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Wang Z, Santa-Maria CA, Popel AS, Sulam J. Bi-level Graph Learning Unveils Prognosis-Relevant Tumor Microenvironment Patterns in Breast Multiplexed Digital Pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590118. [PMID: 38712207 PMCID: PMC11071347 DOI: 10.1101/2024.04.22.590118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The tumor microenvironment is widely recognized for its central role in driving cancer progression and influencing prognostic outcomes. There have been increasing efforts dedicated to characterizing this complex and heterogeneous environment, including developing potential prognostic tools by leveraging modern deep learning methods. However, the identification of generalizable data-driven biomarkers has been limited, in part due to the inability to interpret the complex, black-box predictions made by these models. In this study, we introduce a data-driven yet interpretable approach for identifying patterns of cell organizations in the tumor microenvironment that are associated with patient prognoses. Our methodology relies on the construction of a bi-level graph model: (i) a cellular graph, which models the intricate tumor microenvironment, and (ii) a population graph that captures inter-patient similarities, given their respective cellular graphs, by means of a soft Weisfeiler-Lehman subtree kernel. This systematic integration of information across different scales enables us to identify patient subgroups exhibiting unique prognoses while unveiling tumor microenvironment patterns that characterize them. We demonstrate our approach in a cohort of breast cancer patients and show that the identified tumor microenvironment patterns result in a risk stratification system that provides new complementary information with respect to standard stratification systems. Our results, which are validated in two independent cohorts, allow for new insights into the prognostic implications of the breast tumor microenvironment. This methodology could be applied to other cancer types more generally, providing insights into the cellular patterns of organization associated with different outcomes.
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Rocca G, Galli M, Celant A, Stucchi G, Marongiu L, Cozzi S, Innocenti M, Granucci F. Multiplexed imaging to reveal tissue dendritic cell spatial localisation and function. FEBS Lett 2024. [PMID: 38969618 DOI: 10.1002/1873-3468.14962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/20/2024] [Accepted: 05/28/2024] [Indexed: 07/07/2024]
Abstract
Dendritic cells (DCs) play a pivotal role in immune surveillance, acting as sentinels that coordinate immune responses within tissues. Although differences in the identity and functional states of DC subpopulations have been identified through multiparametric flow cytometry and single-cell RNA sequencing, these methods do not provide information about the spatial context in which the cells are located. This knowledge is crucial for understanding tissue organisation and cellular cross-talk. Recent developments in multiplex imaging techniques can now offer insights into this complex spatial and functional landscape. This review provides a concise overview of these imaging methodologies, emphasising their application in identifying DCs to delineate their tissue-specific functions and aiding newcomers in navigating this field.
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Affiliation(s)
- Giuseppe Rocca
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Marco Galli
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Anna Celant
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Giulia Stucchi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Laura Marongiu
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Stefano Cozzi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Metello Innocenti
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Francesca Granucci
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
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Maskey D, Stevens J, Smith CC, Novelli M, Sutherland GT. Double Chromogen-based Immunohistochemical Staining: An Efficient Approach for Utilizing Long-term Formalin-fixed Tissue in Biobanks. Appl Immunohistochem Mol Morphol 2024; 32:207-214. [PMID: 38712585 DOI: 10.1097/pai.0000000000001199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/28/2024] [Indexed: 05/08/2024]
Abstract
The New South Wales Brain Tissue Resource Centre is a human brain bank that provides top-quality brain tissue for cutting-edge neuroscience research spanning various conditions from alcohol use disorder to neurodegenerative diseases. However, the conventional practice of preserving brain tissue in formalin poses challenges for immunofluorescent staining primarily due to the formalin's tendency, over time, to create cross-links between antigens, which can obscure epitopes of interest. In addition, researchers can encounter issues such as spectral bleeding, limitations in using multiple colors, autofluorescence, and cross-reactivity when working with long-term formalin-fixed brain tissue. The purpose of the study was to test chromogen-based double immunolabeling to negate the issues with immunofluorescent staining. Colocalization of antigens was explored using chromogens 3-amino-9-ethylcarbazole (AEC) and 3,3,-diaminobenzidine in a sequential staining procedure where the AEC signal was eliminated by alcohol treatment. Combinations of 2 or 3 primary antibodies from the same or different species were trialed successfully with this protocol. The colocalization of antigens was also demonstrated with pseudocoloring that mimicked immunofluorescence staining. This staining technique increases the utility of archival formalin-fixed tissue samples.
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Affiliation(s)
- Dhiraj Maskey
- Department of Neuroscience, New South Wales Brain Tissue Research Centre, Charles Perkins Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
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McMahon NP, Solanki A, Wang LG, Montaño AR, Jones JA, Samkoe KS, Tichauer KM, Gibbs SL. In situ single-cell therapeutic response imaging facilitated by the TRIPODD fluorescence imaging platform. Theranostics 2024; 14:2816-2834. [PMID: 38773974 PMCID: PMC11103495 DOI: 10.7150/thno.93256] [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: 12/15/2023] [Accepted: 03/21/2024] [Indexed: 05/24/2024] Open
Abstract
Purpose: Small molecule drugs such as tyrosine kinase inhibitors (TKIs) targeting tumoral molecular dependencies have become standard of care for numerous cancer types. Notably, epidermal growth factor receptor (EGFR) TKIs (e.g., erlotinib, afatinib, osimertinib) are the current first-line treatment for non-small cell lung cancer (NSCLC) due to their improved therapeutic outcomes for EGFR mutated and overexpressing disease over traditional platinum-based chemotherapy. However, many NSCLC tumors develop resistance to EGFR TKI therapy causing disease progression. Currently, the relationship between in situ drug target availability (DTA), local protein expression and therapeutic response cannot be accurately assessed using existing analytical tools despite being crucial to understanding the mechanism of therapeutic efficacy. Procedure: We have previously reported development of our fluorescence imaging platform termed TRIPODD (Therapeutic Response Imaging through Proteomic and Optical Drug Distribution) that is capable of simultaneous quantification of single-cell DTA and protein expression with preserved spatial context within a tumor. TRIPODD combines two complementary fluorescence imaging techniques: intracellular paired agent imaging (iPAI) to measure DTA and cyclic immunofluorescence (cyCIF), which utilizes oligonucleotide conjugated antibodies (Ab-oligos) for spatial proteomic expression profiling on tissue samples. Herein, TRIPODD was modified and optimized to provide a downstream analysis of therapeutic response through single-cell DTA and proteomic response imaging. Results: We successfully performed sequential imaging of iPAI and cyCIF resulting in high dimensional imaging and biomarker assessment to quantify single-cell DTA and local protein expression on erlotinib treated NSCLC models. Pharmacodynamic and pharmacokinetic studies of the erlotinib iPAI probes revealed that administration of 2.5 mg/kg each of the targeted and untargeted probe 4 h prior to tumor collection enabled calculation of DTA values with high Pearson correlation to EGFR, the erlotinib molecular target, expression in the tumors. Analysis of single-cell biomarker expression revealed that a single erlotinib dose was insufficient to enact a measurable decrease in the EGFR signaling cascade protein expression, where only the DTA metric detected the presence of bound erlotinib. Conclusion: We demonstrated the capability of TRIPODD to evaluate therapeutic response imaging to erlotinib treatment as it relates to signaling inhibition, DTA, proliferation, and apoptosis with preserved spatial context.
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Affiliation(s)
- Nathan P. McMahon
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Allison Solanki
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Lei G. Wang
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Antonio R. Montaño
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Jocelyn A. Jones
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Kimberley S. Samkoe
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
- Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Kenneth M. Tichauer
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Summer L. Gibbs
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
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Yan H, Ju X, Huang A, Yuan J. Advancements in technology for characterizing the tumor immune microenvironment. Int J Biol Sci 2024; 20:2151-2167. [PMID: 38617534 PMCID: PMC11008272 DOI: 10.7150/ijbs.92525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/12/2024] [Indexed: 04/16/2024] Open
Abstract
Immunotherapy plays a key role in cancer treatment, however, responses are limited to a small number of patients. The biological basis for the success of immunotherapy is the complex interaction between tumor cells and tumor immune microenvironment (TIME). Historically, research on tumor immune constitution was limited to the analysis of one or two markers, more novel technologies are needed to interpret the complex interactions between tumor cells and TIME. In recent years, major advances have already been made in depicting TIME at a considerably elevated degree of throughput, dimensionality and resolution, allowing dozens of markers to be labeled simultaneously, and analyzing the heterogeneity of tumour-immune infiltrates in detail at the single cell level, depicting the spatial landscape of the entire microenvironment, as well as applying artificial intelligence (AI) to interpret a large amount of complex data from TIME. In this review, we summarized emerging technologies that have made contributions to the field of TIME, and provided prospects for future research.
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Affiliation(s)
- Honglin Yan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | | | | | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
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Kasikova L, Rakova J, Hensler M, Lanickova T, Tomankova J, Pasulka J, Drozenova J, Mojzisova K, Fialova A, Vosahlikova S, Laco J, Ryska A, Dundr P, Kocian R, Brtnicky T, Skapa P, Capkova L, Kovar M, Prochazka J, Praznovec I, Koblizek V, Taskova A, Tanaka H, Lischke R, Mendez FC, Vachtenheim J, Heinzelmann-Schwarz V, Jacob F, McNeish IA, Halaska MJ, Rob L, Cibula D, Orsulic S, Galluzzi L, Spisek R, Fucikova J. Tertiary lymphoid structures and B cells determine clinically relevant T cell phenotypes in ovarian cancer. Nat Commun 2024; 15:2528. [PMID: 38514660 PMCID: PMC10957872 DOI: 10.1038/s41467-024-46873-w] [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: 09/29/2022] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
Intratumoral tertiary lymphoid structures (TLSs) have been associated with improved outcome in various cohorts of patients with cancer, reflecting their contribution to the development of tumor-targeting immunity. Here, we demonstrate that high-grade serous ovarian carcinoma (HGSOC) contains distinct immune aggregates with varying degrees of organization and maturation. Specifically, mature TLSs (mTLS) as forming only in 16% of HGSOCs with relatively elevated tumor mutational burden (TMB) are associated with an increased intratumoral density of CD8+ effector T (TEFF) cells and TIM3+PD1+, hence poorly immune checkpoint inhibitor (ICI)-sensitive, CD8+ T cells. Conversely, CD8+ T cells from immunologically hot tumors like non-small cell lung carcinoma (NSCLC) are enriched in ICI-responsive TCF1+ PD1+ T cells. Spatial B-cell profiling identifies patterns of in situ maturation and differentiation associated with mTLSs. Moreover, B-cell depletion promotes signs of a dysfunctional CD8+ T cell compartment among tumor-infiltrating lymphocytes from freshly isolated HGSOC and NSCLC biopsies. Taken together, our data demonstrate that - at odds with NSCLC - HGSOC is associated with a low density of follicular helper T cells and thus develops a limited number of mTLS that might be insufficient to preserve a ICI-sensitive TCF1+PD1+ CD8+ T cell phenotype. These findings point to key quantitative and qualitative differences between mTLSs in ICI-responsive vs ICI-irresponsive neoplasms that may guide the development of alternative immunotherapies for patients with HGSOC.
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Affiliation(s)
| | | | | | - Tereza Lanickova
- Sotio Biotech a.s., Prague, Czech Republic
- Department of Immunology, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | | | | | - Jana Drozenova
- Department of Pathology, 3rd Faculty of Medicine and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | | | | | | | - Jan Laco
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine and University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ales Ryska
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine and University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Pavel Dundr
- Department of Pathology, 1st Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Roman Kocian
- Department of Gynaecology, Obstetrics and Neonatology, General University Hospital in Prague, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Tomas Brtnicky
- Department of Gynecology and Obstetrics, 1st Faculty of Medicine, Charles University, University Hospital Bulovka, Prague, Czech Republic
| | - Petr Skapa
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Linda Capkova
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Marek Kovar
- Laboratory of Tumor Immunology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Prochazka
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Ivan Praznovec
- Department of Gynecology and Obstetrics, Charles University, Faculty of Medicine and University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Vladimir Koblizek
- Department of Pneumology, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Alice Taskova
- Department of Thoracic Surgery, Charles University, 3rd Faculty of Medicine and Thomayer University Hospital, Prague, Czech Republic
| | - Hisashi Tanaka
- Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Robert Lischke
- 3rd Department of Surgery, First Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Fernando Casas Mendez
- Oncology and Pneumology Department, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jiri Vachtenheim
- 3rd Department of Surgery, First Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Viola Heinzelmann-Schwarz
- Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Francis Jacob
- Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Iain A McNeish
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Michal J Halaska
- Department of Gynecology and Obstetrics, Charles University, 3rd Faculty of Medicine and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Lukas Rob
- Department of Gynecology and Obstetrics, Charles University, 3rd Faculty of Medicine and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - David Cibula
- Department of Gynaecology, Obstetrics and Neonatology, General University Hospital in Prague, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Sandra Orsulic
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA
| | - Radek Spisek
- Sotio Biotech a.s., Prague, Czech Republic
- Department of Immunology, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Jitka Fucikova
- Sotio Biotech a.s., Prague, Czech Republic.
- Department of Immunology, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic.
