1
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Liu Y, Yang C. Computational methods for alignment and integration of spatially resolved transcriptomics data. Comput Struct Biotechnol J 2024; 23:1094-1105. [PMID: 38495555 PMCID: PMC10940867 DOI: 10.1016/j.csbj.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
Most of the complex biological regulatory activities occur in three dimensions (3D). To better analyze biological processes, it is essential not only to decipher the molecular information of numerous cells but also to understand how their spatial contexts influence their behavior. With the development of spatially resolved transcriptomics (SRT) technologies, SRT datasets are being generated to simultaneously characterize gene expression and spatial arrangement information within tissues, organs or organisms. To fully leverage spatial information, the focus extends beyond individual two-dimensional (2D) slices. Two tasks known as slices alignment and data integration have been introduced to establish correlations between multiple slices, enhancing the effectiveness of downstream tasks. Currently, numerous related methods have been developed. In this review, we first elucidate the details and principles behind several representative methods. Then we report the testing results of these methods on various SRT datasets, and assess their performance in representative downstream tasks. Insights into the strengths and weaknesses of each method and the reasons behind their performance are discussed. Finally, we provide an outlook on future developments. The codes and details of experiments are now publicly available at https://github.com/YangLabHKUST/SRT_alignment_and_integration.
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Affiliation(s)
- Yuyao Liu
- Department of Automation, School of Information Science and Technology, Tsinghua University, Beijing, China
| | - Can Yang
- Department of Mathematics, The Hong Kong University of Science and Technology, Hong Kong, China
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2
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Kumar P, Mondal PP. Multicolor iLIFE (m-iLIFE) volume cytometry for high-throughput imaging of multiple organelles. Sci Rep 2024; 14:23798. [PMID: 39394224 DOI: 10.1038/s41598-024-73667-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 09/19/2024] [Indexed: 10/13/2024] Open
Abstract
To be able to resolve multiple organelles at high throughput is an incredible achievement. This will have immediate implications in a range of fields ranging from fundamental cell biology to translational medicine. To realize such a high-throughput multicolor interrogation modality, we have developed a light-sheet based flow imaging system that is capable of visualizing multiple sub-cellular components with organelle-level resolution. This is possible due to the unique optical design that combines an illumination system comprising two collinear light sheets illuminating the flowing cells and a dedicated dual-color 4f-detection, enabling simultaneous recording of multiple organelles. The system PSF sections up to 4 parallel microfluidic channels through which cells are flowing, and multicolor images of cell cross-sections are recorded. The data is then computationally processed (filtered using ML algorithm, shift-corrected, and merged) and combined to reconstruct the 3D multicolor volume. System testing is conducted using multicolor fluorescent nano-beads (size ∼ 175 nm) and flow-based imaging parameters (PSF size, motion-blur, flow rate, frame rate, and number of cell-sections) are determined for quality imaging. Drug treatment studies were carried out for healthy and cancerous HeLa cells to check the performance of the proposed system. The cells were treated with a drug (Vincristine, which is known to promote mitochondrial fission in cells), and the same is compared with untreated control cells. The proposed multicolor iLIFE system could screen ∼ 800 cells/min (at a flow speed of 2490 μ m/s), and the drug treatment studies were carried out up to 24 h. Studies showed the disintegration of mitochondrial network and dysfunctional lysosomes and their accumulation at the cell membrane, which is a clear indication of cell apoptosis. Compared to control cells (untreated), the mortality is highest at a concentration of 500 nM post 12 h of drug treatment. With the capability of multiorganelle interrogation and organelle-level resolution, the multicolor iLIFE cytometry system is suitably placed to assist optical imaging and biomedical research.
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Affiliation(s)
- Prashant Kumar
- Mondal Lab, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Partha Pratim Mondal
- Mondal Lab, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India.
- Centre for Cryogenic Technology, Indian Institute of Science, Bangalore, 560012, India.
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3
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Mougios N, Cotroneo ER, Imse N, Setzke J, Rizzoli SO, Simeth NA, Tsukanov R, Opazo F. NanoPlex: a universal strategy for fluorescence microscopy multiplexing using nanobodies with erasable signals. Nat Commun 2024; 15:8771. [PMID: 39384781 DOI: 10.1038/s41467-024-53030-w] [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: 03/07/2024] [Accepted: 09/27/2024] [Indexed: 10/11/2024] Open
Abstract
Fluorescence microscopy has long been a transformative technique in biological sciences. Nevertheless, most implementations are limited to a few targets, which have been revealed using primary antibodies and fluorescently conjugated secondary antibodies. Super-resolution techniques such as Exchange-PAINT and, more recently, SUM-PAINT have increased multiplexing capabilities, but they require specialized equipment, software, and knowledge. To enable multiplexing for any imaging technique in any laboratory, we developed NanoPlex, a streamlined method based on conventional antibodies revealed by engineered secondary nanobodies that allow the selective removal of fluorescence signals. We develop three complementary signal removal strategies: OptoPlex (light-induced), EnzyPlex (enzymatic), and ChemiPlex (chemical). We showcase NanoPlex reaching 21 targets for 3D confocal analyses and 5-8 targets for dSTORM and STED super-resolution imaging. NanoPlex has the potential to revolutionize multi-target fluorescent imaging methods, potentially redefining the multiplexing capabilities of antibody-based assays.
