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Magness A, Colliver E, Enfield KSS, Lee C, Shimato M, Daly E, Moore DA, Sivakumar M, Valand K, Levi D, Hiley CT, Hobson PS, van Maldegem F, Reading JL, Quezada SA, Downward J, Sahai E, Swanton C, Angelova M. Deep cell phenotyping and spatial analysis of multiplexed imaging with TRACERx-PHLEX. Nat Commun 2024; 15:5135. [PMID: 38879602 PMCID: PMC11180132 DOI: 10.1038/s41467-024-48870-5] [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: 10/11/2023] [Accepted: 05/16/2024] [Indexed: 06/19/2024] Open
Abstract
The growing scale and dimensionality of multiplexed imaging require reproducible and comprehensive yet user-friendly computational pipelines. TRACERx-PHLEX performs deep learning-based cell segmentation (deep-imcyto), automated cell-type annotation (TYPEx) and interpretable spatial analysis (Spatial-PHLEX) as three independent but interoperable modules. PHLEX generates single-cell identities, cell densities within tissue compartments, marker positivity calls and spatial metrics such as cellular barrier scores, along with summary graphs and spatial visualisations. PHLEX was developed using imaging mass cytometry (IMC) in the TRACERx study, validated using published Co-detection by indexing (CODEX), IMC and orthogonal data and benchmarked against state-of-the-art approaches. We evaluated its use on different tissue types, tissue fixation conditions, image sizes and antibody panels. As PHLEX is an automated and containerised Nextflow pipeline, manual assessment, programming skills or pathology expertise are not essential. PHLEX offers an end-to-end solution in a growing field of highly multiplexed data and provides clinically relevant insights.
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Grants
- RF\ERE\231118 Royal Society
- C416/A21999 Cancer Research UK (CRUK)
- CC2041 Wellcome Trust
- CC2041 Arthritis Research UK
- 838540 EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- RF\ERE\210216 Royal Society
- CC2040 Arthritis Research UK
- Wellcome Trust
- 101079113 EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- Francis Crick Institute (Francis Crick Institute Limited)
- Wellcome Trust (Wellcome)
- The TRACERx study (Clinicaltrials.gov no: NCT01888601) is sponsored by University College London (UCL/12/0279) and has been approved by an independent Research Ethics Committee (13/LO/1546). TRACERx is funded by Cancer Research UK (C11496/A17786) and coordinated through the Cancer Research UK and UCL Cancer Trials Centre which has a core grant from CRUK (C444/A15953). We gratefully acknowledge the patients and relatives who participated in TRACERx and PEACE studies. We thank all site personnel, investigators, funders and industry partners that supported the generation of the data within this study. This work was supported by the Francis Crick Institute that receives its core funding from Cancer Research UK (CC2041), the UK Medical Research Council (CC2041), and the Wellcome Trust (CC2041). This work was also supported by the Cancer Research UK Lung Cancer Centre of Excellence and the CRUK City of London Centre Award (C7893/A26233) as well as the UCL Experimental Cancer Medicine Centre. This work was supported by funding as part of a research collaboration with Bristol Myers Squibb. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 101018670). For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. C.S. is a Royal Society Napier Research Professor (RSRP\R\210001). His work is supported by the Francis Crick Institute that receives its core funding from Cancer Research UK (CC2041), the UK Medical Research Council (CC2041), and the Wellcome Trust (CC2041). C.S. is funded by Cancer Research UK (TRACERx (C11496/A17786), PEACE (C416/A21999) and CRUK Cancer Immunotherapy Catalyst Network); Cancer Research UK Lung Cancer Centre of Excellence (C11496/A30025); the Rosetrees Trust, Butterfield and Stoneygate Trusts; NovoNordisk Foundation (ID16584); Royal Society Professorship Enhancement Award (RP/EA/180007 & RF\ERE\231118)); National Institute for Health Research (NIHR) University College London Hospitals Biomedical Research Centre; the Cancer Research UK-University College London Centre; Experimental Cancer Medicine Centre; the Breast Cancer Research Foundation (US; BCRF-22-157); Cancer Research UK Early Detection and Diagnosis Primer Award (Grant EDDPMA-Nov21/100034); and The Mark Foundation for Cancer Research Aspire Award (Grant 21-029-ASP) and ASPIRE II award (23-034-ASP). This work was supported by a Stand Up To Cancer‐LUNGevity-American Lung Association Lung Cancer Interception Dream Team Translational Research Grant (Grant Number: SU2C-AACR-DT23-17 to S.M. Dubinett and A.E. Spira). The indicated Stand Up To Cancer grant is administered by the American Association for Cancer Research, the Scientific Partner of SU2C. C.S. is in receipt of an ERC Advanced Grant (PROTEUS) from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 835297).
- K.S.S.E was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 838540 and is supported by the Royal Society (RF\ERE\210216).
- F.vM. is recipient of the Amsterdam UMC fellowship and receives funding from the European Research Council under the European Union’s Horizon Europe WIDERA work programme (grant agreement No. 101079113).
- E.S. was partly funded by The Mark Foundation for Cancer Research (MFCR ASPIRE 2022- 0384). E.S. is additionally supported by the European Research Council (ERC Advanced Grant CAN_ORGANISE, Grant agreement number 101019366) and the Francis Crick Institute which receives its core funding from Cancer Research UK (CC2040), the UK Medical Research Council (CC2040), and the Wellcome Trust (CC2040).
- M.A. was supported by a fellowship from The Mark Foundation for Cancer Research.
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Affiliation(s)
- Alastair Magness
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Katey S S Enfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Claudia Lee
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Masako Shimato
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emer Daly
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Monica Sivakumar
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Karishma Valand
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Dina Levi
- Flow Cytometry, The Francis Crick Institute, London, UK
| | - Crispin T Hiley
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Febe van Maldegem
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
| | - James L Reading
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Pre-cancer Immunology Laboratory, University College London Cancer Institute, London, UK
- Immune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research, Department of Haematology, University College London Cancer Institute, London, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Immune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research, Department of Haematology, University College London Cancer Institute, London, UK
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Erik Sahai
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
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Beber SA, Moshkelgosha S, White M, Zehong G, Cheung M, Hedley D, Levy L, Samuels J, Renaud-Picard B, Hwang D, Martinu T, Juvet S. The CD8 + T cell content of transbronchial biopsies from patients with a first episode of clinically stable grade A1 cellular rejection is associated with future chronic lung allograft dysfunction. J Heart Lung Transplant 2024:S1053-2498(24)01694-2. [PMID: 38852935 DOI: 10.1016/j.healun.2024.06.001] [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: 01/16/2024] [Revised: 04/05/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND T cells drive acute cellular rejection (ACR) and its progression to chronic lung allograft dysfunction (CLAD) following lung transplantation. International Society for Heart and Lung Transplantation grade A1 ACR without associated allograft dysfunction is often untreated, yet some patients develop progressive graft dysfunction. T-cell composition of A1 ACR lesions may have prognostic value; therefore, protein-level and epigenetic techniques were applied to transbronchial biopsy tissue to determine whether differential T-cell infiltration in recipients experiencing a first episode of stable grade A1 ACR (StA1R) is associated with early CLAD. METHODS Sixty-two patients experiencing a first episode of StA1R were divided into those experiencing CLAD within 2 years (n = 13) and those remaining CLAD-free for 5 or more years (n = 49). Imaging mass cytometry (IMC) was used to profile the spectrum and distribution of intragraft T cell phenotypes on a subcohort (n = 16; 8 early-CLAD and 8 no early-CLAD). Immunofluorescence was used to quantify CD4+, CD8+, and FOXP3+ cells. Separately, CD3+ cells were fluorescently labeled, micro-dissected, and the degree of Treg-specific demethylated region methylation was determined. RESULTS PhenoGraph unsupervised clustering on IMC revealed 50 unique immune cell subpopulations. Methylation and immunofluorescence analyses demonstrated no significant differences in Tregs between early-CLAD and no early-CLAD groups. Immunofluorescence revealed that patients who developed CLAD within 2 years of lung transplantation showed greater CD8+ T cell infiltration compared to those who remained CLAD-free for 5 or more years. CONCLUSIONS In asymptomatic patients with a first episode of A1 rejection, greater CD8+ T cell content may be indicative of worse long-term outlook.
