptor 2, Fms-related tyrosine kinase 3 ligand, C-X-C motif chemokine 10, Epididymal secretory protein E4 and Folate receptor-alpha were decreased, while Interleukin-6 and Interleukin-8 were increased compared to controls. Looking at patients with DIE, we found Chemokine ligand 19, Stem cell factor, Vascular endothelial growth factor D, Interleukin-6 receptor alpha and Melanoma inhibitory activity to be increased compared to endometriosis patients without DIE. We have shown a distinct regulation of the immune response, angiogenesis, cell proliferation, cell adhesion and inhibition of apoptosis in PF of patients with endometriosis compared to controls. The specific protein pattern in the PF of DIE patients provides new evidence that DIE represents a unique entity of extrauterine endometriosis with enhanced angiogenetic and pro-proliferative features.
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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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9
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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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10
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Abstract
The premise of this book is the importance of the tumor microenvironment (TME). Until recently, most research on and clinical attention to cancer biology, diagnosis, and prognosis were focused on the malignant (or premalignant) cellular compartment that could be readily appreciated using standard morphology-based imaging.
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11
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Oon ML, Hoppe MM, Fan S, Phyu T, Phuong HM, Tan SY, Hue SSS, Wang S, Poon LM, Chan HLE, Lee J, Chee YL, Chng WJ, de Mel S, Liu X, Jeyasekharan AD, Ng SB. The contribution of MYC and PLK1 expression to proliferative capacity in diffuse large B-cell lymphoma. Leuk Lymphoma 2019; 60:3214-3224. [PMID: 31259656 DOI: 10.1080/10428194.2019.1633629] [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: 02/16/2019] [Revised: 05/24/2019] [Accepted: 06/11/2019] [Indexed: 10/26/2022]
Abstract
Polo-like kinase-1 (PLK1) regulates the MYC-dependent kinome in aggressive B-cell lymphoma. However, the role of PLK1 and MYC toward proliferation in diffuse large B-cell lymphoma (DLBCL) is unknown. We use multiplexed fluorescent immunohistochemistry (fIHC) to evaluate the co-localization of MYC, PLK1 and Ki67 to study their association with proliferation in DLBCL. The majority (98%, 95% CI 95-100%) of MYC/PLK1-double positive tumor cells expressed Ki67, underscoring the key role of the MYC/PLK1 circuit in proliferation. However, only 38% (95% CI 23-40%) and 51% (95% CI 46-51%) of Ki67-positive cells expressed MYC and PLK1, respectively. Notably, 40% (95% CI 26-43%) of Ki67-positive cells are MYC- and PLK-negative. A stronger correlation exists between PLK1 and Ki67 expression (R = 0.74, p < .001) than with MYC and Ki67 expression (R = 0.52, p < .001). Overall, the results indicate that PLK1 has a higher association than MYC in DLBCL proliferation and there are mechanisms besides MYC and PLK1 influencing DLBCL proliferation.
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Affiliation(s)
- Ming Liang Oon
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
| | - Michal M Hoppe
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shuangyi Fan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - The Phyu
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hoang M Phuong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Soo-Yong Tan
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- A*STAR, Advanced Molecular Pathology Laboratory, Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Susan Swee-Shan Hue
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
- A*STAR, Advanced Molecular Pathology Laboratory, Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Shi Wang
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
| | - Li M Poon
- Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore, Singapore
| | - Hian L E Chan
- Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore, Singapore
| | - Joanne Lee
- Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore, Singapore
| | - Yen L Chee
- Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore, Singapore
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore, Singapore
| | - Sanjay de Mel
- Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore, Singapore
| | - Xin Liu
- Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore, Singapore
| | - Siok-Bian Ng
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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12
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Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Nat Protoc 2019; 14:2900-2930. [PMID: 31534232 DOI: 10.1038/s41596-019-0206-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/03/2019] [Indexed: 12/27/2022]
Abstract
Multiplexed tissue imaging enables precise, spatially resolved enumeration and characterization of cell types and states in human resection specimens. A growing number of methods applicable to formalin-fixed, paraffin-embedded (FFPE) tissue sections have been described, the majority of which rely on antibodies for antigen detection and mapping. This protocol provides step-by-step procedures for confirming the selectivity and specificity of antibodies used in fluorescence-based tissue imaging and for the construction and validation of antibody panels. Although the protocol is implemented using tissue-based cyclic immunofluorescence (t-CyCIF) as an imaging platform, these antibody-testing methods are broadly applicable. We demonstrate assembly of a 16-antibody panel for enumerating and localizing T cells and B cells, macrophages, and cells expressing immune checkpoint regulators. The protocol is accessible to individuals with experience in microscopy and immunofluorescence; some experience in computation is required for data analysis. A typical 30-antibody dataset for 20 FFPE slides can be generated within 2 weeks.