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Affiliation(s)
- Nikolaos Mougios
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, Göttingen, Germany
| | - Elena R Cotroneo
- Institute for Organic and Biomolecular Chemistry, University of Göttingen, Göttingen, Germany
| | - Nils Imse
- Institute for Organic and Biomolecular Chemistry, University of Göttingen, Göttingen, Germany
| | - Jonas Setzke
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, Göttingen, Germany
| | - Silvio O Rizzoli
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Nadja A Simeth
- Institute for Organic and Biomolecular Chemistry, University of Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Roman Tsukanov
- III. Institute of Physics - Biophysics, Georg August University, Göttingen, Germany
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, Göttingen, Germany.
- NanoTag Biotechnologies GmbH, Göttingen, Germany.
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4
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Boudigou M, Frutoso M, Hémon P, Le Dantec C, Chatzis L, Devauchelle V, Jamin C, Cornec D, Pers JO, Le Pottier L, Hillion S. Phenotypic, transcriptomic, and spatial characterization of CD45RB + naïve mature B cells: Implications in Sjögren's disease. Clin Immunol 2024:110378. [PMID: 39393568 DOI: 10.1016/j.clim.2024.110378] [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: 06/11/2024] [Revised: 09/23/2024] [Accepted: 10/05/2024] [Indexed: 10/13/2024]
Abstract
The conventional classification of mature B cells overlooks the diversity within IgD+ CD27- naïve B cells. Here, to identify distinct mature naïve B cells, we categorized CD45RBMEM55- B cells (NA RB-) and CD45RBMEM55+ B cells (NA RB+) and explore their function and localization in circulation and tissues under physiological and pathological conditions. NA RB+ B cells, found in secondary lymphoid organs, differentiate into plasmablasts and secrete IgM. In Sjögren's disease, their numbers decrease, and they show over-activation and abnormal migration, suggesting an adaptive disease response. NA RB+ B cells also appear in inflamed salivary glands, indicating involvement in local immune responses. These findings highlight the distinct roles of NA RB+ B cells in health and Sjögren's disease.
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Affiliation(s)
| | | | | | | | - Loukas Chatzis
- UMR1227, LBAI, Univ Brest, Inserm, Brest, France; Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | | | | | - Divi Cornec
- UMR1227, LBAI, Univ Brest, Inserm, and CHU Brest, Brest, France
| | | | | | - Sophie Hillion
- UMR1227, LBAI, Univ Brest, Inserm, and CHU Brest, Brest, France.
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5
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Ishar J, Tam YM, Mages S, Klughammer J. BoReMi: Bokeh-based jupyter-interface for registering spatio-molecular data to related microscopy images. PLoS Comput Biol 2024; 20:e1012504. [PMID: 39374301 DOI: 10.1371/journal.pcbi.1012504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 09/18/2024] [Indexed: 10/09/2024] Open
Abstract
Spatio-molecular data and microscopy images provide complementary information, essential to study structure and function of spatially organised multicellular systems such as healthy or diseased tissues. However, aligning these two types of data can be challenging due to distortions and differences in resolution, orientation, and position. Manual registration is tedious but may be necessary for challenging samples as well as for the generation of ground-truth data sets that enable benchmarking of existing and emerging automated alignment tools. To make the process of manual registration more convenient, efficient, and integrated, we created BoReMi, a python-based, Jupyter-integrated, visual tool that offers all the relevant functionalities for aligning and registering spatio-molecular data and associated microscopy images. We showcase BoReMi's utility using publicly available data and images and make BoReMi as well as an interactive demo available on GitHub.
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Affiliation(s)
- Jaspreet Ishar
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Yee Man Tam
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Simon Mages
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Johanna Klughammer
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
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6
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Ren J, Luo S, Shi H, Wang X. Spatial omics advances for in situ RNA biology. Mol Cell 2024; 84:3737-3757. [PMID: 39270643 PMCID: PMC11455602 DOI: 10.1016/j.molcel.2024.08.002] [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: 05/21/2024] [Revised: 07/07/2024] [Accepted: 08/02/2024] [Indexed: 09/15/2024]
Abstract
Spatial regulation of RNA plays a critical role in gene expression regulation and cellular function. Understanding spatially resolved RNA dynamics and translation is vital for bringing new insights into biological processes such as embryonic development, neurobiology, and disease pathology. This review explores past studies in subcellular, cellular, and tissue-level spatial RNA biology driven by diverse methodologies, ranging from cell fractionation, in situ and proximity labeling, imaging, spatially indexed next-generation sequencing (NGS) approaches, and spatially informed computational modeling. Particularly, recent advances have been made for near-genome-scale profiling of RNA and multimodal biomolecules at high spatial resolution. These methods enabled new discoveries into RNA's spatiotemporal kinetics, RNA processing, translation status, and RNA-protein interactions in cells and tissues. The evolving landscape of experimental and computational strategies reveals the complexity and heterogeneity of spatial RNA biology with subcellular resolution, heralding new avenues for RNA biology research.