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Affiliation(s)
- Samuel A Beber
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Medicine, New York Medical College, Valhalla, New York
| | - Sajad Moshkelgosha
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Matthew White
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Guan Zehong
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - May Cheung
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - David Hedley
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Liran Levy
- Department of Medicine, Sheba Medical Center, Tel-Aviv University, Tel Aviv, Israel
| | - Joel Samuels
- Department of Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | | | - David Hwang
- Department of Pathology, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Tereza Martinu
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada; Ajmera Transplant Center, Toronto Lung Transplant Program, Toronto, Ontario, Canada; Division of Respirology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Stephen Juvet
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada; Ajmera Transplant Center, Toronto Lung Transplant Program, Toronto, Ontario, Canada; Division of Respirology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
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3
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Enfield KS, Colliver E, Lee C, Magness A, Moore DA, Sivakumar M, Grigoriadis K, Pich O, Karasaki T, Hobson PS, Levi D, Veeriah S, Puttick C, Nye EL, Green M, Dijkstra KK, Shimato M, Akarca AU, Marafioti T, Salgado R, Hackshaw A, Jamal-Hanjani M, van Maldegem F, McGranahan N, Glass B, Pulaski H, Walk E, Reading JL, Quezada SA, Hiley CT, Downward J, Sahai E, Swanton C, Angelova M. Spatial Architecture of Myeloid and T Cells Orchestrates Immune Evasion and Clinical Outcome in Lung Cancer. Cancer Discov 2024; 14:1018-1047. [PMID: 38581685 PMCID: PMC11145179 DOI: 10.1158/2159-8290.cd-23-1380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/27/2024] [Accepted: 03/22/2024] [Indexed: 04/08/2024]
Abstract
Understanding the role of the tumor microenvironment (TME) in lung cancer is critical to improving patient outcomes. We identified four histology-independent archetype TMEs in treatment-naïve early-stage lung cancer using imaging mass cytometry in the TRACERx study (n = 81 patients/198 samples/2.3 million cells). In immune-hot adenocarcinomas, spatial niches of T cells and macrophages increased with clonal neoantigen burden, whereas such an increase was observed for niches of plasma and B cells in immune-excluded squamous cell carcinomas (LUSC). Immune-low TMEs were associated with fibroblast barriers to immune infiltration. The fourth archetype, characterized by sparse lymphocytes and high tumor-associated neutrophil (TAN) infiltration, had tumor cells spatially separated from vasculature and exhibited low spatial intratumor heterogeneity. TAN-high LUSC had frequent PIK3CA mutations. TAN-high tumors harbored recently expanded and metastasis-seeding subclones and had a shorter disease-free survival independent of stage. These findings delineate genomic, immune, and physical barriers to immune surveillance and implicate neutrophil-rich TMEs in metastasis. SIGNIFICANCE This study provides novel insights into the spatial organization of the lung cancer TME in the context of tumor immunogenicity, tumor heterogeneity, and cancer evolution. Pairing the tumor evolutionary history with the spatially resolved TME suggests mechanistic hypotheses for tumor progression and metastasis with implications for patient outcome and treatment. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Katey S.S. Enfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Claudia Lee
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Alastair Magness
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - David A. Moore
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Monica Sivakumar
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Kristiana Grigoriadis
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Takahiro Karasaki
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Philip S. Hobson
- Flow Cytometry, The Francis Crick Institute, London, United Kingdom
| | - Dina Levi
- Flow Cytometry, The Francis Crick Institute, London, United Kingdom
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Clare Puttick
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Emma L. Nye
- Experimental Histopathology, The Francis Crick Institute, London, United Kingdom
| | - Mary Green
- Experimental Histopathology, The Francis Crick Institute, London, United Kingdom
| | - Krijn K. Dijkstra
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Masako Shimato
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ayse U. Akarca
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Allan Hackshaw
- Cancer Research UK and University College London Cancer Trials Centre, London, United Kingdom
| | | | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, United Kingdom
- Department of Oncology, University College London Hospitals, London, United Kingdom
| | - Febe van Maldegem
- Oncogene Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | | | | | | | - James L. Reading
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Pre-cancer Immunology Laboratory, University College London Cancer Institute, London, United Kingdom
- Immune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Sergio A. Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Immune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Crispin T. Hiley
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Erik Sahai
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Department of Oncology, University College London Hospitals, London, United Kingdom
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
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4
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Walsh LA, Quail DF. Decoding the tumor microenvironment with spatial technologies. Nat Immunol 2023; 24:1982-1993. [PMID: 38012408 DOI: 10.1038/s41590-023-01678-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/10/2023] [Indexed: 11/29/2023]
Abstract
Visualization of the cellular heterogeneity and spatial architecture of the tumor microenvironment (TME) is becoming increasingly important to understand mechanisms of disease progression and therapeutic response. This is particularly relevant in the era of cancer immunotherapy, in which the contexture of immune cell positioning within the tumor landscape has been proven to affect efficacy. Although single-cell technologies have mostly replaced conventional approaches to analyze specific cellular subsets within tumors, those that integrate a spatial dimension are now on the rise. In this Review, we assess the strengths and limitations of emerging spatial technologies with a focus on their applications in tumor immunology, as well as forthcoming opportunities for artificial intelligence (AI) and the value of integrating multiomics datasets to achieve a holistic picture of the TME.
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Affiliation(s)
- Logan A Walsh
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada.
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
| | - Daniela F Quail
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada.
- Department of Physiology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.
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5
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Marlin MC, Stephens T, Wright C, Smith M, Wright K, Guthridge JM. A novel process for H&E, immunofluorescence, and imaging mass cytometry on a single slide with a concise analytics pipeline. Cytometry A 2023; 103:1010-1018. [PMID: 37724720 DOI: 10.1002/cyto.a.24789] [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: 02/07/2023] [Revised: 08/04/2023] [Accepted: 08/24/2023] [Indexed: 09/21/2023]
Abstract
Imaging mass cytometry (IMC) is a powerful spatial technology that utilizes cytometry time of flight to acquire multiplexed image datasets with up to 40 markers, via metal-tagged antibodies. Recent advances in IMC have led to the inclusion of RNAScope probes and multiple new analysis pipelines have led to faster analyses and better results. However, IMC still suffers from lower resolution (1 μm2 pixels) and relatively small regions of interest (ROIs) (<2 mm2 ) compared to other, light-based microscope technologies. Capturing higher-resolution images on serial sections causes great difficulty when attempting to align cells and structures across serial sections, especially when observing smaller cell types and structures. Therefore, we demonstrate the combination of H&E and multiplex immunofluorescence imaging, for much higher resolution of the structural and cellular compartments found throughout the entire tissue section, with the high-dimensionality of IMC for specific ROIs on a single slide. Additionally, we demonstrate a simple and effective open-source cell segmentation and IMC analysis pipeline with previously published and freely available software.
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Affiliation(s)
- M Caleb Marlin
- Arthritis & Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Tayte Stephens
- Arthritis & Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Christian Wright
- Arthritis & Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Miles Smith
- Arthritis & Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kyle Wright
- Department of Surgery, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Joel M Guthridge
- Arthritis & Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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6
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Windhager J, Zanotelli VRT, Schulz D, Meyer L, Daniel M, Bodenmiller B, Eling N. An end-to-end workflow for multiplexed image processing and analysis. Nat Protoc 2023; 18:3565-3613. [PMID: 37816904 DOI: 10.1038/s41596-023-00881-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/23/2023] [Indexed: 10/12/2023]
Abstract
Multiplexed imaging enables the simultaneous spatial profiling of dozens of biological molecules in tissues at single-cell resolution. Extracting biologically relevant information, such as the spatial distribution of cell phenotypes from multiplexed tissue imaging data, involves a number of computational tasks, including image segmentation, feature extraction and spatially resolved single-cell analysis. Here, we present an end-to-end workflow for multiplexed tissue image processing and analysis that integrates previously developed computational tools to enable these tasks in a user-friendly and customizable fashion. For data quality assessment, we highlight the utility of napari-imc for interactively inspecting raw imaging data and the cytomapper R/Bioconductor package for image visualization in R. Raw data preprocessing, image segmentation and feature extraction are performed using the steinbock toolkit. We showcase two alternative approaches for segmenting cells on the basis of supervised pixel classification and pretrained deep learning models. The extracted single-cell data are then read, processed and analyzed in R. The protocol describes the use of community-established data containers, facilitating the application of R/Bioconductor packages for dimensionality reduction, single-cell visualization and phenotyping. We provide instructions for performing spatially resolved single-cell analysis, including community analysis, cellular neighborhood detection and cell-cell interaction testing using the imcRtools R/Bioconductor package. The workflow has been previously applied to imaging mass cytometry data, but can be easily adapted to other highly multiplexed imaging technologies. This protocol can be implemented by researchers with basic bioinformatics training, and the analysis of the provided dataset can be completed within 5-6 h. An extended version is available at https://bodenmillergroup.github.io/IMCDataAnalysis/ .