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13
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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: 78] [Impact Index Per Article: 15.6] [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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14
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Gerdes MJ, Gökmen-Polar Y, Sui Y, Pang AS, LaPlante N, Harris AL, Tan PH, Ginty F, Badve SS. Single-cell heterogeneity in ductal carcinoma in situ of breast. Mod Pathol 2018; 31:406-417. [PMID: 29148540 PMCID: PMC6192037 DOI: 10.1038/modpathol.2017.143] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 12/24/2022]
Abstract
Heterogeneous patterns of mutations and RNA expression have been well documented in invasive cancers. However, technological challenges have limited the ability to study heterogeneity of protein expression. This is particularly true for pre-invasive lesions such as ductal carcinoma in situ of the breast. Cell-level heterogeneity in ductal carcinoma in situ was analyzed in a single 5 μm tissue section using a multiplexed immunofluorescence analysis of 11 disease-related markers (EGFR, HER2, HER4, S6, pmTOR, CD44v6, SLC7A5 and CD10, CD4, CD8 and CD20, plus pan-cytokeratin, pan-cadherin, DAPI, and Na+K+ATPase for cell segmentation). Expression was quantified at cell level using a single-cell segmentation algorithm. K-means clustering was used to determine co-expression patterns of epithelial cell markers and immune markers. We document for the first time the presence of epithelial cell heterogeneity within ducts, between ducts and between patients with ductal carcinoma in situ. There was moderate heterogeneity in a distribution of eight clusters within each duct (average Shannon index 0.76; range 0-1.61). Furthermore, within each patient, the average Shannon index across all ducts ranged from 0.33 to 1.02 (s.d. 0.09-0.38). As the distribution of clusters within ducts was uneven, the analysis of eight ducts might be sufficient to represent all the clusters ie within- and between-duct heterogeneity. The pattern of epithelial cell clustering was associated with the presence and type of immune infiltrates, indicating a complex interaction between the epithelial tumor and immune system for each patient. This analysis also provides the first evidence that simultaneous analysis of both the epithelial and immune/stromal components might be necessary to understand the complex milieu in ductal carcinoma in situ lesions.
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Affiliation(s)
- Michael J Gerdes
- GE Global Research, Diagnostics, Imaging and Biotechnology (DIBT), Niskayuna, NY, USA
| | - Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yunxia Sui
- GE Global Research, Diagnostics, Imaging and Biotechnology (DIBT), Niskayuna, NY, USA
| | | | | | - Adrian L Harris
- Department of Oncology, Cancer and Haematology Centre, Oxford University, Oxford, UK
| | - Puay-Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore
| | - Fiona Ginty
- GE Global Research, Diagnostics, Imaging and Biotechnology (DIBT), Niskayuna, NY, USA
| | - Sunil S Badve
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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Gnjatic S, Bronte V, Brunet LR, Butler MO, Disis ML, Galon J, Hakansson LG, Hanks BA, Karanikas V, Khleif SN, Kirkwood JM, Miller LD, Schendel DJ, Tanneau I, Wigginton JM, Butterfield LH. Identifying baseline immune-related biomarkers to predict clinical outcome of immunotherapy. J Immunother Cancer 2017; 5:44. [PMID: 28515944 PMCID: PMC5432988 DOI: 10.1186/s40425-017-0243-4] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 04/26/2017] [Indexed: 12/31/2022] Open
Abstract
As cancer strikes, individuals vary not only in terms of factors that contribute to its occurrence and development, but as importantly, in their capacity to respond to treatment. While exciting new therapeutic options that mobilize the immune system against cancer have led to breakthroughs for a variety of malignancies, success is limited to a subset of patients. Pre-existing immunological features of both the host and the tumor may contribute to how patients will eventually fare with immunotherapy. A broad understanding of baseline immunity, both in the periphery and in the tumor microenvironment, is needed in order to fully realize the potential of cancer immunotherapy. Such interrogation of the tumor, blood, and host immune parameters prior to treatment is expected to identify biomarkers predictive of clinical outcome as well as to elucidate why some patients fail to respond to immunotherapy. To approach these opportunities for progress, the Society for Immunotherapy of Cancer (SITC) reconvened the Immune Biomarkers Task Force. Comprised of an international multidisciplinary panel of experts, Working Group 4 sought to make recommendations that focus on the complexity of the tumor microenvironment, with its diversity of immune genes, proteins, cells, and pathways naturally present at baseline and in circulation, and novel tools to aid in such broad analyses.