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Affiliation(s)
- Jingyi Ren
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shuchen Luo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hailing Shi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Xiao Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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7
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Tang Z, Luo S, Zeng H, Huang J, Sui X, Wu M, Wang X. Search and match across spatial omics samples at single-cell resolution. Nat Methods 2024; 21:1818-1829. [PMID: 39294367 DOI: 10.1038/s41592-024-02410-7] [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: 05/23/2023] [Accepted: 08/12/2024] [Indexed: 09/20/2024]
Abstract
Spatial omics technologies characterize tissue molecular properties with spatial information, but integrating and comparing spatial data across different technologies and modalities is challenging. A comparative analysis tool that can search, match and visualize both similarities and differences of molecular features in space across multiple samples is lacking. To address this, we introduce CAST (cross-sample alignment of spatial omics), a deep graph neural network-based method enabling spatial-to-spatial searching and matching at the single-cell level. CAST aligns tissues based on intrinsic similarities of spatial molecular features and reconstructs spatially resolved single-cell multi-omic profiles. CAST further allows spatially resolved differential analysis (∆Analysis) to pinpoint and visualize disease-associated molecular pathways and cell-cell interactions and single-cell relative translational efficiency profiling to reveal variations in translational control across cell types and regions. CAST serves as an integrative framework for seamless single-cell spatial data searching and matching across technologies, modalities and sample conditions.
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Affiliation(s)
- Zefang Tang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shuchen Luo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hu Zeng
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jiahao Huang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xin Sui
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Morgan Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiao Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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8
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Monasterio G, Morales RA, Bejarano DA, Abalo XM, Fransson J, Larsson L, Schlitzer A, Lundeberg J, Das S, Villablanca EJ. A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract. Nat Protoc 2024; 19:3085-3137. [PMID: 38906985 DOI: 10.1038/s41596-024-01001-2] [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: 04/05/2023] [Accepted: 02/19/2024] [Indexed: 06/23/2024]
Abstract
Tissues are dynamic and complex biological systems composed of specialized cell types that interact with each other for proper biological function. To comprehensively characterize and understand the cell circuitry underlying biological processes within tissues, it is crucial to preserve their spatial information. Here we report a simple mounting technique to maximize the area of the tissue to be analyzed, encompassing the whole length of the murine gastrointestinal (GI) tract, from mouth to rectum. Using this method, analysis of the whole murine GI tract can be performed in a single slide not only by means of histological staining, immunohistochemistry and in situ hybridization but also by multiplexed antibody staining and spatial transcriptomic approaches. We demonstrate the utility of our method in generating a comprehensive gene and protein expression profile of the whole GI tract by combining the versatile tissue-rolling technique with a cutting-edge transcriptomics method (Visium) and two cutting-edge proteomics methods (ChipCytometry and CODEX-PhenoCycler) in a systematic and easy-to-follow step-by-step procedure. The entire process, including tissue rolling, processing and sectioning, can be achieved within 2-3 d for all three methods. For Visium spatial transcriptomics, an additional 2 d are needed, whereas for spatial proteomics assays (ChipCytometry and CODEX-PhenoCycler), another 3-4 d might be considered. The whole process can be accomplished by researchers with skills in performing murine surgery, and standard histological and molecular biology methods.
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Affiliation(s)
- Gustavo Monasterio
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Rodrigo A Morales
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - David A Bejarano
- Quantitative Systems Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Xesús M Abalo
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Jennifer Fransson
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Andreas Schlitzer
- Quantitative Systems Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Srustidhar Das
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden.
- Center of Molecular Medicine, Stockholm, Sweden.
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden.
- Center of Molecular Medicine, Stockholm, Sweden.
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9
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Lacinski RA, Dziadowicz SA, Melemai VK, Fitzpatrick B, Pisquiy JJ, Heim T, Lohse I, Schoedel KE, Llosa NJ, Weiss KR, Lindsey BA. Spatial multiplexed immunofluorescence analysis reveals coordinated cellular networks associated with overall survival in metastatic osteosarcoma. Bone Res 2024; 12:55. [PMID: 39333065 PMCID: PMC11436896 DOI: 10.1038/s41413-024-00359-z] [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: 02/05/2024] [Revised: 06/16/2024] [Accepted: 07/18/2024] [Indexed: 09/29/2024] Open
Abstract
Patients diagnosed with advanced osteosarcoma, often in the form of lung metastases, have abysmal five-year overall survival rates. The complexity of the osteosarcoma immune tumor microenvironment has been implicated in clinical trial failures of various immunotherapies. The purpose of this exploratory study was to spatially characterize the immune tumor microenvironment of metastatic osteosarcoma lung specimens. Knowledge of the coordinating cellular networks within these tissues could then lead to improved outcomes when utilizing immunotherapy for treatment of this disease. Importantly, various cell types, interactions, and cellular neighborhoods were associated with five-year survival status. Of note, increases in cellular interactions between T lymphocytes, positive for programmed cell death protein 1, and myeloid-derived suppressor cells were observed in the 5-year deceased cohort. Additionally, cellular neighborhood analysis identified an Immune-Cold Parenchyma cellular neighborhood, also associated with worse 5-year survival. Finally, the Osteosarcoma Spatial Score, which approximates effector immune activity in the immune tumor microenvironment through the spatial proximity of immune and tumor cells, was increased within 5-year survivors, suggesting improved effector signaling in this patient cohort. Ultimately, these data represent a robust spatial multiplexed immunofluorescence analysis of the metastatic osteosarcoma immune tumor microenvironment. Various communication networks, and their association with survival, were described. In the future, identification of these networks may suggest the use of specific, combinatory immunotherapeutic strategies for improved anti-tumor immune responses and outcomes in osteosarcoma.