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Affiliation(s)
- Jonas Windhager
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland
- SciLifeLab BioImage Informatics Facility and Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Vito Riccardo Tomaso Zanotelli
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel Schulz
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Lasse Meyer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Michelle Daniel
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
- Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
| | - Nils Eling
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
- Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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7
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Akbari B, Huber BR, Sherman JH. Unlocking the Hidden Depths: Multi-Modal Integration of Imaging Mass Spectrometry-Based and Molecular Imaging Techniques. Crit Rev Anal Chem 2023:1-30. [PMID: 37847593 DOI: 10.1080/10408347.2023.2266838] [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: 10/19/2023]
Abstract
Multimodal imaging (MMI) has emerged as a powerful tool in clinical research, combining different imaging modes to acquire comprehensive information and enabling scientists and surgeons to study tissue identification, localization, metabolic activity, and molecular discovery, thus aiding in disease progression analysis. While multimodal instruments are gaining popularity, challenges such as non-standardized characteristics, custom software, inadequate commercial support, and integration issues with other instruments need to be addressed. The field of multimodal imaging or multiplexed imaging allows for simultaneous signal reproduction from multiple imaging strategies. Intraoperatively, MMI can be integrated into frameless stereotactic surgery. Recent developments in medical imaging modalities such as magnetic resonance imaging (MRI), and Positron Emission Topography (PET) have brought new perspectives to multimodal imaging, enabling early cancer detection, molecular tracking, and real-time progression monitoring. Despite the evidence supporting the role of MMI in surgical decision-making, there is a need for comprehensive studies to validate and perform integration at the intersection of multiple imaging technologies. They were integrating mass spectrometry-based technologies (e.g., imaging mass spectrometry (IMS), imaging mass cytometry (IMC), and Ion mobility mass spectrometry ((IM-IM) with medical imaging modalities, offering promising avenues for molecular discovery and clinical applications. This review emphasizes the potential of multi-omics approaches in tissue mapping using MMI integrated into desorption electrospray ionization (DESI) and matrix-assisted laser desorption ionization (MALDI), allowing for sequential analyses of the same section. By addressing existing knowledge gaps, this review encourages future research endeavors toward multi-omics approaches, providing a roadmap for future research and enhancing the value of MMI in molecular pathology for diagnosis.
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Affiliation(s)
- Behnaz Akbari
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Bertrand Russell Huber
- Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
- Boston University Alzheimer's Disease and CTE Center, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
- US Department of Veteran Affairs, VA Boston Healthcare System, Boston, Massachusetts USA
- US Department of Veterans Affairs, National Center for PTSD, Boston, Massachusetts USA
| | - Janet Hope Sherman
- Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
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8
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Welter L, Zheng S, Setayesh SM, Morikado M, Agrawal A, Nevarez R, Naghdloo A, Pore M, Higa N, Kolatkar A, Thiele JA, Sharma P, Moore HCF, Richer JK, Elias A, Pienta KJ, Zurita AJ, Gross ME, Shishido SN, Hicks J, Velasco CR, Kuhn P. Cell State and Cell Type: Deconvoluting Circulating Tumor Cell Populations in Liquid Biopsies by Multi-Omics. Cancers (Basel) 2023; 15:3949. [PMID: 37568766 PMCID: PMC10417732 DOI: 10.3390/cancers15153949] [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: 06/13/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Bi-directional crosstalk between the tumor and the tumor microenvironment (TME) has been shown to increase the rate of tumor evolution and to play a key role in neoplastic progression, therapeutic resistance, and a patient's overall survival. Here, we set out to use a comprehensive liquid-biopsy analysis to study cancer and specific TME cells in circulation and their association with disease status. Cytokeratin+, CD45- circulating rare cells (CRCs) from nine breast and four prostate cancer patients were characterized through morphometrics, single-cell copy number analysis, and targeted multiplexed proteomics to delineate cancer cell lineage from other rare cells originating in the TME. We show that we can detect epithelial circulating tumor cells (EPI.CTC), CTCs undergoing epithelial-to-mesenchymal transition (EMT.CTC) and circulating endothelial cells (CECs) using a universal rare event detection platform (HDSCA). Longitudinal analysis of an index patient finds that CTCs are present at the time of disease progression, while CECs are predominately present at the time of stable disease. In a small cohort of prostate and breast cancer patients, we find high inter-patient and temporal intra-patient variability in the expression of tissue specific markers such as ER, HER2, AR, PSA and PSMA and EpCAM. Our study stresses the importance of the multi-omic characterization of circulating rare cells in patients with breast and prostate carcinomas, specifically highlighting overlapping and cell type defining proteo-genomic characteristics of CTCs and CECs.
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Affiliation(s)
- Lisa Welter
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Serena Zheng
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Sonia Maryam Setayesh
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael Morikado
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Arushi Agrawal
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Rafael Nevarez
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Amin Naghdloo
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Milind Pore
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Nikki Higa
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Anand Kolatkar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Jana-Aletta Thiele
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Priyanka Sharma
- University of Kansas Medical Center, Westwood, KS 66205, USA;
| | - Halle C. F. Moore
- Cleveland Clinic Taussig Cancer Institute, Cleveland, OH 44195, USA;
| | - Jennifer K. Richer
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (J.K.R.); (A.E.)
| | - Anthony Elias
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (J.K.R.); (A.E.)
| | - Kenneth J. Pienta
- The Cancer Ecology Center, Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA;
| | - Amado J. Zurita
- Department of Genitourinary Medical Oncology, MD Anderson, Houston, TX 77230, USA;
| | - Mitchell E. Gross
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA 90064, USA;
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Stephanie N. Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Carmen Ruiz Velasco
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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9
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Bjørnstad OV, Carrasco M, Finne K, Winge I, Askeland C, Arnes JB, Knutsvik G, Kleftogiannis D, Paulo JA, Akslen LA, Vethe H. Global and single-cell proteomics view of the co-evolution between neural progenitors and breast cancer cells in a co-culture model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539050. [PMID: 37205344 PMCID: PMC10187147 DOI: 10.1101/2023.05.03.539050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Tumor neurogenesis, a process by which new nerves invade tumors, is a growing area of interest in cancer research. Nerve presence has been linked to aggressive features of various solid tumors, including breast and prostate cancer. A recent study suggested that the tumor microenvironment may influence cancer progression through recruitment of neural progenitor cells from the central nervous system. However, the presence of neural progenitors in human breast tumors has not been reported. Here, we investigate the presence of Doublecortin (DCX) and Neurofilament-Light (NFL) co-expressing (DCX+/NFL+) cells in patient breast cancer tissue using Imaging Mass Cytometry. To map the interaction between breast cancer cells and neural progenitor cells further, we created an in vitro model mimicking breast cancer innervation, and characterized using mass spectrometry-based proteomics on the two cell types as they co- evolved in co-culture. Our results indicate stromal presence of DCX+/NFL+ cells in breast tumor tissue from a cohort of 107 patient cases, and that neural interaction contribute to drive a more aggressive breast cancer phenotype in our co-culture models. Our results support that neural involvement plays an active role in breast cancer and warrants further studies on the interaction between nervous system and breast cancer progression.
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10
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Gebreyesus ST, Muneer G, Huang CC, Siyal AA, Anand M, Chen YJ, Tu HL. Recent advances in microfluidics for single-cell functional proteomics. LAB ON A CHIP 2023; 23:1726-1751. [PMID: 36811978 DOI: 10.1039/d2lc01096h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Single-cell proteomics (SCP) reveals phenotypic heterogeneity by profiling individual cells, their biological states and functional outcomes upon signaling activation that can hardly be probed via other omics characterizations. This has become appealing to researchers as it enables an overall more holistic view of biological details underlying cellular processes, disease onset and progression, as well as facilitates unique biomarker identification from individual cells. Microfluidic-based strategies have become methods of choice for single-cell analysis because they allow facile assay integrations, such as cell sorting, manipulation, and content analysis. Notably, they have been serving as an enabling technology to improve the sensitivity, robustness, and reproducibility of recently developed SCP methods. Critical roles of microfluidics technologies are expected to further expand rapidly in advancing the next phase of SCP analysis to reveal more biological and clinical insights. In this review, we will capture the excitement of the recent achievements of microfluidics methods for both targeted and global SCP, including efforts to enhance the proteomic coverage, minimize sample loss, and increase multiplexity and throughput. Furthermore, we will discuss the advantages, challenges, applications, and future prospects of SCP.