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Affiliation(s)
- Sacha Gnjatic
- Department of Hematology/Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, S5-105, 1470 Madison Avenue, Box 1128, New York, NY 10029 USA
| | - Vincenzo Bronte
- Head of Immunology Section, University of Verona, Piazzale Le L. A. Scuro, 10, Verona, Italy
| | - Laura Rosa Brunet
- Immodulon Therapeutics Ltd, Stockley Park, 6-9 The Square, Uxbridge, UK
| | - Marcus O Butler
- Princess Margaret Hospital/Ontario Cancer Institute, RM 9-622, 610 University Ave, Toronto, ON Canada
| | - Mary L Disis
- University of Washington, Tumor Vaccine Group, 850 Mercer Street, Box 358050, Seattle, WA 98109 USA
| | - Jérôme Galon
- INSERM - Cordeliers Research Center, Integrative Cancer Immunology Laboratory, 15 rue de l'Ecole de Médecine, Paris, France
| | - Leif G Hakansson
- CanImGuide Therapeutics AB, Domkyrkovägen 23, Hoellviken, Sweden
| | - Brent A Hanks
- Duke University Medical Center, 308 Research Drive, LSRC, Room C203, Box 3819, Durham, NC 27708 USA
| | - Vaios Karanikas
- Roche Innovation Center Zurich, Wagistrasse 18, Schlieren, Switzerland
| | - Samir N Khleif
- Georgia Cancer Center, Augusta University, 1120 15th Street, CN-2101A, Augusta, GA 30912 USA
| | - John M Kirkwood
- University of Pittsburgh, Hillman Cancer Center-Research Pavilion, 5117 Centre Avenue, Suite 1.32, Pittsburg, PA 15213 USA
| | - Lance D Miller
- Wake Forest School of Medicine, 1 Medical Center Blvd, Winston Salem, NC 27157 USA
| | - Dolores J Schendel
- Medigene Immunotherapies GmbH, Lochhamer Strasse 11, Planegg-Martinsried, Germany
| | | | - Jon M Wigginton
- MacroGenics, Inc., 9704 Medical Center Drive, Rockville, MD 20850 USA
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
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16
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Mansfield JR. Phenotyping Multiple Subsets of Immune Cells In Situ in FFPE Tissue Sections: An Overview of Methodologies. Methods Mol Biol 2017; 1546:75-99. [PMID: 27896758 DOI: 10.1007/978-1-4939-6730-8_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The recent clinical success of new cancer immunotherapy agents and methods is driving the need to understand the role of immune cells in solid tissues, especially tumors. Immune cell phenotyping via flow cytometry, while a cornerstone of immunology, is not spatially resolved and cannot analyze immune cell subsets in situ in clinical biopsy sections or to determine their interrelationships. To address this problem, a number of methodologies have been developed in attempts to phenotype immune and other cells in images acquired from tissue sections and to assess their organization in the tumor and its microenvironment. This chapter review the staining and multiplex image analysis methods that have been developed for phenotyping immune and other cells in formalin-fixed, paraffin-embedded (FFPE) tissue sections.