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Affiliation(s)
- Ryan A Lacinski
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, 26506, USA
- Cancer Institute, West Virginia University School of Medicine, Morgantown, WV, 26506, USA
| | - Sebastian A Dziadowicz
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, 26506, USA
- Bioinformatics Core, West Virginia University School of Medicine, Morgantown, WV, 26506, USA
| | - Vincent K Melemai
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, 26506, USA
| | - Brody Fitzpatrick
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, 26506, USA
| | - John J Pisquiy
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, 26506, USA
| | - Tanya Heim
- Department of Orthopaedic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Ines Lohse
- Department of Orthopaedic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Karen E Schoedel
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Nicolas J Llosa
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Kurt R Weiss
- Department of Orthopaedic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Brock A Lindsey
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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10
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Qiu X, Zhou T, Li S, Wu J, Tang J, Ma G, Yang S, Hu J, Wang K, Shen S, Wang H, Chen L. Spatial single-cell protein landscape reveals vimentin high macrophages as immune-suppressive in the microenvironment of hepatocellular carcinoma. NATURE CANCER 2024:10.1038/s43018-024-00824-y. [PMID: 39327501 DOI: 10.1038/s43018-024-00824-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/09/2024] [Indexed: 09/28/2024]
Abstract
Tumor microenvironment heterogeneity in hepatocellular carcinoma (HCC) on a spatial single-cell resolution is unclear. Here, we conducted co-detection by indexing to profile the spatial heterogeneity of 401 HCC samples with 36 biomarkers. By parsing the spatial tumor ecosystem of liver cancer, we identified spatial patterns with distinct prognosis and genomic and molecular features, and unveiled the progressive role of vimentin (VIM)high macrophages. Integration analysis with eight independent cohorts demonstrated that the spatial co-occurrence of VIMhigh macrophages and regulatory T cells promotes tumor progression and favors immunotherapy. Functional studies further demonstrated that VIMhigh macrophages enhance the immune-suppressive activity of regulatory T cells by mechanistically increasing the secretion of interleukin-1β. Our data provide deep insights into the heterogeneity of tumor microenvironment architecture and unveil the critical role of VIMhigh macrophages during HCC progression, which holds potential for personalized cancer prevention and drug discovery and reinforces the need to resolve spatial-informed features for cancer treatment.
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Affiliation(s)
- Xinyao Qiu
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- National Center for Liver Cancer, Shanghai, China
| | - Tao Zhou
- National Center for Liver Cancer, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Shuai Li
- Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Jianmin Wu
- Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Jing Tang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guosheng Ma
- Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Shuai Yang
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ji Hu
- National Center for Liver Cancer, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Kaiting Wang
- Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Siyun Shen
- National Center for Liver Cancer, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Hongyang Wang
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China.
- Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, China.
- Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai, China.
| | - Lei Chen
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- National Center for Liver Cancer, Shanghai, China.
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China.
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, China.
- Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai, China.
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11
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Crouigneau R, Li YF, Auxillos J, Goncalves-Alves E, Marie R, Sandelin A, Pedersen SF. Mimicking and analyzing the tumor microenvironment. CELL REPORTS METHODS 2024:100866. [PMID: 39353424 DOI: 10.1016/j.crmeth.2024.100866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 07/22/2024] [Accepted: 09/09/2024] [Indexed: 10/04/2024]
Abstract
The tumor microenvironment (TME) is increasingly appreciated to play a decisive role in cancer development and response to therapy in all solid tumors. Hypoxia, acidosis, high interstitial pressure, nutrient-poor conditions, and high cellular heterogeneity of the TME arise from interactions between cancer cells and their environment. These properties, in turn, play key roles in the aggressiveness and therapy resistance of the disease, through complex reciprocal interactions between the cancer cell genotype and phenotype, and the physicochemical and cellular environment. Understanding this complexity requires the combination of sophisticated cancer models and high-resolution analysis tools. Models must allow both control and analysis of cellular and acellular TME properties, and analyses must be able to capture the complexity at high depth and spatial resolution. Here, we review the advantages and limitations of key models and methods in order to guide further TME research and outline future challenges.
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Affiliation(s)
- Roxane Crouigneau
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yan-Fang Li
- Department of Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jamie Auxillos
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Eliana Goncalves-Alves
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rodolphe Marie
- Department of Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Albin Sandelin
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
| | - Stine Falsig Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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12
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Coullomb A, Monsarrat P, Pancaldi V. mosna reveals different types of cellular interactions predictive of response to immunotherapies and survival in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.16.532947. [PMID: 36993595 PMCID: PMC10055099 DOI: 10.1101/2023.03.16.532947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Spatially resolved omics enable the discovery of tissue organization of biological or clinical importance. Despite the existence of several methods, performing a rational analysis including multiple algorithms while integrating different conditions such as clinical data is still not trivial. To make such investigations more accessible, we developed mosna, a Python package to analyze spatial omics data with respect to clinical or biological data and to gain insight on cell interaction patterns or tissue architecture of biological relevance. mosna is compatible with all spatial omics methods, it leverages tysserand to build accurate spatial networks, and is compatible with Squidpy. It proposes an analysis pipeline, in which increasingly complex features computed at each step can be explored in integration with clinical data, either with easy-to-use descriptive statistics and data visualization, or by seamlessly training machine learning models and identifying variables with the most predictive power. mosna can take as input any dataset produced by spatial omics methods, including sub-cellular resolved transcriptomics (MERFISH, seqFISH) and proteomics (CODEX, MIBI-TOF, low-plex immuno-fluorescence), as well as spot-based spatial transcriptomics (10x Visium). Integration with experimental metadata or clinical data is adapted to binary conditions, such as biological treatments or response status of patients, and to survival data. We demonstrate the proposed analysis pipeline on two spatially resolved proteomic datasets containing either binary response to immunotherapy or survival data. mosna identifies features describing cellular composition and spatial distribution that can provide biological insight regarding factors that affect response to immunotherapies or survival.