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Affiliation(s)
- Sofani Tafesse Gebreyesus
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Gul Muneer
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | | | - Asad Ali Siyal
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
| | - Mihir Anand
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
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11
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Arnett LP, Rana R, Chung WWY, Li X, Abtahi M, Majonis D, Bassan J, Nitz M, Winnik MA. Reagents for Mass Cytometry. Chem Rev 2023; 123:1166-1205. [PMID: 36696538 DOI: 10.1021/acs.chemrev.2c00350] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mass cytometry (cytometry by time-of-flight detection [CyTOF]) is a bioanalytical technique that enables the identification and quantification of diverse features of cellular systems with single-cell resolution. In suspension mass cytometry, cells are stained with stable heavy-atom isotope-tagged reagents, and then the cells are nebulized into an inductively coupled plasma time-of-flight mass spectrometry (ICP-TOF-MS) instrument. In imaging mass cytometry, a pulsed laser is used to ablate ca. 1 μm2 spots of a tissue section. The plume is then transferred to the CyTOF, generating an image of biomarker expression. Similar measurements are possible with multiplexed ion bean imaging (MIBI). The unit mass resolution of the ICP-TOF-MS detector allows for multiparametric analysis of (in principle) up to 130 different parameters. Currently available reagents, however, allow simultaneous measurement of up to 50 biomarkers. As new reagents are developed, the scope of information that can be obtained by mass cytometry continues to increase, particularly due to the development of new small molecule reagents which enable monitoring of active biochemistry at the cellular level. This review summarizes the history and current state of mass cytometry reagent development and elaborates on areas where there is a need for new reagents. Additionally, this review provides guidelines on how new reagents should be tested and how the data should be presented to make them most meaningful to the mass cytometry user community.
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Affiliation(s)
- Loryn P Arnett
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Rahul Rana
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Wilson Wai-Yip Chung
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Xiaochong Li
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Mahtab Abtahi
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Daniel Majonis
- Standard BioTools Canada Inc. (formerly Fluidigm Canada Inc.), 1380 Rodick Road, Suite 400, Markham, OntarioL3R 4G5, Canada
| | - Jay Bassan
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Mitchell A Winnik
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada.,Department of Chemical Engineering and Applied Chemistry, 200 College Street, Toronto, OntarioM5S 3E5, Canada
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12
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Glasson Y, Chépeaux LA, Dumé AS, Lafont V, Faget J, Bonnefoy N, Michaud HA. Single-cell high-dimensional imaging mass cytometry: one step beyond in oncology. Semin Immunopathol 2023; 45:17-28. [PMID: 36598557 PMCID: PMC9812013 DOI: 10.1007/s00281-022-00978-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/11/2022] [Indexed: 01/05/2023]
Abstract
Solid tumors have a dynamic ecosystem in which malignant and non-malignant (endothelial, stromal, and immune) cell types constantly interact. Importantly, the abundance, localization, and functional orientation of each cell component within the tumor microenvironment vary significantly over time and in response to treatment. Such intratumoral heterogeneity influences the tumor course and its sensitivity to treatments. Recently, high-dimensional imaging mass cytometry (IMC) has been developed to explore the tumor ecosystem at the single-cell level. In the last years, several studies demonstrated that IMC is a powerful tool to decipher the tumor complexity. In this review, we summarize the potential of this technology and how it may be useful for cancer research (from preclinical to clinical studies).
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Affiliation(s)
- Yaël Glasson
- IRCM, Univ Montpellier, ICM, Plateforme de Cytométrie Et d’Imagerie de Masse, Inserm Montpellier, France
| | - Laure-Agnès Chépeaux
- IRCM, Univ Montpellier, ICM, Plateforme de Cytométrie Et d’Imagerie de Masse, Inserm Montpellier, France
| | - Anne-Sophie Dumé
- IRCM, Univ Montpellier, ICM, Plateforme de Cytométrie Et d’Imagerie de Masse, Inserm Montpellier, France
| | | | - Julien Faget
- IRCM, Univ Montpellier, ICM, Inserm Montpellier, France
| | - Nathalie Bonnefoy
- IRCM, Univ Montpellier, ICM, Plateforme de Cytométrie Et d’Imagerie de Masse, Inserm Montpellier, France
| | - Henri-Alexandre Michaud
- IRCM, Univ Montpellier, ICM, Plateforme de Cytométrie Et d'Imagerie de Masse, Inserm Montpellier, France.
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13
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Kong T, Laranjeira ABA, Yang K, Fisher DAC, Yu L, Poittevin De La Frégonnière L, Wang AZ, Ruzinova MB, Fowles JS, Fulbright MC, Cox MJ, Celik H, Challen GA, Huang S, Oh ST. DUSP6 mediates resistance to JAK2 inhibition and drives leukemic progression. NATURE CANCER 2023; 4:108-127. [PMID: 36581736 DOI: 10.1038/s43018-022-00486-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/08/2022] [Indexed: 12/31/2022]
Abstract
Myeloproliferative neoplasms (MPNs) exhibit a propensity for transformation to secondary acute myeloid leukemia (sAML), for which the underlying mechanisms remain poorly understood, resulting in limited treatment options and dismal clinical outcomes. Here, we performed single-cell RNA sequencing on serial MPN and sAML patient stem and progenitor cells, identifying aberrantly increased expression of DUSP6 underlying disease transformation. Pharmacologic dual-specificity phosphatase (DUSP)6 targeting led to inhibition of S6 and Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling while also reducing inflammatory cytokine production. DUSP6 perturbation further inhibited ribosomal S6 kinase (RSK)1, which we identified as a second indispensable candidate associated with poor clinical outcome. Ectopic expression of DUSP6 mediated JAK2-inhibitor resistance and exacerbated disease severity in patient-derived xenograft (PDX) models. Contrastingly, DUSP6 inhibition potently suppressed disease development across Jak2V617F and MPLW515L MPN mouse models and sAML PDXs without inducing toxicity in healthy controls. These findings underscore DUSP6 in driving disease transformation and highlight the DUSP6-RSK1 axis as a vulnerable, druggable pathway in myeloid malignancies.
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Affiliation(s)
- Tim Kong
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Angelo B A Laranjeira
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kangning Yang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Daniel A C Fisher
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - LaYow Yu
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Laure Poittevin De La Frégonnière
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Anthony Z Wang
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Marianna B Ruzinova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jared S Fowles
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mary C Fulbright
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Maggie J Cox
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Hamza Celik
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Grant A Challen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Stephen T Oh
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- Immunomonitoring Laboratory, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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14
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Odunsi K, Qian F, Lugade AA, Yu H, Geller MA, Fling SP, Kaiser JC, Lacroix AM, D'Amico L, Ramchurren N, Morishima C, Disis ML, Dennis L, Danaher P, Warren S, Nguyen VA, Ravi S, Tsuji T, Rosario S, Zha W, Hutson A, Liu S, Lele S, Zsiros E, McGray AJR, Chiello J, Koya R, Chodon T, Morrison CD, Putluri V, Putluri N, Mager DE, Gunawan R, Cheever MA, Battaglia S, Matsuzaki J. Metabolic adaptation of ovarian tumors in patients treated with an IDO1 inhibitor constrains antitumor immune responses. Sci Transl Med 2022; 14:eabg8402. [PMID: 35294258 DOI: 10.1126/scitranslmed.abg8402] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To uncover underlying mechanisms associated with failure of indoleamine 2,3-dioxygenase 1 (IDO1) blockade in clinical trials, we conducted a pilot, window-of-opportunity clinical study in 17 patients with newly diagnosed advanced high-grade serous ovarian cancer before their standard tumor debulking surgery. Patients were treated with the IDO1 inhibitor epacadostat, and immunologic, transcriptomic, and metabolomic characterization of the tumor microenvironment was undertaken in baseline and posttreatment tumor biopsies. IDO1 inhibition resulted in efficient blockade of the kynurenine pathway of tryptophan degradation and was accompanied by a metabolic adaptation that shunted tryptophan catabolism toward the serotonin pathway. This resulted in elevated nicotinamide adenine dinucleotide (NAD+), which reduced T cell proliferation and function. Because NAD+ metabolites could be ligands for purinergic receptors, we investigated the impact of blocking purinergic receptors in the presence or absence of NAD+ on T cell proliferation and function in our mouse model. We demonstrated that A2a and A2b purinergic receptor antagonists, SCH58261 or PSB1115, respectively, rescued NAD+-mediated suppression of T cell proliferation and function. Combining IDO1 inhibition and A2a/A2b receptor blockade improved survival and boosted the antitumor immune signature in mice with IDO1 overexpressing ovarian cancer. These findings elucidate the downstream adaptive metabolic consequences of IDO1 blockade in ovarian cancers that may undermine antitumor T cell responses in the tumor microenvironment.