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Yamada Y, Yamamoto T, Tsutsumi C, Matsumoto T, Noguchi S, Shimada Y, Nakata K, Ohuchida K, Nakamura M, Oda Y. Immature stroma and high infiltration of CD15 + cells are predictive markers of poor prognosis in different subsets of patients with pancreatic cancer. Cancer Sci 2024; 115:1001-1013. [PMID: 38230840 PMCID: PMC10920995 DOI: 10.1111/cas.16060] [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: 09/06/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 01/18/2024] Open
Abstract
Preoperative treatment is commonly carried out for borderline resectable pancreatic ductal adenocarcinoma (PDAC). However, the relationship between the combination of immune cells in the tumor microenvironment and their intratumoral heterogeneity along with their association with histological findings remains unclear, especially in patients receiving preoperative chemotherapy. We aimed to explore the therapeutic strategies for patients with PDAC with poor prognosis after receiving chemotherapy based on histological and immunological microenvironmental classifications. We investigated the correlation between the prognosis and histological immune microenvironmental factors of patients who initially underwent surgery (n = 100) and were receiving gemcitabine plus nab-paclitaxel (GEM + nabPTX) as preoperative chemotherapy (n = 103). Immune profiles were generated based on immune cell infiltration into the tumor, and their correlation with patient outcomes and histological features was analyzed. Tumor-infiltrating neutrophils (TINs) were identified as independent poor prognostic factors using multivariate analysis in both surgery-first and preoperative chemotherapy groups. The patients were further classified into four groups based on immune cell infiltration into the tumor. Patients with high CD15 infiltration into the tumor and immature stroma at the cancer margins showed the worst prognosis in the preoperative chemotherapy group. The analysis of mRNA expression and immunohistochemical features revealed that CXCR2, the receptor for CXCL8, was correlated with disease-free and overall survival. We inferred that patients with immature stroma at the margins and high infiltration of CD15+ neutrophils within the tumor showed the worst prognosis and they could particularly benefit from treatment with inhibitors targeting CXCR2 or CXCL8.
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Affiliation(s)
- Yutaka Yamada
- Department of Anatomic Pathology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
- Department of Surgery and Oncology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Takeo Yamamoto
- Department of Anatomic Pathology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
- Department of Surgery and Oncology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Chikanori Tsutsumi
- Department of Surgery and Oncology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Takashi Matsumoto
- Department of Anatomic Pathology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
- Department of Surgery and Oncology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Shoko Noguchi
- Department of Anatomic Pathology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
- Department of Surgery and Oncology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yuki Shimada
- Department of Anatomic Pathology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
- Department of Surgery and Oncology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Kohei Nakata
- Department of Surgery and Oncology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Kenoki Ohuchida
- Department of Surgery and Oncology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Masafumi Nakamura
- Department of Surgery and Oncology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
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Brogård MB, Nielsen PS, Christensen KB, Georgsen JB, Wandler A, Lade-Keller J, Steiniche T. Immunohistochemical double nuclear staining for cell-specific automated quantification of the proliferation index - A promising diagnostic aid for melanocytic lesions. Pathol Res Pract 2024; 255:155177. [PMID: 38330618 DOI: 10.1016/j.prp.2024.155177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/10/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024]
Abstract
AIMS Pathologists often use immunohistochemical staining of the proliferation marker Ki67 in their diagnostic assessment of melanocytic lesions. However, the interpretation of Ki67 can be challenging. We propose a new workflow to improve the diagnostic utility of the Ki67-index. In this workflow, Ki67 is combined with the melanocytic tumour-cell marker SOX10 in a Ki67/SOX10 double nuclear stain. The Ki67-index is then quantified automatically using digital image analysis (DIA). The aim of this study was to optimise and test three different multiplexing methods for Ki67/SOX10 double nuclear staining. METHODS Multiplex immunofluorescence (mIF), multiplex immunohistochemistry (mIHC), and multiplexed immunohistochemical consecutive staining on single slide (MICSSS) were optimised for Ki67/SOX10 double nuclear staining. DIA applications were designed for automated quantification of the Ki67-index. The methods were tested on a pilot case-control cohort of benign and malignant melanocytic lesions (n = 23). RESULTS Using the Ki67/SOX10 double nuclear stain, malignant melanocytic lesions could be completely distinguished from benign lesions by the Ki67-index. The Ki67-index cut-offs were 1.8% (mIF) and 1.5% (mIHC and MICSSS). The AUC of the automatically quantified Ki67-index based on double nuclear staining was 1.0 (95% CI: 1.0;1.0), whereas the AUC of conventional Ki67 single-stains was 0.87 (95% CI: 0.71;1.00). CONCLUSIONS The novel Ki67/SOX10 double nuclear stain highly improved the diagnostic precision of Ki67 interpretation. Both mIHC and mIF were useful methods for Ki67/SOX10 double nuclear staining, whereas the MICSSS method had challenges in the current setting. The Ki67/SOX10 double nuclear stain shows potential as a valuable diagnostic aid for melanocytic lesions.
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Affiliation(s)
- Mette Bak Brogård
- Department of Pathology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 35, 8200 Aarhus N, Denmark; Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark.
| | - Patricia Switten Nielsen
- Department of Pathology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 35, 8200 Aarhus N, Denmark; Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Kristina Bang Christensen
- Department of Pathology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 35, 8200 Aarhus N, Denmark
| | - Jeanette Bæhr Georgsen
- Department of Pathology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 35, 8200 Aarhus N, Denmark; Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Anne Wandler
- Department of Pathology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 35, 8200 Aarhus N, Denmark
| | - Johanne Lade-Keller
- Department of Pathology, Aalborg University Hospital, Ladegårdsgade 3, 9000 Aalborg, Denmark
| | - Torben Steiniche
- Department of Pathology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 35, 8200 Aarhus N, Denmark; Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
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9
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Schulte SJ, Fornace ME, Hall JK, Shin GJ, Pierce NA. HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples. Development 2024; 151:dev202307. [PMID: 38415752 PMCID: PMC10941662 DOI: 10.1242/dev.202307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/21/2023] [Indexed: 02/29/2024]
Abstract
Signal amplification based on the mechanism of hybridization chain reaction (HCR) provides a unified framework for multiplex, quantitative, high-resolution imaging of RNA and protein targets in highly autofluorescent samples. With conventional bandpass imaging, multiplexing is typically limited to four or five targets owing to the difficulty in separating signals generated by fluorophores with overlapping spectra. Spectral imaging has offered the conceptual promise of higher levels of multiplexing, but it has been challenging to realize this potential in highly autofluorescent samples, including whole-mount vertebrate embryos. Here, we demonstrate robust HCR spectral imaging with linear unmixing, enabling simultaneous imaging of ten RNA and/or protein targets in whole-mount zebrafish embryos and mouse brain sections. Further, we demonstrate that the amplified and unmixed signal in each of the ten channels is quantitative, enabling accurate and precise relative quantitation of RNA and/or protein targets with subcellular resolution, and RNA absolute quantitation with single-molecule resolution, in the anatomical context of highly autofluorescent samples.
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Affiliation(s)
- Samuel J. Schulte
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mark E. Fornace
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John K. Hall
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grace J. Shin
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Niles A. Pierce
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
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Parra ER, Ilié M, Wistuba II, Hofman P. Quantitative multiplexed imaging technologies for single-cell analysis to assess predictive markers for immunotherapy in thoracic immuno-oncology: promises and challenges. Br J Cancer 2023; 129:1417-1431. [PMID: 37391504 PMCID: PMC10628288 DOI: 10.1038/s41416-023-02318-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/05/2023] [Accepted: 06/12/2023] [Indexed: 07/02/2023] Open
Abstract
The past decade has witnessed a revolution in cancer treatment by the shift from conventional drugs (chemotherapies) towards targeted molecular therapies and immune-based therapies, in particular the immune-checkpoint inhibitors (ICIs). These immunotherapies selectively release the host immune system against the tumour and have shown unprecedented durable remission for patients with cancers that were thought incurable such as advanced non-small cell lung cancer (aNSCLC). The prediction of therapy response is based since the first anti-PD-1/PD-L1 molecules FDA and EMA approvals on the level of PD-L1 tumour cells expression evaluated by immunohistochemistry, and recently more or less on tumour mutation burden in the USA. However, not all aNSCLC patients benefit from immunotherapy equally, since only around 30% of them received ICIs and among them 30% have an initial response to these treatments. Conversely, a few aNSCLC patients could have an efficacy ICIs response despite low PD-L1 tumour cells expression. In this context, there is an urgent need to look for additional robust predictive markers for ICIs efficacy in thoracic oncology. Understanding of the mechanisms that enable cancer cells to adapt to and eventually overcome therapy and identifying such mechanisms can help circumvent resistance and improve treatment. However, more than a unique universal marker, the evaluation of several molecules in the tumour at the same time, particularly by using multiplex immunostaining is a promising open room to optimise the selection of patients who benefit from ICIs. Therefore, urgent further efforts are needed to optimise to individualise immunotherapy based on both patient-specific and tumour-specific characteristics. This review aims to rethink the role of multiplex immunostaining in immuno-thoracic oncology, with the current advantages and limitations in the near-daily practice use.
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Affiliation(s)
- Edwin Roger Parra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Biobank Côte d'Azur BB-0033-00025, FHU OncoAge, IHU RespirERA, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Biobank Côte d'Azur BB-0033-00025, FHU OncoAge, IHU RespirERA, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.
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11
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Brockman AA, Khurana R, Bartkowiak T, Thomas PL, Sivagnanam S, Betts CB, Coussens LM, Lovly CM, Irish JM, Ihrie RA. Alignment, segmentation and neighborhood analysis in cyclic immunohistochemistry data using CASSATT. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2023; 104:344-355. [PMID: 36748312 PMCID: PMC10404643 DOI: 10.1002/cyto.b.22114] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/22/2022] [Accepted: 01/12/2023] [Indexed: 02/08/2023]
Abstract
Cyclic immunohistochemistry (cycIHC) uses sequential rounds of colorimetric immunostaining and imaging for quantitative mapping of location and number of cells of interest. Additionally, cycIHC benefits from the speed and simplicity of brightfield microscopy, making the collection of entire tissue sections and slides possible at a trivial cost compared to other high dimensional imaging modalities. However, large cycIHC datasets currently require an expert data scientist to concatenate separate open-source tools for each step of image pre-processing, registration, and segmentation, or the use of proprietary software. Here, we present a unified and user-friendly pipeline for processing, aligning, and analyzing cycIHC data - Cyclic Analysis of Single-Cell Subsets and Tissue Territories (CASSATT). CASSATT registers scanned slide images across all rounds of staining, segments individual nuclei, and measures marker expression on each detected cell. Beyond straightforward single cell data analysis outputs, CASSATT explores the spatial relationships between cell populations. By calculating the log odds of interaction frequencies between cell populations within tissues and tissue regions, this pipeline helps users identify populations of cells that interact-or do not interact-at frequencies that are greater than those occurring by chance. It also identifies specific neighborhoods of cells based on the assortment of neighboring cell types that surround each cell in the sample. The presence and location of these neighborhoods can be compared across slides or within distinct regions within a tissue. CASSATT is a fully open source workflow tool developed to process cycIHC data and will allow greater utilization of this powerful staining technique.
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Affiliation(s)
- Asa A. Brockman
- Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Rohit Khurana
- Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Todd Bartkowiak
- Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
- Departments of Pathology, Microbiology, & Immunology
| | - Portia L. Thomas
- Department of Microbiology, Immunology & Physiology, School of Medicine, Meharry Medical College, Nashville, Tennessee
- Department of School of Graduate Studies & Research, Meharry Medical College, Nashville, Tennessee
| | - Shamilene Sivagnanam
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
- Department of Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Courtney B Betts
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
- Department of Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Lisa M. Coussens
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
- Department of Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Christine M. Lovly
- Department of School of Graduate Studies & Research, Meharry Medical College, Nashville, Tennessee
- Departments of Division of Hematology-Oncology, Department of Medicine
| | - Jonathan M. Irish
- Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
- Departments of Pathology, Microbiology, & Immunology
- Departments of Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Rebecca A. Ihrie
- Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
- Department of School of Graduate Studies & Research, Meharry Medical College, Nashville, Tennessee
- Neurological Surgery
- Departments of Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232
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12
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Schulte SJ, Fornace ME, Hall JK, Pierce NA. HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555626. [PMID: 37693627 PMCID: PMC10491186 DOI: 10.1101/2023.08.30.555626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Signal amplification based on the mechanism of hybridization chain reaction (HCR) provides a unified framework for multiplex, quantitative, high-resolution imaging of RNA and protein targets in highly autofluorescent samples. With conventional bandpass imaging, multiplexing is typically limited to four or five targets due to the difficulty in separating signals generated by fluorophores with overlapping spectra. Spectral imaging has offered the conceptual promise of higher levels of multiplexing, but it has been challenging to realize this potential in highly autofluorescent samples including whole-mount vertebrate embryos. Here, we demonstrate robust HCR spectral imaging with linear unmixing, enabling simultaneous imaging of 10 RNA and/or protein targets in whole-mount zebrafish embryos and mouse brain sections. Further, we demonstrate that the amplified and unmixed signal in each of 10 channels is quantitative, enabling accurate and precise relative quantitation of RNA and/or protein targets with subcellular resolution, and RNA absolute quantitation with single-molecule resolution, in the anatomical context of highly autofluorescent samples. SUMMARY Spectral imaging with signal amplification based on the mechanism of hybridization chain reaction enables robust 10-plex, quantitative, high-resolution imaging of RNA and protein targets in whole-mount vertebrate embryos and brain sections.