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Affiliation(s)
- Alexis Coullomb
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- RESTORE Research Center, Université de Toulouse, INSERM 1301, CNRS 5070, EFS, ENVT, Toulouse, France
| | - Paul Monsarrat
- RESTORE Research Center, Université de Toulouse, INSERM 1301, CNRS 5070, EFS, ENVT, Toulouse, France
- Oral Medicine Department and Hospital of Toulouse - Toulouse Institute of Oral Medicine and Science, CHU de Toulouse, Toulouse, France
- Artificial and Natural Intelligence Toulouse Institute ANITI, Toulouse, France
| | - Vera Pancaldi
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
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13
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Donovan ML, Jhaveri N, Ma N, Cheikh BB, DeRosa J, Mihani R, Berrell N, Suen JY, Monkman J, Fraser JF, Kulasinghe A. Protocol for high-plex, whole-slide imaging of human formalin-fixed paraffin-embedded tissue using PhenoCycler-Fusion. STAR Protoc 2024; 5:103226. [PMID: 39031553 PMCID: PMC11314888 DOI: 10.1016/j.xpro.2024.103226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/03/2024] [Accepted: 07/05/2024] [Indexed: 07/22/2024] Open
Abstract
Single-cell spatial analysis of proteins is rapidly becoming increasingly important in revealing biological insights. Here, we present a protocol for automated high-plex multi-slide immunofluorescence staining and imaging of human head and neck cancer formalin-fixed paraffin-embedded (FFPE) sections using PhenoCycler-Fusion 2.0 technology. We describe steps for preparing human head and neck cancer FFPE tissues, staining with a panel of immunophenotyping markers, and Flow Cell assembly. We then detail procedures for setting up for a PhenoCycler-Fusion run, post-run Flow Cell removal, and downstream analyses. For complete details on the use and execution of this protocol, please refer to Jhaveri et al.1.
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Affiliation(s)
- Meg L Donovan
- Queensland Spatial Biology Centre, Wesley Research Institute, Level 8 East Wing, The Wesley Hospital, Auchenflower, QLD 4066, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Niyati Jhaveri
- Akoya Biosciences, The Spatial Biology Company, Marlborough, MA, USA
| | - Ning Ma
- Akoya Biosciences, The Spatial Biology Company, Marlborough, MA, USA
| | - Bassem Ben Cheikh
- Akoya Biosciences, The Spatial Biology Company, Marlborough, MA, USA
| | - James DeRosa
- Akoya Biosciences, The Spatial Biology Company, Marlborough, MA, USA
| | - Ritu Mihani
- Akoya Biosciences, The Spatial Biology Company, Marlborough, MA, USA
| | - Naomi Berrell
- Queensland Spatial Biology Centre, Wesley Research Institute, Level 8 East Wing, The Wesley Hospital, Auchenflower, QLD 4066, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Jacky Y Suen
- Critical Care Research Group, The Prince Charles Hospital, Brisbane, QLD 4032, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - James Monkman
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - John F Fraser
- Queensland Spatial Biology Centre, Wesley Research Institute, Level 8 East Wing, The Wesley Hospital, Auchenflower, QLD 4066, Australia; Critical Care Research Group, The Prince Charles Hospital, Brisbane, QLD 4032, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Arutha Kulasinghe
- Queensland Spatial Biology Centre, Wesley Research Institute, Level 8 East Wing, The Wesley Hospital, Auchenflower, QLD 4066, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia.
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14
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Ak Ç, Sayar Z, Thibault G, Burlingame EA, Kuykendall MJ, Eng J, Chitsazan A, Chin K, Adey AC, Boniface C, Spellman PT, Thomas GV, Kopp RP, Demir E, Chang YH, Stavrinides V, Eksi SE. Multiplex imaging of localized prostate tumors reveals altered spatial organization of AR-positive cells in the microenvironment. iScience 2024; 27:110668. [PMID: 39246442 PMCID: PMC11379676 DOI: 10.1016/j.isci.2024.110668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/19/2024] [Accepted: 08/01/2024] [Indexed: 09/10/2024] Open
Abstract
Mapping the spatial interactions of cancer, immune, and stromal cell states presents novel opportunities for patient stratification and for advancing immunotherapy. While single-cell studies revealed significant molecular heterogeneity in prostate cancer cells, the impact of spatial stromal cell heterogeneity remains poorly understood. Here, we used cyclic immunofluorescent imaging on whole-tissue sections to uncover novel spatial associations between cancer and stromal cells in low- and high-grade prostate tumors and tumor-adjacent normal tissues. Our results provide a spatial map of single cells and recurrent cellular neighborhoods in the prostate tumor microenvironment of treatment-naive patients. We report unique populations of mast cells that show distinct spatial associations with M2 macrophages and regulatory T cells. Our results show disease-specific neighborhoods that are primarily driven by androgen receptor-positive (AR+) stromal cells and identify inflammatory gene networks active in AR+ prostate stroma.