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Affiliation(s)
- Kunle Odunsi
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA.,Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL, USA.,Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Feng Qian
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA.,Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL, USA.,Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Amit A Lugade
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Han Yu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Melissa A Geller
- Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN, USA
| | - Steven P Fling
- Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Judith C Kaiser
- Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andreanne M Lacroix
- Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Leonard D'Amico
- Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nirasha Ramchurren
- Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chihiro Morishima
- Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Mary L Disis
- Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | | | - Van Anh Nguyen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Sudharshan Ravi
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Takemasa Tsuji
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA.,Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL, USA.,Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Spencer Rosario
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Wenjuan Zha
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Alan Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Shashikant Lele
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Emese Zsiros
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - A J Robert McGray
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jessie Chiello
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Richard Koya
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA.,Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL, USA.,Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Thinle Chodon
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA.,Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL, USA.,Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Carl D Morrison
- Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Vasanta Putluri
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nagireddy Putluri
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Donald E Mager
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA.,Enhanced Pharmacodynamics LLC, Buffalo, NY, USA
| | - Rudiyanto Gunawan
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Martin A Cheever
- Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sebastiano Battaglia
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Junko Matsuzaki
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA.,Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL, USA.,Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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15
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Toothaker JM, Olaloye O, McCourt BT, McCourt CC, Silva TN, Case RM, Liu P, Yimlamai D, Tseng G, Konnikova L. Immune landscape of human placental villi using single-cell analysis. Development 2022; 149:274057. [PMID: 35050308 PMCID: PMC8935213 DOI: 10.1242/dev.200013] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/30/2021] [Indexed: 12/19/2022]
Abstract
Maintenance of a healthy pregnancy is reliant on a successful balance between the fetal and maternal immune systems. Although the maternal mechanisms responsible have been well studied, those used by the fetal immune system remain poorly understood. Using suspension mass cytometry and various imaging modalities, we report a complex immune system within the mid-gestation (17-23 weeks) human placental villi (PV). Consistent with recent reports in other fetal organs, T cells with memory phenotypes, although rare in abundance, were detected within the PV tissue and vasculature. Moreover, we determined that T cells isolated from PV samples may be more proliferative after T cell receptor stimulation than adult T cells at baseline. Collectively, we identified multiple subtypes of fetal immune cells within the PV and specifically highlight the enhanced proliferative capacity of fetal PV T cells.
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Affiliation(s)
- Jessica M. Toothaker
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA,Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | | | - Blake T. McCourt
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Collin C. McCourt
- Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15219, USA
| | - Tatiana N. Silva
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Rebecca M. Case
- Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15219, USA
| | - Peng Liu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Dean Yimlamai
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Liza Konnikova
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA,Department of Pediatrics, Yale University, New Haven, CT 06510, USA,Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University, New Haven, CT 06519, USA,Program in Human and Translational Immunology, Yale University, New Haven, CT 06519, USA,Author for correspondence ()
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16
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A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially-resolved tissue phenotyping at single-cell resolution. Nat Commun 2022; 13:781. [PMID: 35140207 PMCID: PMC8828885 DOI: 10.1038/s41467-022-28470-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/25/2022] [Indexed: 01/08/2023] Open
Abstract
Multiplexed imaging technologies enable the study of biological tissues at single-cell resolution while preserving spatial information. Currently, high-dimension imaging data analysis is technology-specific and requires multiple tools, restricting analytical scalability and result reproducibility. Here we present SIMPLI (Single-cell Identification from MultiPLexed Images), a flexible and technology-agnostic software that unifies all steps of multiplexed imaging data analysis. After raw image processing, SIMPLI performs a spatially resolved, single-cell analysis of the tissue slide as well as cell-independent quantifications of marker expression to investigate features undetectable at the cell level. SIMPLI is highly customisable and can run on desktop computers as well as high-performance computing environments, enabling workflow parallelisation for large datasets. SIMPLI produces multiple tabular and graphical outputs at each step of the analysis. Its containerised implementation and minimum configuration requirements make SIMPLI a portable and reproducible solution for multiplexed imaging data analysis. Software is available at “SIMPLI [https://github.com/ciccalab/SIMPLI]”. Current high-dimension imaging data analysis methods are technology-specific and require multiple tools, restricting analytical scalability and result reproducibility. Here the authors present SIMPLI, a software that overcomes these limitations for single-cell and pixel analysis of multiplexed images at spatial resolution.
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17
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Kuett L, Catena R, Özcan A, Plüss A, Schraml P, Moch H, de Souza N, Bodenmiller B. Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment. NATURE CANCER 2022; 3:122-133. [PMID: 35121992 PMCID: PMC7613779 DOI: 10.1038/s43018-021-00301-w] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 11/03/2021] [Indexed: 11/22/2022]
Abstract
A holistic understanding of tissue and organ structure and function requires the detection of molecular constituents in their original three-dimensional (3D) context. Imaging mass cytometry (IMC) enables simultaneous detection of up to 40 antigens and transcripts using metal-tagged antibodies but has so far been restricted to two-dimensional imaging. Here we report the development of 3D IMC for multiplexed 3D tissue analysis at single-cell resolution and demonstrate the utility of the technology by analysis of human breast cancer samples. The resulting 3D models reveal cellular and microenvironmental heterogeneity and cell-level tissue organization not detectable in two dimensions. 3D IMC will prove powerful in the study of phenomena occurring in 3D space such as tumor cell invasion and is expected to provide invaluable insights into cellular microenvironments and tissue architecture.
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Affiliation(s)
- Laura Kuett
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zürich, Switzerland
| | - Raúl Catena
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Leica Geosystems part of Hexagon, Heerbrugg, St. Gallen, Switzerland
| | - Alaz Özcan
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alex Plüss
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Natalie de Souza
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
- Institute of Molecular Health Sciences, ETH Zurich, Zürich, Switzerland.
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18
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Kakade VR, Weiss M, Cantley LG. Using Imaging Mass Cytometry to Define Cell Identities and Interactions in Human Tissues. Front Physiol 2021; 12:817181. [PMID: 35002783 PMCID: PMC8727440 DOI: 10.3389/fphys.2021.817181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 11/25/2021] [Indexed: 12/30/2022] Open
Abstract
In the evolving landscape of highly multiplexed imaging techniques that can be applied to study complex cellular microenvironments, this review characterizes the use of imaging mass cytometry (IMC) to study the human kidney. We provide technical details for antibody validation, cell segmentation, and data analysis specifically tailored to human kidney samples, and elaborate on phenotyping of kidney cell types and novel insights that IMC can provide regarding pathophysiological processes in the injured or diseased kidney. This review will provide the reader with the necessary background to understand both the power and the limitations of IMC and thus support better perception of how IMC analysis can improve our understanding of human disease pathogenesis and can be integrated with other technologies such as single cell sequencing and proteomics to provide spatial context to cellular data.