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Cardoso dos Santos LM, Avila Y, Schvartz D, Rougemont AL, Bochaton-Piallat ML, Ruchonnet-Metrailler I. Laser microdissection, proteomics, and multiplex immunohistochemistry: a bumpy ride into the study of paraffin-embedded fetal and pediatric lung tissues. Front Med (Lausanne) 2023; 10:1191205. [PMID: 37706027 PMCID: PMC10495683 DOI: 10.3389/fmed.2023.1191205] [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: 03/22/2023] [Accepted: 07/28/2023] [Indexed: 09/15/2023] Open
Abstract
Background Knowledge about lung development or lung disease is mainly derived from data extrapolated from mouse models. This has obvious drawbacks in developmental diseases, particularly due to species differences. Our objective is to describe the development of complementary analysis methods that will allow a better understanding of the molecular mechanisms involved in the pathogenesis of rare congenital diseases. Methods Paraffin-embedded human pediatric and fetal lung samples were laser microdissected to enrich different lung regions, namely, bronchioli or alveoli. These samples were analyzed by data-independent acquisition-based quantitative proteomics, and the lung structures were subsequently compared. To confirm the proteomic data, we employed an optimized Sequential ImmunoPeroxidase Labeling and Erasing (SIMPLE) staining for specific proteins of interest. Results By quantitative proteomics, we identified typical pulmonary proteins from being differentially expressed in different regions. While the receptor for advanced glycation end products (RAGE) and the surfactant protein C (SFTPC) were downregulated, tubulin beta 4B (TUBB4B) was upregulated in bronchioli, compared to alveoli. In fetal tissues, CD31 was downregulated in fetal bronchioli compared to canaliculi. Moreover, we confirmed their presence using SIMPLE staining. Some expected proteins did not show up in the proteomic data, such as SOX-9, which was only detected by means of immunohistochemistry in the SIMPLE analysis. Conclusion Our data underline the robustness and applicability of this type of experimental approach, especially for rare paraffin-embedded tissue samples. It also strengthens the importance of these methods for future studies, particularly when considering developmental lung diseases, such as congenital lung anomalies.
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Affiliation(s)
- Luis M. Cardoso dos Santos
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Pediatric Pulmonary Unit, Department of Pediatrics, Gynecology, and Obstetrics, University Hospital of Geneva, Geneva, Switzerland
| | - Yannick Avila
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Pediatric Pulmonary Unit, Department of Pediatrics, Gynecology, and Obstetrics, University Hospital of Geneva, Geneva, Switzerland
| | - Domitille Schvartz
- Proteomics Core Facility, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Bioinformatic Support Platform, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | | | - Isabelle Ruchonnet-Metrailler
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Pediatric Pulmonary Unit, Department of Pediatrics, Gynecology, and Obstetrics, University Hospital of Geneva, Geneva, Switzerland
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14
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Bolognesi MM, Antoranz A, Bosisio FM, Cattoretti G. Quantitative multiplex immunohistochemistry with colorimetric staining (QUIVER) may still benefit from MILAN. Acta Neuropathol Commun 2023; 11:91. [PMID: 37287032 DOI: 10.1186/s40478-023-01585-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/09/2023] Open
Affiliation(s)
- Maddalena M Bolognesi
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Via Cadore 48, Monza, MI, Italy
| | - Asier Antoranz
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- The Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Francesca Maria Bosisio
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Giorgio Cattoretti
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Via Cadore 48, Monza, MI, Italy.
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15
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Elhanani O, Ben-Uri R, Keren L. Spatial profiling technologies illuminate the tumor microenvironment. Cancer Cell 2023; 41:404-420. [PMID: 36800999 DOI: 10.1016/j.ccell.2023.01.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/01/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023]
Abstract
The tumor microenvironment (TME) is composed of many different cellular and acellular components that together drive tumor growth, invasion, metastasis, and response to therapies. Increasing realization of the significance of the TME in cancer biology has shifted cancer research from a cancer-centric model to one that considers the TME as a whole. Recent technological advancements in spatial profiling methodologies provide a systematic view and illuminate the physical localization of the components of the TME. In this review, we provide an overview of major spatial profiling technologies. We present the types of information that can be extracted from these data and describe their applications, findings and challenges in cancer research. Finally, we provide a future perspective of how spatial profiling could be integrated into cancer research to improve patient diagnosis, prognosis, stratification to treatment and development of novel therapeutics.
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Affiliation(s)
- Ofer Elhanani
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Raz Ben-Uri
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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16
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Galactosidase-catalyzed fluorescence amplification method (GAFAM): sensitive fluorescent immunohistochemistry using novel fluorogenic β-galactosidase substrates and its application in multiplex immunostaining. Histochem Cell Biol 2023; 159:233-246. [PMID: 36374321 DOI: 10.1007/s00418-022-02162-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2022] [Indexed: 11/16/2022]
Abstract
Multiplex immunohistochemistry/multiplex immunofluorescence (mIHC/mIF) enables the simultaneous detection of multiple markers in a single tissue section by visualizing the markers in different colors. Currently, tyramide signal amplification (TSA) is the most commonly used method because it is heat resistant to multiplexing. SPiDER-βGal (6'-(diethylamino)-4'-(fluoromethyl)spiro[isobenzofuran-1(3H),9'-[9H]xanthen]-3'-yl β-D-galactopyranoside), a novel fluorogenic substrate of β-galactosidase (β-gal) was reported recently. Its properties are favorable for application in sensitive mIF based on quinone methide chemistry. Combining SPiDER-βGal with its related substrates, a novel, sensitive fluorescent IHC method for formalin-fixed paraffin-embedded (FFPE) sections was developed, named the galactosidase-catalyzed fluorescence amplification method (GAFAM). Evaluation of GAFAM indicated the following characteristics: (1) the entire GAFAM procedure was complete within a few hours; (2) the optimal working concentration of the substrates was 20 μM; (3) the fluorescent product was heat resistant; (4) the GAFAM exhibited sensitivity comparable with that of TSA, which was higher than that of conventional IF; and (5) the GAFAM was applicable to mIF and multispectral imaging. GAFAM is expected to be applicable to IF (or mIF in combination with TSA), and is a promising tool for facilitating morphological research in various fields of life science.
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17
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Behanova A, Avenel C, Andersson A, Chelebian E, Klemm A, Wik L, Östman A, Wählby C. Visualization and quality control tools for large-scale multiplex tissue analysis in TissUUmaps3. BIOLOGICAL IMAGING 2023; 3:e6. [PMID: 38487686 PMCID: PMC10936381 DOI: 10.1017/s2633903x23000053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/18/2023] [Accepted: 02/13/2023] [Indexed: 03/17/2024]
Abstract
Large-scale multiplex tissue analysis aims to understand processes such as development and tumor formation by studying the occurrence and interaction of cells in local environments in, for example, tissue samples from patient cohorts. A typical procedure in the analysis is to delineate individual cells, classify them into cell types, and analyze their spatial relationships. All steps come with a number of challenges, and to address them and identify the bottlenecks of the analysis, it is necessary to include quality control tools in the analysis workflow. This makes it possible to optimize the steps and adjust settings in order to get better and more precise results. Additionally, the development of automated approaches for tissue analysis requires visual verification to reduce skepticism with regard to the accuracy of the results. Quality control tools could be used to build users' trust in automated approaches. In this paper, we present three plugins for visualization and quality control in large-scale multiplex tissue analysis of microscopy images. The first plugin focuses on the quality of cell staining, the second one was made for interactive evaluation and comparison of different cell classification results, and the third one serves for reviewing interactions of different cell types.
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Affiliation(s)
- Andrea Behanova
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
| | - Christophe Avenel
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
| | - Axel Andersson
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
| | - Eduard Chelebian
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
| | - Anna Klemm
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
| | - Lina Wik
- Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Arne Östman
- Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Carolina Wählby
- Department of Information Technology and SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, Sweden
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18
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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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McMahon NP, Jones JA, Anderson AN, Dietz MS, Wong MH, Gibbs SL. Flexible Cyclic Immunofluorescence (cyCIF) Using Oligonucleotide Barcoded Antibodies. Cancers (Basel) 2023; 15:827. [PMID: 36765785 PMCID: PMC9913741 DOI: 10.3390/cancers15030827] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Advances in our understanding of the complex, multifaceted interactions between tumor epithelia, immune infiltrate, and tumor microenvironmental cells have been driven by highly multiplexed imaging technologies. These techniques are capable of labeling many more biomarkers than conventional immunostaining methods. However, multiplexed imaging techniques suffer from low detection sensitivity, cell loss-particularly in fragile samples-, and challenges with antibody labeling. Herein, we developed and optimized an oligonucleotide antibody barcoding strategy for cyclic immunofluorescence (cyCIF) that can be amplified to increase the detection efficiency of low-abundance antigens. Stained fluorescence signals can be readily removed using ultraviolet light treatment, preserving tissue and fragile cell sample integrity. We also extended the oligonucleotide barcoding strategy to secondary antibodies to enable the inclusion of difficult-to-label primary antibodies in a cyCIF panel. Using both the amplification oligonucleotides to label DNA barcoded antibodies and in situ hybridization of multiple fluorescently labeled oligonucleotides resulted in signal amplification and increased signal-to-background ratios. This procedure was optimized through the examination of staining parameters including staining oligonucleotide concentration, staining temperature, and oligonucleotide sequence design, resulting in a robust amplification technique. As a proof-of-concept, we demonstrate the flexibility of our cyCIF strategy by simultaneously imaging with the original oligonucleotide conjugated antibody (Ab-oligo) cyCIF strategy, the novel Ab-oligo cyCIF amplification strategy, as well as direct and indirect immunofluorescence to generate highly multiplexed images.
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Affiliation(s)
- Nathan P. McMahon
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Jocelyn A. Jones
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Ashley N. Anderson
- Department of Cell, Development & Cancer Biology Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Matthew S. Dietz
- Department of Cell, Development & Cancer Biology Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Melissa H. Wong
- Department of Cell, Development & Cancer Biology Department, Oregon Health & Science University, Portland, OR 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Summer L. Gibbs
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
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20
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Involvement of angiogenesis in cancer-associated acinar-to-ductal metaplasia lesion of pancreatic cancer invasive front. J Cancer Res Clin Oncol 2023:10.1007/s00432-022-04554-5. [PMID: 36592214 DOI: 10.1007/s00432-022-04554-5] [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: 11/16/2022] [Accepted: 12/21/2022] [Indexed: 01/03/2023]
Abstract
PURPOSE This study aimed to demonstrate the involvement of angiogenesis in cancer-associated acinar-to-ductal metaplasia (CA-ADM) lesion of invasive front pancreatic ductal adenocarcinoma (PDAC) and investigate the possible mechanism. METHODS Tissue samples from 128 patients with PDAC and 36 LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx-1-Cre mice were analyzed. Immunohistochemical assay was performed using HE, anti-CK19 and anti-amylase to confirm the presence of CA-ADM lesions, using anti-CD34 and anti-CD31 to measure microvessel density (MVD), and using anti-CD68, anti-CD163, anti-iNOS, or anti-MMP9 to evaluate the immune microenvironment. We performed multiplex immunohistochemical assay to detect the co-expression of MMP9 and CD68 on macrophage. We examined clinical outcomes and other clinicopathological factors to determine the significance of high-level MVD of CA-ADM on survival and liver metastasis. We performed tube formation assay to evaluate the effect of macrophage on angiogenic capacity in vitro. RESULTS Angiogenesis was significantly abundant in CA-ADM lesions compared with that in PDAC lesions in human and mouse tissues. High-level MVD in CA-ADM lesions was an independent predictor of poor prognosis (P = 0.0047) and the recurrence of liver metastasis (P = 0.0027). More CD68-positive and CD163-positive macrophages were detected in CA-ADM lesions than in PDAC. The percentage of CD68-positive macrophages was positively correlated with MVD in CA-ADM lesions. Multiplex-immunostaining revealed that MMP9 was expressed in CD68-positive macrophages of CA-ADM lesions. In CA-ADM lesions, the percentage of macrophages was positively correlated with MMP9 expression, which positively correlated with microvessel density. CONCLUSION CA-ADM related angiogenesis is a promising predictive marker for poor prognosis of PDAC and may provide an attractive therapeutic target for PDAC.