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Affiliation(s)
- Çiğdem Ak
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR 97239, USA
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR 97209, USA
| | - Zeynep Sayar
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR 97239, USA
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR 97209, USA
| | - Guillaume Thibault
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR 97209, USA
| | - Erik A Burlingame
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR 97209, USA
| | - M J Kuykendall
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR 97239, USA
| | - Jennifer Eng
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR 97209, USA
| | - Alex Chitsazan
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR 97239, USA
| | - Koei Chin
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR 97239, USA
| | - Andrew C Adey
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Knight Cancer Institute, OHSU, Portland, OR 97239, USA
| | - Christopher Boniface
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR 97239, USA
| | - Paul T Spellman
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Knight Cancer Institute, OHSU, Portland, OR 97239, USA
| | - George V Thomas
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR 97239, USA
- Department of Pathology & Laboratory Medicine, School of Medicine, OHSU, Portland, OR 97239, USA
| | - Ryan P Kopp
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR 97239, USA
- Department of Urology, School of Medicine, Knight Cancer Institute, Portland, OR 97239, USA
| | - Emek Demir
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR 97239, USA
- Division of Oncological Sciences, School of Medicine, OHSU, Portland, OR 97239, USA
| | - Young Hwan Chang
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR 97209, USA
| | | | - Sebnem Ece Eksi
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR 97239, USA
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR 97209, USA
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15
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Kwon Y, Woo J, Yu F, Williams SM, Markillie LM, Moore RJ, Nakayasu ES, Chen J, Campbell-Thompson M, Mathews CE, Nesvizhskii AI, Qian WJ, Zhu Y. Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. Mol Cell Proteomics 2024:100841. [PMID: 39307423 DOI: 10.1016/j.mcpro.2024.100841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 08/19/2024] [Accepted: 08/23/2024] [Indexed: 09/25/2024] Open
Abstract
Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in healthy and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in a whole tissue section or region of interest, has attracted significant interest because it holds great potential to directly reveal diagnostic biomarkers and therapeutic targets. While many approaches are available, however, proteome mapping still exhibits significant technical challenges in both protein coverage and analytical throughput. Since many of these existing challenges are associated with mass spectrometry-based protein identification and quantification, we performed a detailed benchmarking study of three protein quantification methods for spatial proteome mapping, including label-free, TMT-MS2, and TMT-MS3. Our study indicates label-free method provided the deepest coverages of ∼3500 proteins at a spatial resolution of 50 μm and the highest quantification dynamic range, while TMT-MS2 method holds great benefit in mapping throughput at >125 pixels per day. The evaluation also indicates both label-free and TMT-MS2 provide robust protein quantifications in identifying differentially abundant proteins and spatially co-variable clusters. In the study of pancreatic islet microenvironment, we demonstrated deep proteome mapping not only enables the identification of protein markers specific to different cell types, but more importantly, it also reveals unknown or hidden protein patterns by spatial co-expression analysis.
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Affiliation(s)
- Yumi Kwon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Jongmin Woo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Jing Chen
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Clayton E Mathews
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, United States; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States.
| | - Ying Zhu
- Department of Proteomic and Genomic Technologies, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
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16
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Wu M, Tao H, Xu T, Zheng X, Wen C, Wang G, Peng Y, Dai Y. Spatial proteomics: unveiling the multidimensional landscape of protein localization in human diseases. Proteome Sci 2024; 22:7. [PMID: 39304896 DOI: 10.1186/s12953-024-00231-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 09/01/2024] [Indexed: 09/22/2024] Open
Abstract
Spatial proteomics is a multidimensional technique that studies the spatial distribution and function of proteins within cells or tissues across both spatial and temporal dimensions. This field multidimensionally reveals the complex structure of the human proteome, including the characteristics of protein spatial distribution, dynamic protein translocation, and protein interaction networks. Recently, as a crucial method for studying protein spatial localization, spatial proteomics has been applied in the clinical investigation of various diseases. This review summarizes the fundamental concepts and characteristics of tissue-level spatial proteomics, its research progress in common human diseases such as cancer, neurological disorders, cardiovascular diseases, autoimmune diseases, and anticipates its future development trends. The aim is to highlight the significant impact of spatial proteomics on understanding disease pathogenesis, advancing diagnostic methods, and developing potential therapeutic targets in clinical research.
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Affiliation(s)
- Mengyao Wu
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Huihui Tao
- School of Medicine, Anhui University of Science & Technology, Huainan, China.