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Affiliation(s)
| | | | - Lloyd G. Cantley
- Section of Nephrology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
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19
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Rana R, Chang Q, Bassan J, Chow S, Hedley D, Nitz M. An Iodinated DAPI-Based Reagent for Mass Cytometry. Chembiochem 2020; 22:532-538. [PMID: 32897623 DOI: 10.1002/cbic.202000369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/02/2020] [Indexed: 01/04/2023]
Abstract
Multiparametric single-cell analysis has seen dramatic improvements with the introduction of mass cytometry (MC) and imaging mass cytometry (IMC™ ). These technologies expanded the number of biomarkers that can be identified simultaneously by using heavy-isotope-tagged antibody reagents. Small-molecule probes bearing heavy isotopes are emerging as additional useful functional reporters of cellular features. Realizing this, we explored the iodination of DAPI to produce a heavy-atom-substituted derivative of the commonly used fluorescent DNA stain. Although exhibiting a drastically reduced fluorescence emission profile, I-DAPI retains strong binding affinity for DNA. I-DAPI was used to detect cellular DNA in MC and IMC™ assays with comparable efficiency to known Ir-containing DNA intercalators. This work suggests repurposing well-known colorimetric stains through simple reactions could be an effective strategy to develop new, functional MC and IMC™ reagents.
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Affiliation(s)
- Rahul Rana
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Qing Chang
- Fluidigm Canada Inc., 1380 Rodick Road, Markham, ON L3R 4G5, Canada
| | - Jay Bassan
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada.,BIMDAQ Ltd, 9 Lessness Avenue, Bexleyheath, DA7 5SH, UK
| | - Sue Chow
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON M5G 2 M9, Canada
| | - David Hedley
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON M5G 2 M9, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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20
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Tan WCC, Nerurkar SN, Cai HY, Ng HHM, Wu D, Wee YTF, Lim JCT, Yeong J, Lim TKH. Overview of multiplex immunohistochemistry/immunofluorescence techniques in the era of cancer immunotherapy. Cancer Commun (Lond) 2020; 40:135-153. [PMID: 32301585 PMCID: PMC7170662 DOI: 10.1002/cac2.12023] [Citation(s) in RCA: 288] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/20/2020] [Indexed: 12/17/2022] Open
Abstract
Conventional immunohistochemistry (IHC) is a widely used diagnostic technique in tissue pathology. However, this technique is associated with a number of limitations, including high inter-observer variability and the capacity to label only one marker per tissue section. This review details various highly multiplexed techniques that have emerged to circumvent these constraints, allowing simultaneous detection of multiple markers on a single tissue section and the comprehensive study of cell composition, cellular functional and cell-cell interactions. Among these techniques, multiplex Immunohistochemistry/Immunofluorescence (mIHC/IF) has emerged to be particularly promising. mIHC/IF provides high-throughput multiplex staining and standardized quantitative analysis for highly reproducible, efficient and cost-effective tissue studies. This technique has immediate potential for translational research and clinical practice, particularly in the era of cancer immunotherapy.
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Affiliation(s)
- Wei Chang Colin Tan
- Yong Loo Lin School of MedicineNational University of SingaporeSingapore169856Singapore
| | | | - Hai Yun Cai
- Yong Loo Lin School of MedicineNational University of SingaporeSingapore169856Singapore
| | - Harry Ho Man Ng
- Department of Anatomical PathologySingapore General HospitalSingapore169856Singapore
- Duke‐NUS Medical SchoolSingapore169856Singapore
| | - Duoduo Wu
- Yong Loo Lin School of MedicineNational University of SingaporeSingapore169856Singapore
| | - Yu Ting Felicia Wee
- Department of Anatomical PathologySingapore General HospitalSingapore169856Singapore
| | - Jeffrey Chun Tatt Lim
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR)Singapore169856Singapore
| | - Joe Yeong
- Department of Anatomical PathologySingapore General HospitalSingapore169856Singapore
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR)Singapore169856Singapore
- Singapore Immunology NetworkAgency of Science (SIgN)Technology and Research (A*STAR)Singapore169856Singapore
| | - Tony Kiat Hon Lim
- Department of Anatomical PathologySingapore General HospitalSingapore169856Singapore
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21
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Hartmann FJ, Bendall SC. Immune monitoring using mass cytometry and related high-dimensional imaging approaches. Nat Rev Rheumatol 2020; 16:87-99. [PMID: 31892734 PMCID: PMC7232872 DOI: 10.1038/s41584-019-0338-z] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2019] [Indexed: 02/07/2023]
Abstract
The cellular complexity and functional diversity of the human immune system necessitate the use of high-dimensional single-cell tools to uncover its role in multifaceted diseases such as rheumatic diseases, as well as other autoimmune and inflammatory disorders. Proteomic technologies that use elemental (heavy metal) reporter ions, such as mass cytometry (also known as CyTOF) and analogous high-dimensional imaging approaches (including multiplexed ion beam imaging (MIBI) and imaging mass cytometry (IMC)), have been developed from their low-dimensional counterparts, flow cytometry and immunohistochemistry, to meet this need. A growing number of studies have been published that use these technologies to identify functional biomarkers and therapeutic targets in rheumatic diseases, but the full potential of their application to rheumatic disease research has yet to be fulfilled. This Review introduces the underlying technologies for high-dimensional immune monitoring and discusses aspects necessary for their successful implementation, including study design principles, analytical tools and future developments for the field of rheumatology.
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Affiliation(s)
- Felix J Hartmann
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA.
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22
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Theiner S, Schweikert A, Haberler C, Peyrl A, Koellensperger G. Laser ablation-ICP-TOFMS imaging of germ cell tumors of patients undergoing platinum-based chemotherapy. Metallomics 2020; 12:1246-1252. [DOI: 10.1039/d0mt00080a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A low dispersion laser ablation setup in combination with inductively coupled plasma-time-of-flight mass spectrometry (LA-ICP-TOFMS) was applied to clinical samples of patients undergoing platinum-based chemotherapy.
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Affiliation(s)
- Sarah Theiner
- Institute of Analytical Chemistry
- University of Vienna
- 1090 Vienna
- Austria
| | - Andreas Schweikert
- Institute of Analytical Chemistry
- University of Vienna
- 1090 Vienna
- Austria
- Institute of Inorganic Chemistry
| | - Christine Haberler
- Clinical Institute of Neurology
- Medical University of Vienna
- 1090 Vienna
- Austria
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine
- Medical University of Vienna
- 1090 Vienna
- Austria
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23
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Aoki T, Chong LC, Takata K, Milne K, Hav M, Colombo A, Chavez EA, Nissen M, Wang X, Miyata-Takata T, Lam V, Viganò E, Woolcock BW, Telenius A, Li MY, Healy S, Ghesquiere C, Kos D, Goodyear T, Veldman J, Zhang AW, Kim J, Saberi S, Ding J, Farinha P, Weng AP, Savage KJ, Scott DW, Krystal G, Nelson BH, Mottok A, Merchant A, Shah SP, Steidl C. Single-Cell Transcriptome Analysis Reveals Disease-Defining T-cell Subsets in the Tumor Microenvironment of Classic Hodgkin Lymphoma. Cancer Discov 2019; 10:406-421. [PMID: 31857391 DOI: 10.1158/2159-8290.cd-19-0680] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/13/2019] [Accepted: 12/13/2019] [Indexed: 12/22/2022]
Abstract
Hodgkin lymphoma is characterized by an extensively dominant tumor microenvironment (TME) composed of different types of noncancerous immune cells with rare malignant cells. Characterization of the cellular components and their spatial relationship is crucial to understanding cross-talk and therapeutic targeting in the TME. We performed single-cell RNA sequencing of more than 127,000 cells from 22 Hodgkin lymphoma tissue specimens and 5 reactive lymph nodes, profiling for the first time the phenotype of the Hodgkin lymphoma-specific immune microenvironment at single-cell resolution. Single-cell expression profiling identified a novel Hodgkin lymphoma-associated subset of T cells with prominent expression of the inhibitory receptor LAG3, and functional analyses established this LAG3+ T-cell population as a mediator of immunosuppression. Multiplexed spatial assessment of immune cells in the microenvironment also revealed increased LAG3+ T cells in the direct vicinity of MHC class II-deficient tumor cells. Our findings provide novel insights into TME biology and suggest new approaches to immune-checkpoint targeting in Hodgkin lymphoma. SIGNIFICANCE: We provide detailed functional and spatial characteristics of immune cells in classic Hodgkin lymphoma at single-cell resolution. Specifically, we identified a regulatory T-cell-like immunosuppressive subset of LAG3+ T cells contributing to the immune-escape phenotype. Our insights aid in the development of novel biomarkers and combination treatment strategies targeting immune checkpoints.See related commentary by Fisher and Oh, p. 342.This article is highlighted in the In This Issue feature, p. 327.