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21
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Li Z, Muench G, Goebel S, Uhland K, Wenhart C, Reimann A. Flow chamber staining modality for real-time inspection of dynamic phenotypes in multiple histological stains. PLoS One 2023; 18:e0284444. [PMID: 37141296 PMCID: PMC10159194 DOI: 10.1371/journal.pone.0284444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/30/2023] [Indexed: 05/05/2023] Open
Abstract
Traditional histological stains, such as hematoxylin-eosin (HE), special stains, and immunofluorescence (IF), have defined myriads of cellular phenotypes and tissue structures in a separate stained section. However, the precise connection of information conveyed by the various stains in the same section, which may be important for diagnosis, is absent. Here, we present a new staining modality-Flow chamber stain, which complies with the current staining workflow but possesses newly additional features non-seen in conventional stains, allowing for (1) quickly switching staining modes between destain and restain for multiplex staining in one single section from routinely histological preparation, (2) real-time inspecting and digitally capturing each specific stained phenotype, and (3) efficiently synthesizing graphs containing the tissue multiple-stained components at site-specific regions. Comparisons of its stains with those by the conventional staining fashions using the microscopic images of mouse tissues (lung, heart, liver, kidney, esophagus, and brain), involving stains of HE, Periodic acid-Schiff, Sirius red, and IF for Human IgG, and mouse CD45, hemoglobin, and CD31, showed no major discordance. Repetitive experiments testing on targeted areas of stained sections confirmed the method is reliable with accuracy and high reproducibility. Using the technique, the targets of IF were easily localized and seen structurally in HE- or special-stained sections, and the unknown or suspected components or structures in HE-stained sections were further determined in histological special stains or IF. By the technique, staining processing was videoed and made a backup for off-site pathologists, which facilitates tele-consultation or -education in current digital pathology. Mistakes, which might occur during the staining process, can be immediately found and amended accordingly. With the technique, a single section can provide much more information than the traditional stained counterpart. The staining mode bears great potential to become a common supplementary tool for traditional histopathology.
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22
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Niu J, Hagen J, Yu F, Kalyuzhny AE, Tsourkas A. Labeling of Phospho-Specific Antibodies with oYo-Link® Epitope Tags for Multiplex Immunostaining. Methods Mol Biol 2023; 2593:113-126. [PMID: 36513927 PMCID: PMC10730302 DOI: 10.1007/978-1-0716-2811-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Spatial proteomics has recently garnered significant interest, as it offers to provide unprecedented insight into biological processes in both health and disease, by connecting protein expression patterns from the subcellular level to the tissue or even organism level. These high-content approaches generally rely on a high degree of multiplexing, whereby multiple proteins can be detected simultaneously. The most versatile multiplexing approaches utilize antibodies to confer specificity for various intracellular proteins of interest. Therefore, these methods must be able to differentiate many antibodies at once. In this chapter, we describe a simple and rapid approach to labeling antibodies with distinct epitope tags in a site-specific manner. This allows multiple antibodies, even from the same host species, to be uniquely identified and detected and offers a simple approach for spatial proteomic applications.
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Affiliation(s)
| | | | | | | | - Andrew Tsourkas
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
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23
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Rangamuwa K, Aloe C, Christie M, Asselin-Labat ML, Batey D, Irving L, John T, Bozinovski S, Leong TL, Steinfort D. Methods for assessment of the tumour microenvironment and immune interactions in non-small cell lung cancer. A narrative review. Front Oncol 2023; 13:1129195. [PMID: 37143952 PMCID: PMC10151669 DOI: 10.3389/fonc.2023.1129195] [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: 12/21/2022] [Accepted: 03/28/2023] [Indexed: 05/06/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is one of the leading causes of cancer death worldwide. Immunotherapy with immune checkpoint inhibitors (ICI) has significantly improved outcomes in some patients, however 80-85% of patients receiving immunotherapy develop primary resistance, manifesting as a lack of response to therapy. Of those that do have an initial response, disease progression may occur due to acquired resistance. The make-up of the tumour microenvironment (TME) and the interaction between tumour infiltrating immune cells and cancer cells can have a large impact on the response to immunotherapy. Robust assessment of the TME with accurate and reproducible methods is vital to understanding mechanisms of immunotherapy resistance. In this paper we will review the evidence of several methodologies to assess the TME, including multiplex immunohistochemistry, imaging mass cytometry, flow cytometry, mass cytometry and RNA sequencing.
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Affiliation(s)
- Kanishka Rangamuwa
- Department of Respiratory Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine Royal Melbourne Hospital (RMH), University of Melbourne, Parkville, VIC, Australia
- *Correspondence: Kanishka Rangamuwa,
| | - Christian Aloe
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Michael Christie
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | | | - Daniel Batey
- Personalised Oncology Division, Walter Eliza Hall Institute, Melbourne, VIC, Australia
| | - Lou Irving
- Department of Respiratory Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Thomas John
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Steven Bozinovski
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Tracy L. Leong
- Personalised Oncology Division, Walter Eliza Hall Institute, Melbourne, VIC, Australia
- Department of Respiratory Medicine, Austin Hospital, Heidelberg, VIC, Australia
| | - Daniel Steinfort
- Department of Respiratory Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine Royal Melbourne Hospital (RMH), University of Melbourne, Parkville, VIC, Australia
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24
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Kang W, Santella A, Rosiek E, Pulina M, Chan E, Fan N, Tipping MJ, Barlas A, Romin Y, Manova-Todorova K. Multiplex Spatial Protein Detection by Combining Immunofluorescence with Immunohistochemistry. Methods Mol Biol 2022; 2593:233-244. [PMID: 36513935 DOI: 10.1007/978-1-0716-2811-9_15] [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: 12/15/2022]
Abstract
Technologies for staining and imaging multiple antigens in single tissue sections are developing rapidly due to their potential to uncover spatial relationships between proteins with cellular resolution. Detections are performed simultaneously or sequentially depending on the approach. However, several technologies can detect limited numbers of antigens or require expensive equipment and reagents. Another serious concern is the lack of flexibility. Most commercialized reagents are validated for defined antibody panels, and introducing any changes is laborious and costly. In this chapter, we describe a method where we combine, for the first time, multiplexed IF followed by sequential immunohistochemistry (IHC) with AEC chromogen on Leica Bond staining processors with paraffin tissue sections. We present data for successful detection of 10 antigens in a single tissue section with preserved tissue integrity. Our method is designed for use with any combination of antibodies of interest, with images collected using whole slide scanners. We include an image viewing and image analysis workflow using nonlinear warping to combine all staining passes in a single full-resolution image of the entire tissue section, aligned at the single cell level.
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Affiliation(s)
- Wenfei Kang
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Anthony Santella
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Rosiek
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Pulina
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Chan
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ning Fan
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Murray J Tipping
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Afsar Barlas
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yevgeniy Romin
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katia Manova-Todorova
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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25
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Zhu H, Shen W, Luo C, Liu F. An integrated microfluidic device for multiplexed imaging of spatial gene expression patterns of Drosophila embryos. LAB ON A CHIP 2022; 22:4081-4092. [PMID: 36165088 DOI: 10.1039/d2lc00514j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To reveal the underlying mechanism of the biological function of multicellular systems, it is important to obtain comprehensive spatial gene expression profiles. Among the emerging single-cell spatial-omics techniques, immunofluorescence (IF)-based iterative multiplexed imaging is a promising approach. However, the conventional method is usually costly, time-consuming, labor-intensive, and has low throughput. Moreover, it has yet to be demonstrated in intact multicellular organisms. Here, we developed an integrated microfluidic system to overcome these challenges for quantitatively measuring multiple protein profiles sequentially in situ in the same Drosophila embryo. We designed an array of hydrodynamic trapping sites to automatically capture over ten Drosophila embryos with orientation selectivity at more than 90% trapping rates. We also optimized the geometry of confinement and the on-chip IF protocol to achieve the same high signal-to-noise ratio as the off-chip traditional IF experiments. Moreover, we developed an efficient de-staining protocol by combining on-chip antibody stripping and fluorophore bleaching. Using the same secondary antibody to sequentially stain different genes, we confirmed that the de-stained genes have no detectable interference with the subsequently stained genes, and the gene expression profiles are preserved after multiple cycles of staining and de-staining processes. This preliminary test shows that our newly developed integrated microfluidic system can be a powerful tool for multiplexed imaging of Drosophila embryos. Our work opens a new avenue to design microfluidic chips for multicellular organisms and single-cell spatial-omics techniques.
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Affiliation(s)
- Hongcun Zhu
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China.
| | - Wenting Shen
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China.
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
| | - Feng Liu
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
- Key Laboratory of Hebei Province for Molecular Biophysics, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300130, China
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26
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Bosisio FM, Van Herck Y, Messiaen J, Bolognesi MM, Marcelis L, Van Haele M, Cattoretti G, Antoranz A, De Smet F. Next-Generation Pathology Using Multiplexed Immunohistochemistry: Mapping Tissue Architecture at Single-Cell Level. Front Oncol 2022; 12:918900. [PMID: 35992810 PMCID: PMC9389457 DOI: 10.3389/fonc.2022.918900] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/20/2022] [Indexed: 01/23/2023] Open
Abstract
Single-cell omics aim at charting the different types and properties of all cells in the human body in health and disease. Over the past years, myriads of cellular phenotypes have been defined by methods that mostly required cells to be dissociated and removed from their original microenvironment, thus destroying valuable information about their location and interactions. Growing insights, however, are showing that such information is crucial to understand complex disease states. For decades, pathologists have interpreted cells in the context of their tissue using low-plex antibody- and morphology-based methods. Novel technologies for multiplexed immunohistochemistry are now rendering it possible to perform extended single-cell expression profiling using dozens of protein markers in the spatial context of a single tissue section. The combination of these novel technologies with extended data analysis tools allows us now to study cell-cell interactions, define cellular sociology, and describe detailed aberrations in tissue architecture, as such gaining much deeper insights in disease states. In this review, we provide a comprehensive overview of the available technologies for multiplexed immunohistochemistry, their advantages and challenges. We also provide the principles on how to interpret high-dimensional data in a spatial context. Similar to the fact that no one can just “read” a genome, pathological assessments are in dire need of extended digital data repositories to bring diagnostics and tissue interpretation to the next level.
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Affiliation(s)
- Francesca Maria Bosisio
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- *Correspondence: Frederik De Smet, ; Francesca Maria Bosisio,
| | | | - Julie Messiaen
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- The Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Maddalena Maria Bolognesi
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Monza, Italy
- Department of Pathology, Azienda Socio Sanitaria Territoriale (ASST) Monza, Ospedale San Gerardo, Monza, Italy
| | - Lukas Marcelis
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Matthias Van Haele
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Giorgio Cattoretti
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Monza, Italy
- Department of Pathology, Azienda Socio Sanitaria Territoriale (ASST) Monza, Ospedale San Gerardo, Monza, Italy
| | - Asier Antoranz
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- The Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Frederik De Smet
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- The Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- *Correspondence: Frederik De Smet, ; Francesca Maria Bosisio,
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27
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Kawabe Y, Tanaka T, Isonishi A, Nakahara K, Tatsumi K, Wanaka A. Characterization of Glial Populations in the Aging and Remyelinating Mouse Corpus Callosum. Neurochem Res 2022; 47:2826-2838. [PMID: 35859078 DOI: 10.1007/s11064-022-03676-z] [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: 03/30/2022] [Revised: 06/15/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
Cells in the white matter of the adult brain have a characteristic distribution pattern in which several cells are contiguously connected to each other, making a linear array (LA) resembling pearls-on-a-string parallel to the axon axis. We have been interested in how this pattern of cell distribution changes during aging and remyelination after demyelination. In the present study, with a multiplex staining method, semi-quantitative analysis of the localization of oligodendrocyte lineage cells (oligodendrocyte progenitors, premyelinating oligodendrocytes, and mature oligodendrocytes), astrocytes, and microglia in 8-week-old (young adult) and 32-week-old (aged) corpus callosum showed that young adult cells still include immature oligodendrocytes and that LAs contain a higher proportion of microglia than isolated cells. In aged mice, premyelinating oligodendrocytes were decreased, but microglia continued to be present in the LAs. These results suggest that the presence of microglia is important for the characteristic cell localization pattern of LAs. In a cuprizone-induced demyelination model, we observed re-formation of LAs after completion of cuprizone treatment, concurrent with remyelination. These re-formed LAs again contained more microglia than the isolated cells. This finding supports the hypothesis that microglia contribute to the formation and maintenance of LAs. In addition, regardless of the distribution of cells (LAs or isolated cells), astrocytes were found to be more abundant than in the normal corpus callosum at 24 weeks after cuprizone treatment when remyelination is completed. This suggests that astrocytes are involved in maintaining the functions of remyelinated white matter.