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institutes, Huainan, China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Huainan, China.
| | - Tiantian Xu
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Xuejia Zheng
- The First Hospital of Anhui University of Science and Technology, Huainan, China
| | - Chunmei Wen
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Guoying Wang
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Yali Peng
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Yong Dai
- School of Medicine, Anhui University of Science & Technology, Huainan, China
- The First Hospital of Anhui University of Science and Technology, Huainan, China
- Joint Research Center for Occupational Medicine and Health of IHM, Anhui University of Science and Technology, Huainan, China
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17
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Pang M, Roy TK, Wu X, Tan K. CelloType: A Unified Model for Segmentation and Classification of Tissue Images. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.15.613139. [PMID: 39345491 PMCID: PMC11429831 DOI: 10.1101/2024.09.15.613139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Cell segmentation and classification are critical tasks in spatial omics data analysis. We introduce CelloType, an end-to-end model designed for cell segmentation and classification of biomedical microscopy images. Unlike the traditional two-stage approach of segmentation followed by classification, CelloType adopts a multi-task learning approach that connects the segmentation and classification tasks and simultaneously boost the performance of both tasks. CelloType leverages Transformer-based deep learning techniques for enhanced accuracy of object detection, segmentation, and classification. It outperforms existing segmentation methods using ground-truths from public databases. In terms of classification, CelloType outperforms a baseline model comprised of state-of-the-art methods for individual tasks. Using multiplexed tissue images, we further demonstrate the utility of CelloType for multi-scale segmentation and classification of both cellular and non-cellular elements in a tissue. The enhanced accuracy and multi-task-learning ability of CelloType facilitate automated annotation of rapidly growing spatial omics data.
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18
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Xiong X, Wang X, Liu CC, Shao ZM, Yu KD. Deciphering breast cancer dynamics: insights from single-cell and spatial profiling in the multi-omics era. Biomark Res 2024; 12:107. [PMID: 39294728 PMCID: PMC11411917 DOI: 10.1186/s40364-024-00654-1] [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: 06/28/2024] [Accepted: 09/10/2024] [Indexed: 09/21/2024] Open
Abstract
As one of the most common tumors in women, the pathogenesis and tumor heterogeneity of breast cancer have long been the focal point of research, with the emergence of tumor metastasis and drug resistance posing persistent clinical challenges. The emergence of single-cell sequencing (SCS) technology has introduced novel approaches for gaining comprehensive insights into the biological behavior of malignant tumors. SCS is a high-throughput technology that has rapidly developed in the past decade, providing high-throughput molecular insights at the individual cell level. Furthermore, the advent of multitemporal point sampling and spatial omics also greatly enhances our understanding of cellular dynamics at both temporal and spatial levels. The paper provides a comprehensive overview of the historical development of SCS, and highlights the most recent advancements in utilizing SCS and spatial omics for breast cancer research. The findings from these studies will serve as valuable references for future advancements in basic research, clinical diagnosis, and treatment of breast cancer.
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Affiliation(s)
- Xin Xiong
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xin Wang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Cui-Cui Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ke-Da Yu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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19
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Xiao Y, Li Y, Zhao H. Spatiotemporal metabolomic approaches to the cancer-immunity panorama: a methodological perspective. Mol Cancer 2024; 23:202. [PMID: 39294747 PMCID: PMC11409752 DOI: 10.1186/s12943-024-02113-9] [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: 07/03/2024] [Accepted: 09/05/2024] [Indexed: 09/21/2024] Open
Abstract
Metabolic reprogramming drives the development of an immunosuppressive tumor microenvironment (TME) through various pathways, contributing to cancer progression and reducing the effectiveness of anticancer immunotherapy. However, our understanding of the metabolic landscape within the tumor-immune context has been limited by conventional metabolic measurements, which have not provided comprehensive insights into the spatiotemporal heterogeneity of metabolism within TME. The emergence of single-cell, spatial, and in vivo metabolomic technologies has now enabled detailed and unbiased analysis, revealing unprecedented spatiotemporal heterogeneity that is particularly valuable in the field of cancer immunology. This review summarizes the methodologies of metabolomics and metabolic regulomics that can be applied to the study of cancer-immunity across single-cell, spatial, and in vivo dimensions, and systematically assesses their benefits and limitations.
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Affiliation(s)
- Yang Xiao
- Chongqing University Cancer Hospital, School of Medicine, Chongqing University, Chongqing, 400044, China
| | - Yongsheng Li
- Chongqing University Cancer Hospital, School of Medicine, Chongqing University, Chongqing, 400044, China.
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China.
| | - Huakan Zhao
- Chongqing University Cancer Hospital, School of Medicine, Chongqing University, Chongqing, 400044, China.
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China.
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20
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Li NY, Zhang W, Haensel D, Jussila AR, Pan C, Gaddam S, Plevritis SK, Oro AE. Basal-to-inflammatory transition and tumor resistance via crosstalk with a pro-inflammatory stromal niche. Nat Commun 2024; 15:8134. [PMID: 39289380 PMCID: PMC11408617 DOI: 10.1038/s41467-024-52394-3] [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: 01/24/2024] [Accepted: 09/05/2024] [Indexed: 09/19/2024] Open
Abstract
Cancer-associated inflammation is a double-edged sword possessing both pro- and anti-tumor properties through ill-defined tumor-immune dynamics. While we previously identified a carcinoma tumor-intrinsic resistance pathway, basal-to-squamous cell carcinoma transition, here, employing a multipronged single-cell and spatial-omics approach, we identify an inflammation and therapy-enriched tumor state we term basal-to-inflammatory transition. Basal-to-inflammatory transition signature correlates with poor overall patient survival in many epithelial tumors. Basal-to-squamous cell carcinoma transition and basal-to-inflammatory transition occur in adjacent but distinct regions of a single tumor: basal-to-squamous cell carcinoma transition arises within the core tumor nodule, while basal-to-inflammatory transition emerges from a specialized inflammatory environment defined by a tumor-associated TREM1 myeloid signature. TREM1 myeloid-derived cytokines IL1 and OSM induce basal-to-inflammatory transition in vitro and in vivo through NF-κB, lowering sensitivity of patient basal cell carcinoma explant tumors to Smoothened inhibitor treatment. This work deepens our knowledge of the heterogeneous local tumor microenvironment and nominates basal-to-inflammatory transition as a drug-resistant but targetable tumor state driven by a specialized inflammatory microenvironment.