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Affiliation(s)
- Tomohiro Aoki
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lauren C Chong
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Katy Milne
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Monirath Hav
- Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Elizabeth A Chavez
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Michael Nissen
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Xuehai Wang
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Tomoko Miyata-Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Vivian Lam
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Elena Viganò
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce W Woolcock
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Adèle Telenius
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Michael Y Li
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shannon Healy
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Chanel Ghesquiere
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Daniel Kos
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Talia Goodyear
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Johanna Veldman
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Allen W Zhang
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jubin Kim
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Saeed Saberi
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Jiarui Ding
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Pedro Farinha
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Kerry J Savage
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Gerald Krystal
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Brad H Nelson
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anja Mottok
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Akil Merchant
- Cedars-Sinai Medical Center, Los Angeles, California
| | - Sohrab P Shah
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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24
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Klufa J, Bauer T, Hanson B, Herbold C, Starkl P, Lichtenberger B, Srutkova D, Schulz D, Vujic I, Mohr T, Rappersberger K, Bodenmiller B, Kozakova H, Knapp S, Loy A, Sibilia M. Hair eruption initiates and commensal skin microbiota aggravate adverse events of anti-EGFR therapy. Sci Transl Med 2019; 11:eaax2693. [PMID: 31826981 DOI: 10.1126/scitranslmed.aax2693] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/30/2019] [Accepted: 10/11/2019] [Indexed: 12/11/2022]
Abstract
Epidermal growth factor receptor (EGFR)-targeted anticancer therapy induces stigmatizing skin toxicities affecting patients' quality of life and therapy adherence. The lack of mechanistic details underlying these adverse events hampers their management. We found that EGFR/ERK signaling is required in LRIG1-positive stem cells during de novo hair eruption to secure barrier integrity and prevent the invasion of commensal microbiota and inflammatory skin disease. EGFR-deficient epidermis is permissive for microbiota outgrowth and displays an atopic-like TH2-dominated signature. The opening of the follicular ostia during hair eruption allows invasion of commensal microbiota into the hair follicle, initiating an additional TH1 and TH17 response culminating in chronic folliculitis. Restoration of epidermal ERK signaling via prophylactic FGF7 treatment or transgenic SOS expression rescues the barrier defect in the absence of EGFR, highlighting a therapeutic anchor point. These data reveal that commensal skin microbiota provoke atopic-like inflammatory skin diseases by invading into the follicular opening of erupting hair.
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Affiliation(s)
- Jörg Klufa
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna and Comprehensive Cancer Center, Vienna 1090, Austria
| | - Thomas Bauer
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna and Comprehensive Cancer Center, Vienna 1090, Austria.
| | - Buck Hanson
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna 1090, Austria
| | - Craig Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna 1090, Austria
| | - Philipp Starkl
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Laboratory of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna 1090, Austria
| | - Beate Lichtenberger
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna and Comprehensive Cancer Center, Vienna 1090, Austria
| | - Dagmar Srutkova
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, v.v.i., Novy Hradek 549 22, Czech Republic
| | - Daniel Schulz
- Institute of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
| | - Igor Vujic
- Department of Dermatology and Venereology, Medical Institution Rudolfstiftung, Vienna 1030, Austria
- Department of Dermatology, Medical University of Vienna, Vienna 1090, Austria
| | - Thomas Mohr
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna and Comprehensive Cancer Center, Vienna 1090, Austria
| | - Klemens Rappersberger
- Department of Dermatology and Venereology, Medical Institution Rudolfstiftung, Vienna 1030, Austria
| | - Bernd Bodenmiller
- Institute of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
| | - Hana Kozakova
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, v.v.i., Novy Hradek 549 22, Czech Republic
| | - Sylvia Knapp
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Laboratory of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna 1090, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna 1090, Austria
| | - Maria Sibilia
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna and Comprehensive Cancer Center, Vienna 1090, Austria.
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25
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Baharlou H, Canete NP, Cunningham AL, Harman AN, Patrick E. Mass Cytometry Imaging for the Study of Human Diseases-Applications and Data Analysis Strategies. Front Immunol 2019; 10:2657. [PMID: 31798587 PMCID: PMC6868098 DOI: 10.3389/fimmu.2019.02657] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/28/2019] [Indexed: 01/09/2023] Open
Abstract
High parameter imaging is an important tool in the life sciences for both discovery and healthcare applications. Imaging Mass Cytometry (IMC) and Multiplexed Ion Beam Imaging (MIBI) are two relatively recent technologies which enable clinical samples to be simultaneously analyzed for up to 40 parameters at subcellular resolution. Importantly, these "Mass Cytometry Imaging" (MCI) modalities are being rapidly adopted for studies of the immune system in both health and disease. In this review we discuss, first, the various applications of MCI to date. Second, due to the inherent challenge of analyzing high parameter spatial data, we discuss the various approaches that have been employed for the processing and analysis of data from MCI experiments.
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Affiliation(s)
- Heeva Baharlou
- The Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Nicolas P. Canete
- The Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Anthony L. Cunningham
- The Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Andrew N. Harman
- The Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Ellis Patrick
- The Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia
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26
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Bassan J, Nitz M. Methods for analyzing tellurium imaging mass cytometry data. PLoS One 2019; 14:e0221714. [PMID: 31479470 PMCID: PMC6719864 DOI: 10.1371/journal.pone.0221714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/13/2019] [Indexed: 11/21/2022] Open
Abstract
Imaging mass cytometry (IMC) is a technique allowing visualization and quantification of over 40 biological parameters in a single experiment with subcellular spatial resolution, however most IMC experiments are limited to endpoint analysis with antibodies and DNA stains. Small molecules containing tellurium are promising probes for IMC due to their cell permeability, synthetic versatility, and most importantly their application to sequential labelling with isotopologous probes (SLIP) experiments. SLIP experiments with tellurium-containing probes allow quantification of intracellular biology at multiple timepoints with IMC. Despite the promise of tellurium in IMC, there are unique challenges in image processing associated with tellurium IMC data. Here, we address some of these issues by demonstrating the removal of xenon background signal, combining channels to improve signal-to-noise ratio, and calculating isotope transmission efficiency biases. These developments add accuracy to the unique temporal resolution afforded by tellurium IMC probes.
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Affiliation(s)
- Jay Bassan
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- BIMDAQ Ltd, Bexleyheath, United Kingdom
- * E-mail:
| | - Mark Nitz
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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27
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Elyada E, Bolisetty M, Laise P, Flynn WF, Courtois ET, Burkhart RA, Teinor JA, Belleau P, Biffi G, Lucito MS, Sivajothi S, Armstrong TD, Engle DD, Yu KH, Hao Y, Wolfgang CL, Park Y, Preall J, Jaffee EM, Califano A, Robson P, Tuveson DA. Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts. Cancer Discov 2019; 9:1102-1123. [PMID: 31197017 DOI: 10.1158/2159-8290.cd-19-0094] [Citation(s) in RCA: 1025] [Impact Index Per Article: 205.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/18/2019] [Accepted: 05/30/2019] [Indexed: 12/21/2022]
Abstract
Cancer-associated fibroblasts (CAF) are major players in the progression and drug resistance of pancreatic ductal adenocarcinoma (PDAC). CAFs constitute a diverse cell population consisting of several recently described subtypes, although the extent of CAF heterogeneity has remained undefined. Here we use single-cell RNA sequencing to thoroughly characterize the neoplastic and tumor microenvironment content of human and mouse PDAC tumors. We corroborate the presence of myofibroblastic CAFs and inflammatory CAFs and define their unique gene signatures in vivo. Moreover, we describe a new population of CAFs that express MHC class II and CD74, but do not express classic costimulatory molecules. We term this cell population "antigen-presenting CAFs" and find that they activate CD4+ T cells in an antigen-specific fashion in a model system, confirming their putative immune-modulatory capacity. Our cross-species analysis paves the way for investigating distinct functions of CAF subtypes in PDAC immunity and progression. SIGNIFICANCE: Appreciating the full spectrum of fibroblast heterogeneity in pancreatic ductal adenocarcinoma is crucial to developing therapies that specifically target tumor-promoting CAFs. This work identifies MHC class II-expressing CAFs with a capacity to present antigens to CD4+ T cells, and potentially to modulate the immune response in pancreatic tumors.See related commentary by Belle and DeNardo, p. 1001.This article is highlighted in the In This Issue feature, p. 983.