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Affiliation(s)
- Yoshie Kawabe
- Department of Anatomy and Neuroscience, Nara Medical University, Faculty of Medicine, 840 Shijo-cho, Kashihara City, Nara, 634-8521, Japan
| | - Tatsuhide Tanaka
- Department of Anatomy and Neuroscience, Nara Medical University, Faculty of Medicine, 840 Shijo-cho, Kashihara City, Nara, 634-8521, Japan
| | - Ayami Isonishi
- Department of Anatomy and Neuroscience, Nara Medical University, Faculty of Medicine, 840 Shijo-cho, Kashihara City, Nara, 634-8521, Japan
| | - Kazuki Nakahara
- Department of Anatomy and Neuroscience, Nara Medical University, Faculty of Medicine, 840 Shijo-cho, Kashihara City, Nara, 634-8521, Japan
| | - Kouko Tatsumi
- Department of Anatomy and Neuroscience, Nara Medical University, Faculty of Medicine, 840 Shijo-cho, Kashihara City, Nara, 634-8521, Japan.
| | - Akio Wanaka
- Department of Anatomy and Neuroscience, Nara Medical University, Faculty of Medicine, 840 Shijo-cho, Kashihara City, Nara, 634-8521, Japan
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28
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Ozbek B, Ertunc O, Erickson A, Vidal ID, Gomes-Alexandre C, Guner G, Hicks JL, Jones T, Taube JM, Sfanos KS, Yegnasubramanian S, De Marzo AM. Multiplex immunohistochemical phenotyping of T cells in primary prostate cancer. Prostate 2022; 82:706-722. [PMID: 35188986 DOI: 10.1002/pros.24315] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/03/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Most prostate cancers are "immune cold" and poorly responsive to immune checkpoint inhibitors. However, the mechanisms responsible for the lack of a robust antitumor adaptive immune response in the prostate are poorly understood, which hinders the development of novel immunotherapeutic approaches. AIMS Most inflammatory infiltrates in the prostate are centered around benign glands and stroma, which can confound the molecular characterization of the antitumor immune response. We sought to analytically validate a chromogenic-based multiplex immunohistochemistry (IHC) approach applicable to whole slide digital image analysis to quantify T cell subsets from the tumor microenvironment of primary prostatic adenocarcinomas. As an initial application, we tested the hypothesis that PTEN loss leads to an altered antitumor immune response by comparing matched regions of tumors within the same individual with and without PTEN loss. MATERIALS & METHODS Using the HALO Image Analysis Platform (Indica Labs), we trained a classifier to quantify the densities of eight T cell phenotypes separately in the tumor epithelial and stromal subcompartments. RESULTS The iterative chromogenic approach using 7 different antibodies on the same slide provides highly similar findings to results using individually stained slides with single antibodies. Our main findings in carcinomas (benign removed) include the following: i) CD4+ T cells are present at higher density than CD8+ T cells; ii) all T cell subsets are present at higher densities in the stromal compartment compared to the epithelial tumor compartment; iii) most CD4+ and CD8+ T cells are PD1+; iv) cancer foci with PTEN loss harbored increased numbers of T cells compared to regions without PTEN loss, in both stromal and epithelial compartments; and v) the increases in T cells in PTEN loss regions were associated with ERG gene fusion status. DISCUSSION This modular approach can apply to any IHC-validated antibody combination and sets the groundwork for more detailed spatial analyses. CONCLUSION Iterative chromogenic IHC can be used for whole slide analysis of prostate tissue samples and can complement transcriptomic results including those using single cell and spatial genomic approaches.
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Affiliation(s)
- Busra Ozbek
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Onur Ertunc
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Erickson
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Igor D Vidal
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Carolina Gomes-Alexandre
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Gunes Guner
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jessica L Hicks
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tracy Jones
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Janis M Taube
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, Maryland, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins University, Baltimore, Maryland, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Karen S Sfanos
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, Maryland, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Brady Urological Research Institute, Johns Hopkins, Baltimore, Maryland, USA
| | - Srinivasan Yegnasubramanian
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, Maryland, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Brady Urological Research Institute, Johns Hopkins, Baltimore, Maryland, USA
| | - Angelo M De Marzo
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, Maryland, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Brady Urological Research Institute, Johns Hopkins, Baltimore, Maryland, USA
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29
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Pontelli MC, Castro IA, Martins RB, La Serra L, Veras FP, Nascimento DC, Silva CM, Cardoso RS, Rosales R, Gomes R, Lima TM, Souza JP, Vitti BC, Caetité DB, de Lima MHF, Stumpf SD, Thompson CE, Bloyet LM, Kawahisa JTE, Giannini MC, Bonjorno LP, Lopes MIF, Batah SS, Li S, Assad RL, Almeida SCL, Oliveira FR, Benatti MN, Pontes LLF, Santana RC, Vilar FC, Martins MA, Shi PY, Cunha TM, Calado RT, Alves-Filho JC, Zamboni DS, Fabro A, Louzada-Junior P, Oliveira RDR, Whelan SPJ, Cunha FQ, Arruda E. SARS-CoV-2 productively infects primary human immune system cells in vitro and in COVID-19 patients. J Mol Cell Biol 2022; 14:6572370. [PMID: 35451490 PMCID: PMC9384834 DOI: 10.1093/jmcb/mjac021] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 12/30/2021] [Accepted: 04/19/2022] [Indexed: 12/04/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with a hyperinflammatory state and lymphocytopenia, a hallmark that appears as both signature and prognosis of disease severity outcome. Although cytokine storm and a sustained inflammatory state are commonly associated with immune cell depletion, it is still unclear whether direct SARS-CoV-2 infection of immune cells could also play a role in this scenario by harboring viral replication. We found that monocytes, as well as both B and T lymphocytes, were susceptible to SARS-CoV-2 infection in vitro, accumulating double-stranded RNA consistent with viral RNA replication and ultimately leading to expressive T cell apoptosis. In addition, flow cytometry and immunofluorescence analysis revealed that SARS-CoV-2 was frequently detected in monocytes and B lymphocytes from coronavirus disease 2019 (COVID-19) patients. The rates of SARS-CoV-2-infected monocytes in peripheral blood mononuclear cells from COVID-19 patients increased over time from symptom onset, with SARS-CoV-2-positive monocytes, B cells, and CD4+ T lymphocytes also detected in postmortem lung tissue. These results indicated that SARS-CoV-2 infection of blood-circulating leukocytes in COVID-19 patients might have important implications for disease pathogenesis and progression, immune dysfunction, and virus spread within the host.
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Affiliation(s)
- Marjorie C Pontelli
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Italo A Castro
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Ronaldo B Martins
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Leonardo La Serra
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Flávio P Veras
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Daniele C Nascimento
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Camila M Silva
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Ricardo S Cardoso
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Roberta Rosales
- Department of Cell and Molecular Biology, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Rogério Gomes
- Blood Center of Ribeirao Preto, 14049-900, Ribeirao Preto, São Paulo, Brazil
| | - Thais M Lima
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Juliano P Souza
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Brenda C Vitti
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Diego B Caetité
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Mikhael H F de Lima
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Spencer D Stumpf
- Department of Biochemistry & Molecular Biology, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Cassandra E Thompson
- Department of Biochemistry & Molecular Biology, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Louis-Marie Bloyet
- Department of Biochemistry & Molecular Biology, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Juliana T E Kawahisa
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Marcela C Giannini
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Divisions of Clinical Immunology, Infectious Diseases and Intensive Care Unit, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Letícia P Bonjorno
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Divisions of Clinical Immunology, Infectious Diseases and Intensive Care Unit, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Maria I F Lopes
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Divisions of Clinical Immunology, Infectious Diseases and Intensive Care Unit, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Sabrina S Batah
- Department of Pathology, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Siyuan Li
- Department of Pathology, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Rodrigo L Assad
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Divisions of Clinical Immunology, Infectious Diseases and Intensive Care Unit, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Sergio C L Almeida
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Divisions of Clinical Immunology, Infectious Diseases and Intensive Care Unit, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Fabiola R Oliveira
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Divisions of Clinical Immunology, Infectious Diseases and Intensive Care Unit, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Maíra N Benatti
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Divisions of Clinical Immunology, Infectious Diseases and Intensive Care Unit, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Lorena L F Pontes
- Blood Center of Ribeirao Preto, 14049-900, Ribeirao Preto, São Paulo, Brazil
| | - Rodrigo C Santana
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Divisions of Clinical Immunology, Infectious Diseases and Intensive Care Unit, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Fernando C Vilar
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Divisions of Clinical Immunology, Infectious Diseases and Intensive Care Unit, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Maria A Martins
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Divisions of Clinical Immunology, Infectious Diseases and Intensive Care Unit, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Pei-Yong Shi
- Department of Biochemistry & Molecular Biology, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Thiago M Cunha
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Rodrigo T Calado
- Blood Center of Ribeirao Preto, 14049-900, Ribeirao Preto, São Paulo, Brazil
| | - José C Alves-Filho
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Dario S Zamboni
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Department of Cell and Molecular Biology, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Alexandre Fabro
- Department of Pathology, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Paulo Louzada-Junior
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Divisions of Clinical Immunology, Infectious Diseases and Intensive Care Unit, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Rene D R Oliveira
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Divisions of Clinical Immunology, Infectious Diseases and Intensive Care Unit, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University in St. Louis, Saint Louis, MO 63110, USA
| | - Fernando Q Cunha
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
| | - Eurico Arruda
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil.,Department of Cell and Molecular Biology, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900, Ribeirao Preto, Sao Paulo, Brazil
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30
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Taatjes DJ, Ghule PN, Bouffard NA, Lee K, DeLance NM, Evans MF, Weaver DL, Deakin N, Carr FE, Sprague BL, Stein GS, Stein JL. The Shared Core Resource as a Partner in Innovative Scientific Research: Illustration from an Academic Microscopy Imaging Center. J Biomol Tech 2022; 33:3fc1f5fe.2507f36c. [PMID: 35836997 PMCID: PMC9258914 DOI: 10.7171/3fc1f5fe.2507f36c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Core facilities have a ubiquitous and increasingly valuable presence at research institutions. Although many shared cores were originally created to provide routine services and access to complex and expensive instrumentation for the research community, they are frequently called upon by investigators to design protocols and procedures to help answer complex research questions. For instance, shared microscopy resources are evolving from providing access to and training on complex imaging instruments to developing detailed innovative protocols and experimental strategies, including sample preparation techniques, staining, complex imaging parameters, and high-level image analyses. These approaches require close intellectual collaboration between core staff and research investigators to formulate and coordinate plans for protocol development suited to the research question. Herein, we provide an example of such coordinated collaboration between a shared microscopy facility and a team of scientists and clinician-investigators to approach a complex multiprobe immunostaining, imaging, and image analysis project investigating the tumor microenvironment from human breast cancer samples. Our hope is that this example may be used to convey to institute administrators the critical importance of the intellectual contributions of the scientific staff in core facilities to research endeavors.
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Affiliation(s)
- Douglas J. Taatjes
- Department of Pathology and Laboratory Medicine,
Microscopy Imaging Center, and University of Vermont Cancer Center, University of VermontBurlington, VT 05405USA
| | - Prachi N. Ghule
- University of Vermont Cancer Center and Department of Biochemistry,
University of VermontBurlington,
VT 05405USA
| | - Nicole A. Bouffard
- Department of Pathology and Laboratory Medicine and Microscopy Imaging Center,
University of VermontBurlington,
VT 05405USA
| | - Kyra Lee
- Department of Biochemistry,
University of VermontBurlington,
VT 05405USA
| | - Nicole M. DeLance
- Department of Pathology and Laboratory Medicine and Microscopy Imaging Center,
University of VermontBurlington,
VT 05405USA
| | - Mark F. Evans
- Department of Pathology and Laboratory Medicine and University of Vermont Cancer Center,
University of VermontBurlington,
VT 05405USA
| | - Donald L. Weaver
- Department of Pathology and Laboratory Medicine and University of Vermont Cancer Center,
University of VermontBurlington,
VT 05405USA
| | | | - Frances E. Carr
- University of Vermont Cancer Center and Department of Pharmacology,
University of VermontBurlington,
VT 05405USA
| | - Brian L. Sprague
- University of Vermont Cancer Center and Department of Surgery,
Larner College of Medicine, University of VermontBurlington,
VT 05405USA
| | - Gary S. Stein
- University of Vermont Cancer Center and Department of Biochemistry,
University of VermontBurlington,
VT 05405USA
| | - Janet L. Stein
- University of Vermont Cancer Center and Department of Biochemistry,
University of VermontBurlington,
VT 05405USA
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31
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Davis B, Shi P, Gaddes E, Lai J, Wang Y. Bidirectional Supramolecular Display and Signal Amplification on the Surface of Living Cells. Biomacromolecules 2022; 23:1403-1412. [PMID: 35189058 DOI: 10.1021/acs.biomac.1c01627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to display exogenous molecules or nanomaterials on the surface of cells holds great potential for biomedical applications such as cell imaging and delivery. Numerous methods have been well established to enhance the display of biomolecules and nanomaterials on the cell surface. However, it is challenging to remove these biomolecules or nanomaterials from the cell surface. The purpose of this study was to investigate the reversible display of supramolecular nanomaterials on the surface of living cells. The data show that DNA initiators could induce the self-assembly of DNA-alginate conjugates to form supramolecular nanomaterials and amplify the fluorescence signals on the cell surface. Complementary DNA (cDNA), DNase, and alginase could all trigger the reversal of the signals from the cell surface. However, these three molecules exhibited different triggering efficiencies in the order cDNA > alginase > DNase. The combination of cDNA and alginase led to the synergistic reversal of nanomaterials and fluorescent signals from the cell surface. Thus, this study has successfully demonstrated a method for the bidirectional display of supramolecular nanomaterials on the surface of living cells. This method may find its application in numerous fields such as intact cell imaging and separation.
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Affiliation(s)
- Brandon Davis
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Peng Shi
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Erin Gaddes
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jinping Lai
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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32
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Lonardi S, Bugatti M, Valzelli A, Facchetti F. Immunohistochemical Detection of SARS-CoV-2 Antigens by Single and Multiple Immunohistochemistry. Methods Mol Biol 2022; 2452:291-303. [PMID: 35554913 DOI: 10.1007/978-1-0716-2111-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can be demonstrated in tissue sections by immunohistochemistry (IHC), which has the power to localize in bright field specific antigens in cells and tissues. The use of double or triple immunostains is capable of highlighting which cells are infected and/or the relationship of infected cell with other cells and tissue structures. In addition, immunoenzymatic multi-staining permits the simultaneous identification, localization, and enumeration of different cellular epitopes. Moreover, this method improves analytical precision, decreasing the time required for morphometric quantification, maximizing the information obtained from a single slide of paraffin-embedded tissue.