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17
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Awad MM, Jones RE, Liu H, Lizotte PH, Ivanova EV, Kulkarni M, Herter-Sprie GS, Liao X, Santos AA, Bittinger MA, Keogh L, Koyama S, Almonte C, English JM, Barlow J, Richards WG, Barbie DA, Bass AJ, Rodig SJ, Hodi FS, Wucherpfennig KW, Jänne PA, Sholl LM, Hammerman PS, Wong KK, Bueno R. Cytotoxic T Cells in PD-L1–Positive Malignant Pleural Mesotheliomas Are Counterbalanced by Distinct Immunosuppressive Factors. Cancer Immunol Res 2016; 4:1038-1048. [DOI: 10.1158/2326-6066.cir-16-0171] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/22/2016] [Accepted: 10/19/2016] [Indexed: 11/16/2022]
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18
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Cellular-level characterization of B cells infiltrating pulmonary MALT lymphoma tissues. Virchows Arch 2016; 469:575-580. [DOI: 10.1007/s00428-016-2012-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/24/2016] [Accepted: 08/29/2016] [Indexed: 10/21/2022]
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19
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Distinguishing Classical Hodgkin Lymphoma, Gray Zone Lymphoma, and Large B-cell Lymphoma: A Proposed Scoring System. Appl Immunohistochem Mol Morphol 2016; 24:535-40. [DOI: 10.1097/pai.0000000000000236] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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20
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Multiplexed imaging of intracellular protein networks. Cytometry A 2016; 89:761-75. [DOI: 10.1002/cyto.a.22876] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 12/19/2022]
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21
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Levenson RM, Borowsky AD, Angelo M. Immunohistochemistry and mass spectrometry for highly multiplexed cellular molecular imaging. J Transl Med 2015; 95:397-405. [PMID: 25730370 PMCID: PMC7062454 DOI: 10.1038/labinvest.2015.2] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 01/02/2023] Open
Abstract
The role of immunohistochemistry (IHC) in the management of cancer has expanded to provide improved diagnostic classification, as well as guidance on disease prognosis, therapy, and relapse. These new tasks require evaluation of an increasing number of protein targets; however, conventional multiplexing, usually achieved using serial tissue sections stained for a single analyte per slide, can exhaust small biopsy specimens, complicate slide-to-slide protein expression correlation, and leave insufficient material for additional molecular assays. A new approach, mass spectrometry immunohistochemistry (MSIHC), compatible with high levels of target multiplexing and suitable for use on formalin-fixed, paraffin-embedded samples can circumvent many of these issues. The strategy employs antibodies that are labeled with elemental mass tags, such as isotopically pure lanthanides not typically found in biological specimens, rather than with typical fluorophores or chromogens. The metal-labeled antibodies are then detected in tissue using lasers or ion beams to liberate the tags for subsequent mass spectrometry detection. Within a given multiplexed IHC panel, the metal labels are selected so that their respective masses do not overlap. More than 30 antibodies have been imaged simultaneously, and up to 100 antibodies could potentially be detected at once if the full available mass spectrum is deployed. MSIHC has a number of advantages over conventional IHC techniques. Background due to autofluorescence is absent and the dynamic range is 10(5), exceeding immunofluorescence and chromogenic IHC by 100-fold and 1000-fold, respectively. Detection of labeled primary antibodies improves assay linearity over both chromogenic and fluorescent IHC. Multiplexed mass-tagged antibodies incubated simultaneously with tissue do not appear to cross-interfere, and because the mass tags do not degrade, samples are stable indefinitely. The imaging resolution of multiplexed ion-beam imaging can be better than light microscopy. With appropriate instrumentation, MSIHC has the potential to transform research and clinical pathology practice.
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Affiliation(s)
- Richard M Levenson
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, CA, USA
| | - Alexander D Borowsky
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Palo Alto, CA, USA
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22
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Gerdes MJ, Sood A, Sevinsky C, Pris AD, Zavodszky MI, Ginty F. Emerging understanding of multiscale tumor heterogeneity. Front Oncol 2014; 4:366. [PMID: 25566504 PMCID: PMC4270176 DOI: 10.3389/fonc.2014.00366] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/02/2014] [Indexed: 12/12/2022] Open
Abstract
Cancer is a multifaceted disease characterized by heterogeneous genetic alterations and cellular metabolism, at the organ, tissue, and cellular level. Key features of cancer heterogeneity are summarized by 10 acquired capabilities, which govern malignant transformation and progression of invasive tumors. The relative contribution of these hallmark features to the disease process varies between cancers. At the DNA and cellular level, germ-line and somatic gene mutations are found across all cancer types, causing abnormal protein production, cell behavior, and growth. The tumor microenvironment and its individual components (immune cells, fibroblasts, collagen, and blood vessels) can also facilitate or restrict tumor growth and metastasis. Oncology research is currently in the midst of a tremendous surge of comprehension of these disease mechanisms. This will lead not only to novel drug targets but also to new challenges in drug discovery. Integrated, multi-omic, multiplexed technologies are essential tools in the quest to understand all of the various cellular changes involved in tumorigenesis. This review examines features of cancer heterogeneity and discusses how multiplexed technologies can facilitate a more comprehensive understanding of these features.
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Affiliation(s)
- Michael J. Gerdes
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Anup Sood
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Christopher Sevinsky
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Andrew D. Pris
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Maria I. Zavodszky
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Fiona Ginty
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
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23
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New developments in the pathology of malignant lymphoma. A review of the literature published from June–August 2014. J Hematop 2014. [DOI: 10.1007/s12308-014-0218-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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