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Affiliation(s)
- Ela Elyada
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Mohan Bolisetty
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Bristol-Myers Squibb, Pennington, New Jersey
| | - Pasquale Laise
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York
| | - William F Flynn
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Elise T Courtois
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Richard A Burkhart
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Jonathan A Teinor
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Pascal Belleau
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Giulia Biffi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Matthew S Lucito
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | | | - Todd D Armstrong
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Dannielle D Engle
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York.,Salk institute for Biological Studies, La Jolla, California
| | - Kenneth H Yu
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuan Hao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Christopher L Wolfgang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Youngkyu Park
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | | | - Elizabeth M Jaffee
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York.,J.P. Sulzberger Columbia Genome Center, Columbia University, New York, New York.,Department of Biomedical Informatics, Columbia University, New York, New York.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut. .,Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut, Farmington, Connecticut
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York. .,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
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28
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Van Acker T, Buckle T, Van Malderen SJM, van Willigen DM, van Unen V, van Leeuwen FWB, Vanhaecke F. High-resolution imaging and single-cell analysis via laser ablation-inductively coupled plasma-mass spectrometry for the determination of membranous receptor expression levels in breast cancer cell lines using receptor-specific hybrid tracers. Anal Chim Acta 2019; 1074:43-53. [PMID: 31159938 DOI: 10.1016/j.aca.2019.04.064] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/16/2019] [Accepted: 04/26/2019] [Indexed: 02/07/2023]
Abstract
This work evaluates the possibility of placement of high-resolution imaging and single-cell analysis via laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) within precision medicine by assessing the suitability of LA-ICP-MS as a micro-analytical technique for the localization and quantification of membranous receptors in heterogeneous cell samples that express both the membrane-bound receptors C-X-C chemokine receptor type 4 (CXCR4) and epidermal growth factor receptor (EGFR). Staining of the breast cancer cell lines MDA-MB-231 X4 and MDA-MB-468 was achieved using receptor-specific hybrid tracers, containing both a fluorophore and a DTPA single-lanthanide chelate. Prior to LA-ICP-MS imaging, fluorescence confocal microscopy (FCM) imaging was performed to localize the receptors, hereby enabling direct comparison. Based on the different expression levels of CXCR4 and EGFR, a distinction could be made between the cell lines using both imaging modalities. Furthermore, FCM and LA-ICP-MS demonstrated complementary characteristics, as a more distinct discrimination could be made between both cell lines based on the EGFR-targeting hybrid tracer via LA-ICP-MS, due to the intrinsic CXCR4-related green fluorescent protein (GFP) signal present in the MDA-MB-231 X4 cells. Employing state-of-the-art LA-ICP-MS instrumentation in bidirectional area scanning mode for sub-cellular imaging of MDA-MB-231 X4 cells enabled the specific binding of the CXCR4-targeting hybrid tracer to the cell membrane to be clearly demonstrated. The stretching of cells over the glass substrate led to a considerably higher signal response for pixels at the cell edges, relative to the more central pixels. The determination of the expression levels of CXCR4 and EGFR for the MDA-MB-468 cell line was performed using LA-ICP-MS single-cell analysis (sc-LA-ICP-MS) and external calibration, based on the quantitative ablation of Ho-spiked dried gelatin droplet standards. Additionally, a second calibration approach was applied based on spot ablation of highly homogeneous dried gelatin gels in combination with the determination of the ablated volume using atomic force microscopy (AFM) and yielded results which were in good agreement with the expression levels determined via flow cytometry (FC) and mass cytometry (MC). Hybrid tracers enable a direct comparison between (i) FCM and LA-ICP-MS imaging for the evaluation of the microscopic binding pattern and between (ii) FC, MC and sc-LA-ICP-MS for the quantification of receptor expression levels in single cells.
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Affiliation(s)
- Thibaut Van Acker
- Ghent University, Department of Chemistry, Atomic & Mass Spectrometry - A&MS Research Unit, Campus Sterre, Krijgslaan 281-S12, 9000, Ghent, Belgium.
| | - Tessa Buckle
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, the Netherlands.
| | - Stijn J M Van Malderen
- Ghent University, Department of Chemistry, Atomic & Mass Spectrometry - A&MS Research Unit, Campus Sterre, Krijgslaan 281-S12, 9000, Ghent, Belgium; Ghent University, Department of Chemistry, X-ray Microspectroscopy and Imaging Research Unit, Campus Sterre, Krijgslaan 281-S12, 9000, Ghent, Belgium.
| | - Danny M van Willigen
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, the Netherlands.
| | - Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, the Netherlands.
| | - Fijs W B van Leeuwen
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, the Netherlands.
| | - Frank Vanhaecke
- Ghent University, Department of Chemistry, Atomic & Mass Spectrometry - A&MS Research Unit, Campus Sterre, Krijgslaan 281-S12, 9000, Ghent, Belgium.
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29
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Van Malderen SJM, Van Acker T, Laforce B, De Bruyne M, de Rycke R, Asaoka T, Vincze L, Vanhaecke F. Three-dimensional reconstruction of the distribution of elemental tags in single cells using laser ablation ICP-mass spectrometry via registration approaches. Anal Bioanal Chem 2019; 411:4849-4859. [PMID: 30790022 DOI: 10.1007/s00216-019-01677-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/22/2019] [Accepted: 02/06/2019] [Indexed: 12/15/2022]
Abstract
This paper describes a workflow towards the reconstruction of the three-dimensional elemental distribution profile within human cervical carcinoma cells (HeLa), at a spatial resolution down to 1 μm, employing state-of-the-art laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) instrumentation. The suspended cells underwent a series of fixation/embedding protocols and were stained with uranyl acetate and an Ir-based DNA intercalator. A priori, laboratory-based absorption micro-computed tomography (μ-CT) was applied to acquire a reference frame of the morphology of the cells and their spatial distribution before sectioning. After CT analysis, a trimmed 300 × 300 × 300 μm3 block was sectioned into a sequential series of 132 sections with a thickness of 2 μm, which were subjected to LA-ICP-MS imaging. A pixel acquisition rate of 250 pixels s-1 was achieved, through a bidirectional scanning strategy. After acquisition, the two-dimensional elemental images were reconstructed using the timestamps in the laser log file. The synchronization of the data required an improved optimization algorithm, which forces the pixels of scans in different ablation directions to be spatially coherent in the direction orthogonal to the scan direction. The volume was reconstructed using multiple registration approaches. Registration using the section outline itself as a fiducial marker resulted into a volume which was in good agreement with the morphology visualized in the μ-CT volume. The 3D μ-CT volume could be registered to the LA-ICP-MS volume, consisting of 2.9 × 107 voxels, and the nucleus dimensions in 3D space could be derived.
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Affiliation(s)
- Stijn J M Van Malderen
- Atomic & Mass Spectrometry (A&MS) Research Unit, Department of Chemistry, Ghent University, Campus Sterre, Krijgslaan 281 - S12, 9000, Ghent, Belgium
| | - Thibaut Van Acker
- Atomic & Mass Spectrometry (A&MS) Research Unit, Department of Chemistry, Ghent University, Campus Sterre, Krijgslaan 281 - S12, 9000, Ghent, Belgium
| | - Brecht Laforce
- X-ray Microspectroscopy and Imaging (XMI) Research Unit, Department of Chemistry, Ghent University, Campus Sterre, Krijgslaan 281 - S12, 9000, Ghent, Belgium
| | - Michiel De Bruyne
- Department of Biomedical Molecular Biology and VIB Center for Inflammation Research, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- Ghent University Expertise Centre for Transmission Electron Microscopy and VIB BioImaging Core, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Riet de Rycke
- Department of Biomedical Molecular Biology and VIB Center for Inflammation Research, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- Ghent University Expertise Centre for Transmission Electron Microscopy and VIB BioImaging Core, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Tomoko Asaoka
- Department of Biomedical Molecular Biology and VIB Center for Inflammation Research, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Laszlo Vincze
- X-ray Microspectroscopy and Imaging (XMI) Research Unit, Department of Chemistry, Ghent University, Campus Sterre, Krijgslaan 281 - S12, 9000, Ghent, Belgium
| | - Frank Vanhaecke
- Atomic & Mass Spectrometry (A&MS) Research Unit, Department of Chemistry, Ghent University, Campus Sterre, Krijgslaan 281 - S12, 9000, Ghent, Belgium.
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