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Affiliation(s)
- Silvia Lonardi
- Section of Pathology, Department of Molecular and Translational Medicine, University of Brescia, Spedali Civili di Brescia, Brescia, Italy
| | - Mattia Bugatti
- Section of Pathology, Department of Molecular and Translational Medicine, University of Brescia, Spedali Civili di Brescia, Brescia, Italy.
| | - Arianna Valzelli
- Section of Pathology, Department of Molecular and Translational Medicine, University of Brescia, Spedali Civili di Brescia, Brescia, Italy
| | - Fabio Facchetti
- Section of Pathology, Department of Molecular and Translational Medicine, University of Brescia, Spedali Civili di Brescia, Brescia, Italy.
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33
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Oligonucleotide conjugated antibody strategies for cyclic immunostaining. Sci Rep 2021; 11:23844. [PMID: 34903759 PMCID: PMC8668956 DOI: 10.1038/s41598-021-03135-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022] Open
Abstract
A number of highly multiplexed immunostaining and imaging methods have advanced spatial proteomics of cancer for improved treatment strategies. While a variety of methods have been developed, the most widely used methods are limited by harmful signal removal techniques, difficulties with reagent production and antigen sensitivity. Multiplexed immunostaining employing oligonucleotide (oligos)-barcoded antibodies is an alternative approach that is growing in popularity. However, challenges remain in consistent conjugation of oligos to antibodies with maintained antigenicity as well as non-destructive, robust and cost-effective signal removal methods. Herein, a variety of oligo conjugation and signal removal methods were evaluated in the development of a robust oligo conjugated antibody cyclic immunofluorescence (Ab-oligo cyCIF) methodology. Both non- and site-specific conjugation strategies were assessed to label antibodies, where site-specific conjugation resulted in higher retained binding affinity and antigen-specific staining. A variety of fluorescence signal removal methods were also evaluated, where incorporation of a photocleavable link (PCL) resulted in full fluorescence signal removal with minimal tissue disruption. In summary, this work resulted in an optimized Ab-oligo cyCIF platform capable of generating high dimensional images to characterize the spatial proteomics of the hallmarks of cancer.
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34
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Schwarzkopf M, Liu MC, Schulte SJ, Ives R, Husain N, Choi HMT, Pierce NA. Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization. Development 2021; 148:dev199847. [PMID: 35020875 PMCID: PMC8645210 DOI: 10.1242/dev.199847] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022]
Abstract
RNA in situ hybridization based on the mechanism of the hybridization chain reaction (HCR) enables multiplexed, quantitative, high-resolution RNA imaging in highly autofluorescent samples, including whole-mount vertebrate embryos, thick brain slices and formalin-fixed paraffin-embedded tissue sections. Here, we extend the benefits of one-step, multiplexed, quantitative, isothermal, enzyme-free HCR signal amplification to immunohistochemistry, enabling accurate and precise protein relative quantitation with subcellular resolution in an anatomical context. Moreover, we provide a unified framework for simultaneous quantitative protein and RNA imaging with one-step HCR signal amplification performed for all target proteins and RNAs simultaneously.
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Affiliation(s)
- Maayan Schwarzkopf
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mike C. Liu
- Molecular Instruments, Los Angeles, CA 90041, USA
| | - Samuel J. Schulte
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rachel Ives
- Molecular Instruments, Los Angeles, CA 90041, USA
| | - Naeem Husain
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Niles A. Pierce
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
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35
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Giri AK, Ianevski A. High-throughput screening for drug discovery targeting the cancer cell-microenvironment interactions in hematological cancers. Expert Opin Drug Discov 2021; 17:181-190. [PMID: 34743621 DOI: 10.1080/17460441.2022.1991306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION The interactions between leukemic blasts and cells within the bone marrow environment affect oncogenesis, cancer stem cell survival, as well as drug resistance in hematological cancers. The importance of this interaction is increasingly being recognized as a potentially important target for future drug discoveries and developments. Recent innovations in the high throughput drug screening-related technologies, novel ex-vivo disease-models, and freely available machine-learning algorithms are advancing the drug discovery process by targeting earlier undruggable proteins, complex pathways, as well as physical interactions (e.g. leukemic cell-bone microenvironment interaction). AREA COVERED In this review, the authors discuss the recent methodological advancements and existing challenges to target specialized hematopoietic niches within the bone marrow during leukemia and suggest how such methods can be used to identify drugs targeting leukemic cell-bone microenvironment interactions. EXPERT OPINION The recent development in cell-cell communication scoring technology and culture conditions can speed up the drug discovery by targeting the cell-microenvironment interaction. However, to accelerate this process, collecting clinical-relevant patient tissues, developing culture model systems, and implementing computational algorithms, especially trained to predict drugs and their combination targeting the cancer cell-bone microenvironment interaction are needed.
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Affiliation(s)
- Anil K Giri
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Aleksander Ianevski
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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36
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Qi J, Liu X, Yan P, He S, Lin Y, Huang Z, Zhang S, Xie S, Li Y, Lu X, Wu Y, Zhou Y, Yuan J, Cai T, Zheng X, Ding Y, Yang W. Analysis of Immune Landscape Reveals Prognostic Significance of Cytotoxic CD4 + T Cells in the Central Region of pMMR CRC. Front Oncol 2021; 11:724232. [PMID: 34631551 PMCID: PMC8493090 DOI: 10.3389/fonc.2021.724232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/06/2021] [Indexed: 12/22/2022] Open
Abstract
Background Mismatch repair proficient colorectal cancer (pMMR CRC) lacks effective treatments and has a poor prognosis, which can be attributed to the complexity of tumor microenvironment. The coordinated function of immune cells is vital to anti-tumor immunity. However, the spatial characteristics of immune cells in the pMMR CRC immune microenvironment and their relationship with clinical prognosis are not fully understood. Meanwhile, the immune modulatory effect of neoadjuvant chemotherapy (NCT), which is the first-line treatment of pMMR CRC, needs further investigation. Therefore, this study aims to explore the spatial dynamics of immune cells and its prognostic value in pMMR CRC. Methods We analyzed the various immune cells in formalin-fixed, paraffin-embedded tumor tissues which were collected from 77 patients with stage II/III of pMMR CRC, including 39 non-NCT treated and 38 NCT treated patients. We used the optimized multiplex immunohistochemistry (mIHC) to identify and quantify the density, type and location of immune cells in pMMR CRC. Multivariate survival analysis was performed to assess the relationship of immune profiles and clinical prognosis of pMMR CRC patients. Results The densities of most T cell subsets, B cells and macrophages were higher in the central region of the pMMR CRC than in the invasion margin. Tumor infiltrating lymphocytes (TILs), especially the infiltration of CD4+ GzmB+ T cells in the central region of the tumor was identified to be positively correlated with the prognosis of the patients. Multivariate analysis confirmed that CD4+ GzmB+ T cells population was an independent predictor of disease-free survival (DFS) in non-NCT group. Meanwhile, NCT enhanced the infiltration of CD4+ GzmB+ T cells in the central region of the pMMR CRC, which was also identified as an independent protective factor of overall survival (OS) and DFS in NCT group. Conclusion We demonstrated that the level of CD4+ GzmB+ T cells located in the center of tumor could provide great prognostic value for pMMR CRC patients. And the application of neoadjuvant chemotherapy further improves the infiltration of CD4+ GzmB+ T cells in the central compartment. Further studies into the application of CD4+ GzmB+ T cells in tumor immunotherapy are needed.
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Affiliation(s)
- Jingwen Qi
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
| | - Xiaoyan Liu
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
| | - Peian Yan
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
| | - Shangwen He
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yuhao Lin
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zhiwei Huang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Shenyan Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
| | - Siyu Xie
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
| | - Yanfeng Li
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
| | - Xiaofei Lu
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
| | - Yingjun Wu
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
| | - Yangshu Zhou
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
| | - Juanjuan Yuan
- Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ting Cai
- Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiaojun Zheng
- Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yanqing Ding
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
| | - Wei Yang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
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Boisson A, Noël G, Saiselet M, Rodrigues-Vitória J, Thomas N, Fontsa ML, Sofronii D, Naveaux C, Duvillier H, Craciun L, Larsimont D, Awada A, Detours V, Willard-Gallo K, Garaud S. Fluorescent Multiplex Immunohistochemistry Coupled With Other State-Of-The-Art Techniques to Systematically Characterize the Tumor Immune Microenvironment. Front Mol Biosci 2021; 8:673042. [PMID: 34621785 PMCID: PMC8490683 DOI: 10.3389/fmolb.2021.673042] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/11/2021] [Indexed: 02/06/2023] Open
Abstract
Our expanding knowledge of the interactions between tumor cells and their microenvironment has helped to revolutionize cancer treatments, including the more recent development of immunotherapies. Immune cells are an important component of the tumor microenvironment that influence progression and treatment responses, particularly to the new immunotherapies. Technological advances that help to decipher the complexity and diversity of the tumor immune microenvironment (TIME) are increasingly used in translational research and biomarker studies. Current techniques that facilitate TIME evaluation include flow cytometry, multiplex bead-based immunoassays, chromogenic immunohistochemistry (IHC), fluorescent multiplex IHC, immunofluorescence, and spatial transcriptomics. This article offers an overview of our representative data, discusses the application of each approach to studies of the TIME, including their advantages and challenges, and reviews the potential clinical applications. Flow cytometry and chromogenic and fluorescent multiplex IHC were used to immune profile a HER2+ breast cancer, illustrating some points. Spatial transcriptomic analysis of a luminal B breast tumor demonstrated that important additional insight can be gained from this new technique. Finally, the development of a multiplex panel to identify proliferating B cells, Tfh, and Tfr cells on the same tissue section demonstrates their co-localization in tertiary lymphoid structures.
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Affiliation(s)
- Anaïs Boisson
- Molecular Immunology Unit, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Grégory Noël
- Molecular Immunology Unit, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | | | | | - Noémie Thomas
- Molecular Immunology Unit, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Mireille Langouo Fontsa
- Molecular Immunology Unit, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Doïna Sofronii
- Molecular Immunology Unit, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Céline Naveaux
- Molecular Immunology Unit, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Hugues Duvillier
- Flow Cytometry Facility, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Ligia Craciun
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Denis Larsimont
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Ahmad Awada
- Oncology Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Karen Willard-Gallo
- Molecular Immunology Unit, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Soizic Garaud
- Molecular Immunology Unit, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
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38
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Zirbes A, Joseph J, Lopez JC, Sayaman RW, Basam M, Seewaldt VL, LaBarge MA. Changes in Immune Cell Types with Age in Breast are Consistent with a Decline in Immune Surveillance and Increased Immunosuppression. J Mammary Gland Biol Neoplasia 2021; 26:247-261. [PMID: 34341887 PMCID: PMC8566425 DOI: 10.1007/s10911-021-09495-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/19/2021] [Indexed: 12/22/2022] Open
Abstract
A majority of breast cancers (BC) are age-related and we seek to determine what cellular and molecular changes occur in breast tissue with age that make women more susceptible to cancer initiation. Immune-epithelial cell interactions are important during mammary gland development and the immune system plays an important role in BC progression. The composition of human immune cell populations is known to change in peripheral blood with age and in breast tissue during BC progression. Less is known about changes in immune populations in normal breast tissue and how their interactions with mammary epithelia change with age. We quantified densities of T cells, B cells, and macrophage subsets in pathologically normal breast tissue from 122 different women who ranged in age from 24 to 74 years old. Donor-matched peripheral blood from a subset of 20 donors was analyzed by flow cytometry. Tissue immune cell densities and localizations relative to the epithelium were quantified in situ with machine learning-based image analyses of multiplex immunohistochemistry-stained tissue sections. In situ results were corroborated with flow cytometry analyses of peri-epithelial immune cells from primary breast tissue preparations and transcriptome analyses of public data from bulk tissue reduction mammoplasties. Proportions of immune cell subsets in breast tissue and donor-matched peripheral blood were not correlated. Density (cells/mm2) of T and B lymphocytes in situ decreased with age. T cells and macrophages preferentially localized near or within epithelial bilayers, rather than the intralobular stroma. M2 macrophage density was higher than M1 macrophage density and this difference was due to higher density of M2 in the intralobular stroma. Transcriptional signature analyses suggested age-dependent decline in adaptive immune cell populations and functions and increased innate immune cell activity. T cells and macrophages are so intimately associated with the epithelia that they are embedded within the bilayer, suggesting an important role for immune-epithelial cell interactions. Age-associated decreased T cell density in peri-epithelial regions, and increased M2 macrophage density in intralobular stroma suggests the emergence of a tissue microenvironment that is simultaneously immune-senescent and immunosuppressive with age.
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Affiliation(s)
- Arrianna Zirbes
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, USA
| | - Jesuchristopher Joseph
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
| | - Jennifer C Lopez
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
| | - Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
- Center for Cancer and Aging, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Cancer Metabolism Training Program, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Mudaser Basam
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
| | - Victoria L Seewaldt
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA.
- Center for Cancer and Aging, Beckman Research Institute, City of Hope, Duarte, CA, USA.
- Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway.
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39
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9-Cyanopyronin probe palette for super-multiplexed vibrational imaging. Nat Commun 2021; 12:4518. [PMID: 34312393 PMCID: PMC8313527 DOI: 10.1038/s41467-021-24855-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 07/05/2021] [Indexed: 11/08/2022] Open
Abstract
Multiplexed optical imaging provides holistic visualization on a vast number of molecular targets, which has become increasingly essential for understanding complex biological processes and interactions. Vibrational microscopy has great potential owing to the sharp linewidth of vibrational spectra. In 2017, we demonstrated the coupling between electronic pre-resonant stimulated Raman scattering (epr-SRS) microscopy with a proposed library of 9-cyanopyronin-based dyes, named Manhattan Raman Scattering (MARS). Herein, we develop robust synthetic methodology to build MARS probes with different core atoms, expansion ring numbers, and stable isotope substitutions. We discover a predictive model to correlate their vibrational frequencies with structures, which guides rational design of MARS dyes with desirable Raman shifts. An expanded library of MARS probes with diverse functionalities is constructed. When coupled with epr-SRS microscopy, these MARS probes allow us to demonstrate not only many versatile labeling modalities but also increased multiplexing capacity. Hence, this work opens up next-generation vibrational imaging with greater utilities.
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40
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Brockman AA, Mobley BC, Ihrie RA. Histological Studies of the Ventricular-Subventricular Zone as Neural Stem Cell and Glioma Stem Cell Niche. J Histochem Cytochem 2021; 69:819-834. [PMID: 34310246 DOI: 10.1369/00221554211032003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The neural stem cell niche of the ventricular-subventricular zone supports the persistence of stem and progenitor cells in the mature brain. This niche has many notable cytoarchitectural features that affect the activity of stem cells and may also support the survival and growth of invading tumor cells. Histochemical studies of the niche have revealed many proteins that, in combination, can help to reveal stem-like cells in the normal or cancer context, although many caveats persist in the quest to consistently identify these cells in the human brain. Here, we explore the complex relationship between the persistent proliferative capacity of the neural stem cell niche and the malignant proliferation of brain tumors, with a special focus on histochemical identification of stem cells and stem-like tumor cells and an eye toward the potential application of high-dimensional imaging approaches to the field.
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Affiliation(s)
- Asa A Brockman
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Bret C Mobley
- Departments of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Rebecca A Ihrie
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Departments of Neurological Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
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41
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Shafique MR, Fisher TL, Evans EE, Leonard JE, Pastore DRE, Mallow CL, Smith E, Mishra V, Schröder A, Chin KM, Beck JT, Baumgart MA, Govindan R, Gabrail NY, Spira AI, Seetharamu N, Lou Y, Mansfield AS, Sanborn RE, Goldman JW, Zauderer M. A Phase Ib/II Study of Pepinemab in Combination with Avelumab in Advanced Non-Small Cell Lung Cancer. Clin Cancer Res 2021; 27:3630-3640. [PMID: 33820783 DOI: 10.1158/1078-0432.ccr-20-4792] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/11/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE The CLASSICAL-Lung clinical trial tested the combination of pepinemab, an IgG4 humanized mAb targeting semaphorin 4D, with the PD-L1 inhibitor avelumab to assess the effects of coupling increased T-cell infiltration and reversal of immune suppression via pepinemab with sustained T-cell activation via checkpoint inhibition. PATIENTS AND METHODS This phase Ib/II, single-arm study was designed to evaluate the safety, tolerability, and efficacy of pepinemab in combination with avelumab in 62 patients with advanced non-small cell lung cancer (NSCLC), including immunotherapy-naïve (ION) patients and patients whose tumors progressed following anti-PD-1/L1 monotherapy (IOF). The main objectives were to evaluate safety/tolerability, establish a recommended phase 2 dose (RP2D), obtain a preliminary evaluation of antitumor activity, and investigate candidate biomarker activity. RESULTS The combination was well tolerated with no major safety signals identified. Pepinemab, 10 mg/kg with avelumab, 10 mg/kg, every 2 weeks, was selected as the RP2D. Among 21 evaluable ION patients, 5 patients experienced partial responses (PR), 4 patients evidenced clinical benefit ≥1 year, and the disease control rate (DCR) was 81%. Notably, overall response rate with the combination therapy was higher than previously reported for single-agent avelumab in the PD-L1-negative/low population. Among 29 evaluable IOF patients, the combination resulted in a DCR of 59%, including 2 PR and 7 patients with durable clinical benefit of ≥23 weeks. Biomarker analysis of biopsies demonstrated increased CD8 T-cell density correlating with RECIST response criteria. CONCLUSIONS The combination of pepinemab with avelumab was well tolerated in NSCLC and showed signs of antitumor activity in immunotherapy-resistant and PD-L1-negative/low tumors.
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Affiliation(s)
- Michael R Shafique
- Department of Thoracic Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | | | | | | | | | | | | | | | | | - Kevin M Chin
- EMD Serono Research & Development, Inc., Billerica, Massachusetts; an affiliate of Merck KGaA, Darmstadt, Germany
| | | | | | | | | | - Alexander I Spira
- Virginia Cancer Specialists and US Oncology Research, The Woodlands, Texas
| | | | - Yanyan Lou
- Department of Hematology and Oncology, Jacksonville, Florida
| | | | - Rachel E Sanborn
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon
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42
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Rajagopalan A, Venkatesh I, Aslam R, Kirchenbuechler D, Khanna S, Cimbaluk D, Kordower JH, Gupta V. SeqStain is an efficient method for multiplexed, spatialomic profiling of human and murine tissues. CELL REPORTS METHODS 2021; 1:100006. [PMID: 34766102 PMCID: PMC8579778 DOI: 10.1016/j.crmeth.2021.100006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/11/2021] [Accepted: 03/17/2021] [Indexed: 01/16/2023]
Abstract
Spatial organization of molecules and cells in complex tissue microenvironments provides essential organizational cues in health and disease. A significant need exists for improved visualization of these spatial relationships. Here, we describe a multiplex immunofluorescence imaging method, termed SeqStain, that uses fluorescent-DNA-labeled antibodies for immunofluorescent staining and nuclease treatment for de-staining that allows selective enzymatic removal of the fluorescent signal. SeqStain can be used with primary antibodies, secondary antibodies, and antibody fragments to efficiently analyze complex cells and tissues. Additionally, incorporation of specific endonuclease restriction sites in antibody labels allows for selective removal of fluorescent signals while retaining other signals that can serve as marks for subsequent analyses. The application of SeqStain on human kidney tissue provided a spatialomic profile of the organization of >25 markers in the kidney, highlighting it as a versatile, easy-to-use, and gentle new technique for spatialomic analyses of complex microenvironments.
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Affiliation(s)
- Anugraha Rajagopalan
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
| | - Ishwarya Venkatesh
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
| | - Rabail Aslam
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
| | - David Kirchenbuechler
- Center for Advanced Microscopy, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shreyaa Khanna
- University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
| | - David Cimbaluk
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Pathology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Jeffrey H. Kordower
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, USA
| | - Vineet Gupta
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
- Division of Hematology, Oncology and Cell Therapy, Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
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43
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Viana RMM, Souza JP, Jorge DMM, Martins RB, Castro IA, Cardoso RS, Volpini LPB, de Souza Luna LK, Spano LC, Bellei NCJ, Chahud F, Arruda E, A Hyppolito M. Detection of respiratory viruses in primary cholesteatoma tissues. J Med Virol 2021; 93:6132-6139. [PMID: 34050944 DOI: 10.1002/jmv.27107] [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: 03/25/2021] [Revised: 05/17/2021] [Accepted: 05/24/2021] [Indexed: 11/08/2022]
Abstract
Cholesteatomas are frequent middle ear benign tumors of unknown etiology. Infectious agents have been considered as possible contributing factors in the pathogenesis of cholesteatomas. Aiming to investigate the presence of respiratory viruses in primary cholesteatoma tissues, 26 formalin-fixed paraffin-embedded primary cholesteatoma tissues obtained from patients seen at the of the Clinical Hospital of the University of São Paulo School of Medicine, in Ribeirão Preto, Brazil were tested by real-time polymerase chain reaction (PCR). Considering the PCR results, 35% of the tissues were positive for human rhinovirus (HRV), 15.3% for human enterovirus (EV), 3.8% for human metapneumovirus (HMPV), and 3.8% for human bocavirus (HBoV). Serial immunohistochemistry for virus antigens and cell surface markers evidenced that the viruses were associated with fibroblasts, dendritic cells, macrophages, B lymphocytes, CD4+ , and CD8+ T lymphocytes. These findings indicate for the first time the presence of active respiratory virus infection in primary cholesteatoma tissues, suggesting that persisting virus infection in the middle could play a role in the pathogenesis and evolution of cholesteatomas.
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Affiliation(s)
- Rosa M M Viana
- Department of Ophthalmology, Otorhinolaryngology, and Head and Neck Surgery, Ribeirão Preto School of Medicine, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil.,Department of Molecular and Cell Biology, Ribeirão Preto School of Medicine, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Juliano P Souza
- Department of Molecular and Cell Biology, Ribeirão Preto School of Medicine, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Daniel M M Jorge
- Department of Molecular and Cell Biology, Ribeirão Preto School of Medicine, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Ronaldo B Martins
- Department of Molecular and Cell Biology, Ribeirão Preto School of Medicine, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Italo A Castro
- Department of Molecular and Cell Biology, Ribeirão Preto School of Medicine, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Ricardo S Cardoso
- Department of Molecular and Cell Biology, Ribeirão Preto School of Medicine, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Lays P B Volpini
- Post-Graduate Program in infectious Diseases, Federal University of Espírito Santo, Vitória, Brazil
| | - Luciano K de Souza Luna
- Medicine Department, Clinical Virology Laboratory, Infectious Diseases Unit, São Paulo Federal University, São Paulo, Brazil
| | - Liliana C Spano
- Post-Graduate Program in infectious Diseases, Federal University of Espírito Santo, Vitória, Brazil.,Departament of Pathology, Center of Health Sciences, Federal University of Espírito Santo, Vitória, Brazil
| | - Nancy C J Bellei
- Medicine Department, Clinical Virology Laboratory, Infectious Diseases Unit, São Paulo Federal University, São Paulo, Brazil
| | - Fernando Chahud
- Department of Pathology and Forensic Medicine, Ribeirão Preto School of Medicine, University of São Paulo (USP), São Paulo, Brazil
| | - Eurico Arruda
- Department of Molecular and Cell Biology, Ribeirão Preto School of Medicine, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Miguel A Hyppolito
- Department of Ophthalmology, Otorhinolaryngology, and Head and Neck Surgery, Ribeirão Preto School of Medicine, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
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44
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Willemsen M, Krebbers G, Bekkenk MW, Teunissen MB, Luiten RM. Improvement of Opal Multiplex Immunofluorescence Workflow for Human Tissue Sections. J Histochem Cytochem 2021; 69:339-346. [PMID: 33797290 PMCID: PMC8091416 DOI: 10.1369/00221554211007793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/17/2021] [Indexed: 01/27/2023] Open
Abstract
The Opal multiplex technique is an established methodology for the detection of multiple biomarkers in one section. The protocol encompasses iterative single stainings and heating-mediated removal of the primary and secondary antibodies after each staining round, leaving untouched the Opal fluorophores which are deposited onto the antigen of interest. According to our experience, repetitive heating of skin sections often results in tissue damage, indicating an urgent need for milder alternatives to strip immunoglobulins. In this study, we demonstrate that considerable heating-related damage was found not only in skin but also in tissues of different origin, mostly characterized by low cell density. Importantly, the morphology remained fully intact when sections were repetitively exposed to β-mercaptoethanol-containing stripping buffer instead of multiple heating cycles. However, target epitopes appeared sensitive at a differential degree to multiple treatments with stripping buffer, as shown by loss in staining intensity, but in all cases, the staining intensity could be restored by increment of the primary antibody concentrations. Application of β-mercaptoethanol-containing stripping buffer instead of heating for antibody removal markedly improved the quality of the Opal multiplex technique, as a substantial higher number of differently colored cells could be visualized within a well-conserved morphological context.
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Affiliation(s)
- Marcella Willemsen
- Department of Dermatology, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Institute for Pigment Disorders, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gabrielle Krebbers
- Department of Dermatology, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Institute for Pigment Disorders, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marcel W. Bekkenk
- Department of Dermatology, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Institute for Pigment Disorders, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marcel B.M. Teunissen
- Department of Dermatology, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Rosalie M. Luiten
- Department of Dermatology, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Institute for Pigment Disorders, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
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45
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Mungenast F, Fernando A, Nica R, Boghiu B, Lungu B, Batra J, Ecker RC. Next-Generation Digital Histopathology of the Tumor Microenvironment. Genes (Basel) 2021; 12:538. [PMID: 33917241 PMCID: PMC8068063 DOI: 10.3390/genes12040538] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/11/2022] Open
Abstract
Progress in cancer research is substantially dependent on innovative technologies that permit a concerted analysis of the tumor microenvironment and the cellular phenotypes resulting from somatic mutations and post-translational modifications. In view of a large number of genes, multiplied by differential splicing as well as post-translational protein modifications, the ability to identify and quantify the actual phenotypes of individual cell populations in situ, i.e., in their tissue environment, has become a prerequisite for understanding tumorigenesis and cancer progression. The need for quantitative analyses has led to a renaissance of optical instruments and imaging techniques. With the emergence of precision medicine, automated analysis of a constantly increasing number of cellular markers and their measurement in spatial context have become increasingly necessary to understand the molecular mechanisms that lead to different pathways of disease progression in individual patients. In this review, we summarize the joint effort that academia and industry have undertaken to establish methods and protocols for molecular profiling and immunophenotyping of cancer tissues for next-generation digital histopathology-which is characterized by the use of whole-slide imaging (brightfield, widefield fluorescence, confocal, multispectral, and/or multiplexing technologies) combined with state-of-the-art image cytometry and advanced methods for machine and deep learning.
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Affiliation(s)
- Felicitas Mungenast
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria
- TissueGnostics GmbH, 1020 Vienna, Austria;
| | - Achala Fernando
- Translational Research Institute, 37 Kent Street, Woolloongabba, QLD 4102, Australia; (A.F.); (J.B.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
| | | | - Bogdan Boghiu
- TissueGnostics SRL, 700028 Iasi, Romania; (B.B.); (B.L.)
| | - Bianca Lungu
- TissueGnostics SRL, 700028 Iasi, Romania; (B.B.); (B.L.)
| | - Jyotsna Batra
- Translational Research Institute, 37 Kent Street, Woolloongabba, QLD 4102, Australia; (A.F.); (J.B.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
| | - Rupert C. Ecker
- TissueGnostics GmbH, 1020 Vienna, Austria;
- Translational Research Institute, 37 Kent Street, Woolloongabba, QLD 4102, Australia; (A.F.); (J.B.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
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46
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Chandrasekaran SN, Ceulemans H, Boyd JD, Carpenter AE. Image-based profiling for drug discovery: due for a machine-learning upgrade? Nat Rev Drug Discov 2021; 20:145-159. [PMID: 33353986 PMCID: PMC7754181 DOI: 10.1038/s41573-020-00117-w] [Citation(s) in RCA: 151] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2020] [Indexed: 12/20/2022]
Abstract
Image-based profiling is a maturing strategy by which the rich information present in biological images is reduced to a multidimensional profile, a collection of extracted image-based features. These profiles can be mined for relevant patterns, revealing unexpected biological activity that is useful for many steps in the drug discovery process. Such applications include identifying disease-associated screenable phenotypes, understanding disease mechanisms and predicting a drug's activity, toxicity or mechanism of action. Several of these applications have been recently validated and have moved into production mode within academia and the pharmaceutical industry. Some of these have yielded disappointing results in practice but are now of renewed interest due to improved machine-learning strategies that better leverage image-based information. Although challenges remain, novel computational technologies such as deep learning and single-cell methods that better capture the biological information in images hold promise for accelerating drug discovery.
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Affiliation(s)
| | - Hugo Ceulemans
- Discovery Data Sciences, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Justin D Boyd
- High Content Imaging Technology Center, Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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47
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Meneveau MO, Sahli ZT, Lynch KT, Mauldin IS, Slingluff CL. Immunotyping and Quantification of Melanoma Tumor-Infiltrating Lymphocytes. Methods Mol Biol 2021; 2265:515-528. [PMID: 33704737 DOI: 10.1007/978-1-0716-1205-7_36] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The density of tumour-infiltrating lymphocytes (TILs) in melanoma is correlated with improved clinical prognosis; however, standardized TIL immunotyping and quantification protocols are lacking. Herein, we provide a review of the technologies being utilized for the immunotyping and quantification of melanoma TILs.
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Affiliation(s)
- Max O Meneveau
- Department of Surgery, The University of Virginia Health System, Charlottesville, VA, USA
| | - Zeyad T Sahli
- Department of Surgery, The University of Virginia Health System, Charlottesville, VA, USA
| | - Kevin T Lynch
- Department of Surgery, The University of Virginia Health System, Charlottesville, VA, USA
| | - Ileana S Mauldin
- Department of Surgery, The University of Virginia Health System, Charlottesville, VA, USA
| | - Craig L Slingluff
- Department of Surgery, The University of Virginia Health System, Charlottesville, VA, USA.
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48
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Paulsen JD, Zeck B, Sun K, Simoes C, Theise ND, Chiriboga L. Keratin 19 and mesenchymal markers for evaluation of epithelial-mesenchymal transition and stem cell niche components in primary biliary cholangitis by sequential elution-stripping multiplex immunohistochemistry. J Histotechnol 2020; 43:163-173. [PMID: 32998669 DOI: 10.1080/01478885.2020.1807228] [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: 10/23/2022]
Abstract
Multiplexed immunohistochemical techniques give insight into contextual cellular relationships by offering the ability to collect cell-specific data with spatial information from formalin-fixed, paraffin-embedded tissue sections. We established an automated sequential elution-stripping multiplex immunohistochemical assay to address two controversial scientific questions in the field of hepatopathology: 1) whether epithelial-to-mesenchymal transition or mesenchymal-to-epithelial transition occurs during liver injury and repair of a chronic liver disease and 2) if there is a stromal:epithelial relationship along the canals of Hering that would support the concept of this biliary structure being a stem/progenitor cell niche. Our 4-plex assay includes both epithelial and mesenchymal clinical immunohistochemical markers and was performed on clinical human liver specimens in patients with primary biliary cholangitis. The assay demonstrated that in each specimen, co-expression of epithelial and mesenchymal markers was observed in extraportal cholangiocytes. In regard to possible mesenchymal components in a stem cell niche, 82.3% ± 5.5% of extraportal cholangiocytes were intimately associated with a vimentin-positive cell. Co-expression of epithelial and mesenchymal markers by extraportal cholangiocytes is evidence for epithelial to mesenchymal transition in primary biliary cholangitis. Vimentin-positive stromal cells are frequently juxtaposed to extraportal cholangiocytes, supporting an epithelial:mesenchymal relationship within the hepatobiliary stem cell niche. Our automated sequential elution-stripping multiplex immunohistochemical assay is a cost-effective multiplexing technique that can be readily applied to a small series of clinical pathology samples in order to answer scientific questions involving cell:cell relationships and cellular antibody expression.
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Affiliation(s)
- John David Paulsen
- Department of Pathology, NYU Langone Health , New York, USA.,Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai/The Mount Sinai Hospital , New York, USA
| | - Briana Zeck
- NYU Langone Health, Center for Biospecimen Research and Development , New York, USA
| | - Katherine Sun
- Department of Pathology, NYU Langone Health , New York, USA
| | - Camila Simoes
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai/The Mount Sinai Hospital , New York, USA
| | - Neil D Theise
- Department of Pathology, NYU Langone Health , New York, USA
| | - Luis Chiriboga
- Department of Pathology, NYU Langone Health , New York, USA.,NYU Langone Health, Center for Biospecimen Research and Development , New York, USA
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49
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Roy-Luzarraga M, Abdel-Fatah T, Reynolds LE, Clear A, Taylor JG, Gribben JG, Chan S, Jones L, Hodivala-Dilke K. Association of Low Tumor Endothelial Cell pY397-Focal Adhesion Kinase Expression With Survival in Patients With Neoadjuvant-Treated Locally Advanced Breast Cancer. JAMA Netw Open 2020; 3:e2019304. [PMID: 33107920 PMCID: PMC7592032 DOI: 10.1001/jamanetworkopen.2020.19304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
IMPORTANCE Determining the risk of relapse after neoadjuvant chemotherapy in patients with locally advanced breast cancer is required to offer alternative therapeutic strategies. OBJECTIVE To examine whether endothelial cell phosphorylated-focal adhesion kinase (EC-pY397-FAK) expression in patients with treatment-naive locally advanced breast cancer is a biomarker for chemotherapy sensitivity and is associated with survival after neoadjuvant chemotherapy. DESIGN, SETTING, AND PARTICIPANTS In this prognostic study, expression levels of EC-pY397-FAK and tumor cell (TC)-pY397-FAK were determined by immunohistochemistry in prechemotherapy core biopsies from 82 female patients with locally advanced breast cancer treated with anthracycline-based combination neoadjuvant chemotherapy at Nottingham City Hospital in Nottingham, UK. Median follow-up time was 67 months. The study was conducted from December 1, 2010, to September 28, 2019, and data analysis was performed from October 2, 2019, to March 31, 2020. EXPOSURES All women underwent surgery followed by adjuvant radiotherapy and, if tumors were estrogen receptor-positive, 5-year tamoxifen treatment. MAIN OUTCOMES AND MEASURES Outcomes were pathologic complete response and 5-year relapse-free survival examined using Kaplan-Meier, univariable logistic, multivariable logistic, and Cox proportional hazards models. RESULTS A total of 82 women (age, 29-76 years) with locally advanced breast cancer (stage IIA-IIIC) were included. Of these, 21 women (26%) had high EC-pY397-FAK expression that was associated with estrogen receptor positivity (71% vs 46%; P = .04), progesterone receptor positivity (67% vs 39%; P = .03), high Ki67 (86% vs 41%; P < .001), 4-immunohistochemically stained luminal-B (52% vs 8%; P < .001), higher tumor category (T3/T4 category: 90% vs 59%; P = .01), high lymph node category (N2-3 category: 43% vs 5%; P < .001), and high tumor node metastasis stage (IIIA-IIIC: 90% vs 66%; P = .03). Of 21 patients with high EC-pY397-FAK expression levels, none showed pathologic complete response, compared with 11 of 61 patients with low EC-pY397-FAK expression levels who showed pathologic complete response (odds ratio, 0.70; 95% CI, 0.61-0.82; P = .04). High EC-pY397-FAK expression levels and high blood vessel density (BVD) were associated with shorter 5-year relapse-free survival compared with those with low EC-pY397-FAK expression levels (hazard ratio [HR], 2.21; 95% CI, 1.17-4.20; P = .01) and low BVD (HR, 2.2; 95% CI, 1.15-4.35; P = .02). High TC-pY397-FAK expression levels in 15 of 82 women (18%) were not associated significantly with pathologic complete response or 5-year relapse-free survival. A multivariable Cox regression model for 5-year relapse-free survival indicated that high EC-pY397-FAK expression levels was an independent poor prognostic factor after controlling for other validated prognostic factors (HR, 3.91; 95% CI, 1.42-10.74; P = .01). Combined analysis of EC-pY397-FAK expression levels, TC-pY397-FAK expression levels, and BVD improved prognostic significance over individually tested features. CONCLUSIONS AND RELEVANCE The findings of this study suggest that low EC-pY397-FAK expression levels are associated with chemotherapy sensitivity and improved 5-year relapse-free survival after systemic therapy. Combined analysis of high EC-pY397-FAK expression levels, high TC-pY397-FAK expression levels, and high BVD appeared to identify a high-risk population.
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Affiliation(s)
- Marina Roy-Luzarraga
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, United Kingdom
| | - Tarek Abdel-Fatah
- Department of Clinical Oncology, University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Pathology Department, National Liver Institute, Minoufyia University, Al Minufiyah, Egypt
| | - Louise E. Reynolds
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, United Kingdom
| | - Andrew Clear
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, United Kingdom
| | - Joseph G. Taylor
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, United Kingdom
| | - John G. Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, United Kingdom
| | - Stephen Chan
- Department of Clinical Oncology, University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Louise Jones
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, United Kingdom
| | - Kairbaan Hodivala-Dilke
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, United Kingdom
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Pontelli MC, Castro IA, Martins RB, Veras FP, Serra LL, Nascimento DC, Cardoso RS, Rosales R, Lima TM, Souza JP, Caetité DB, de Lima MHF, Kawahisa JT, Giannini MC, Bonjorno LP, Lopes MIF, Batah SS, Siyuan L, Assad RL, Almeida SCL, Oliveira FR, Benatti MN, Pontes LLF, Santana RC, Vilar FC, Martins MA, Cunha TM, Calado RT, Alves-Filho JC, Zamboni DS, Fabro A, Louzada-Junior P, Oliveira RDR, Cunha FQ, Arruda E. Infection of human lymphomononuclear cells by SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 34013264 PMCID: PMC8132220 DOI: 10.1101/2020.07.28.225912] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although SARS-CoV-2 severe infection is associated with a hyperinflammatory state, lymphopenia is an immunological hallmark, and correlates with poor prognosis in COVID-19. However, it remains unknown if circulating human lymphocytes and monocytes are susceptible to SARS-CoV-2 infection. In this study, SARS-CoV-2 infection of human peripheral blood mononuclear cells (PBMCs) was investigated both in vitro and in vivo . We found that in vitro infection of whole PBMCs from healthy donors was productive of virus progeny. Results revealed that monocytes, as well as B and T lymphocytes, are susceptible to SARS-CoV-2 active infection and viral replication was indicated by detection of double-stranded RNA. Moreover, flow cytometry and immunofluorescence analysis revealed that SARS-CoV-2 was frequently detected in monocytes and B lymphocytes from COVID-19 patients, and less frequently in CD4 + T lymphocytes. The rates of SARS-CoV-2-infected monocytes in PBMCs from COVID-19 patients increased over time from symptom onset. Additionally, SARS-CoV-2-positive monocytes and B and CD4+T lymphocytes were detected by immunohistochemistry in post mortem lung tissue. SARS-CoV-2 infection of blood circulating leukocytes in COVID-19 patients may have important implications for disease pathogenesis, immune dysfunction, and virus spread within the host.
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