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Affiliation(s)
- Nancy Yanzhe Li
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Weiruo Zhang
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Haensel
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna R Jussila
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Cory Pan
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sadhana Gaddam
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sylvia K Plevritis
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Anthony E Oro
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.
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21
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Dos Santos Peixoto R, Miller BF, Brusko MA, Aihara G, Atta L, Anant M, Atkinson MA, Brusko TM, Wasserfall CH, Fan J. Characterizing cell-type spatial relationships across length scales in spatially resolved omics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.05.560733. [PMID: 39314450 PMCID: PMC11418938 DOI: 10.1101/2023.10.05.560733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Spatially resolved omics (SRO) technologies enable the identification of cell types while preserving their organization within tissues. Application of such technologies offers the opportunity to delineate cell-type spatial relationships, particularly across different length scales, and enhance our understanding of tissue organization and function. To quantify such multi-scale cell-type spatial relationships, we developed CRAWDAD, Cell-type Relationship Analysis Workflow Done Across Distances, as an open-source R package with source code and additional documentation at https://jef.works/CRAWDAD/. To demonstrate the utility of such multi-scale characterization, recapitulate expected cell-type spatial relationships, and evaluate against other cell-type spatial analyses, we applied CRAWDAD to various simulated and real SRO datasets of diverse tissues assayed by diverse SRO technologies. We further demonstrate how such multi-scale characterization enabled by CRAWDAD can be used to compare cell-type spatial relationships across multiple samples. Finally, we applied CRAWDAD to SRO datasets of the human spleen to identify consistent as well as patient and sample-specific cell-type spatial relationships. In general, we anticipate such multi-scale analysis of SRO data enabled by CRAWDAD will provide useful quantitative metrics to facilitate the identification, characterization, and comparison of cell-type spatial relationships across axes of interest.
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Affiliation(s)
- Rafael Dos Santos Peixoto
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21211
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Brendan F Miller
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21211
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Maigan A Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610
| | - Gohta Aihara
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21211
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Lyla Atta
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21211
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Manjari Anant
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21211
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205
| | - Mark A Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610
| | - Todd M Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610
| | - Clive H Wasserfall
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610
| | - Jean Fan
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21211
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
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22
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Liang W, Zhu Z, Xu D, Wang P, Guo F, Xiao H, Hou C, Xue J, Zhi X, Ran R. The burgeoning spatial multi-omics in human gastrointestinal cancers. PeerJ 2024; 12:e17860. [PMID: 39285924 PMCID: PMC11404479 DOI: 10.7717/peerj.17860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/14/2024] [Indexed: 09/19/2024] Open
Abstract
The development and progression of diseases in multicellular organisms unfold within the intricate three-dimensional body environment. Thus, to comprehensively understand the molecular mechanisms governing individual development and disease progression, precise acquisition of biological data, including genome, transcriptome, proteome, metabolome, and epigenome, with single-cell resolution and spatial information within the body's three-dimensional context, is essential. This foundational information serves as the basis for deciphering cellular and molecular mechanisms. Although single-cell multi-omics technology can provide biological information such as genome, transcriptome, proteome, metabolome, and epigenome with single-cell resolution, the sample preparation process leads to the loss of spatial information. Spatial multi-omics technology, however, facilitates the characterization of biological data, such as genome, transcriptome, proteome, metabolome, and epigenome in tissue samples, while retaining their spatial context. Consequently, these techniques significantly enhance our understanding of individual development and disease pathology. Currently, spatial multi-omics technology has played a vital role in elucidating various processes in tumor biology, including tumor occurrence, development, and metastasis, particularly in the realms of tumor immunity and the heterogeneity of the tumor microenvironment. Therefore, this article provides a comprehensive overview of spatial transcriptomics, spatial proteomics, and spatial metabolomics-related technologies and their application in research concerning esophageal cancer, gastric cancer, and colorectal cancer. The objective is to foster the research and implementation of spatial multi-omics technology in digestive tumor diseases. This review will provide new technical insights for molecular biology researchers.
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Affiliation(s)
- Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei province, China
| | - Zhenpeng Zhu
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
- Hebei North University, Zhangjiakou, Hebei Province, China
| | - Dandan Xu
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei province, China
| | - Peng Wang
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
- Hebei North University, Zhangjiakou, Hebei Province, China
| | - Fei Guo
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
| | - Haoshan Xiao
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
- Hebei North University, Zhangjiakou, Hebei Province, China
| | - Chenyang Hou
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
- Hebei North University, Zhangjiakou, Hebei Province, China
| | - Jun Xue
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
| | - Xuejun Zhi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei province, China
| | - Rensen Ran
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei province, China
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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23
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Pati P, Karkampouna S, Bonollo F, Compérat E, Radić M, Spahn M, Martinelli A, Wartenberg M, Kruithof-de Julio M, Rapsomaniki M. Accelerating histopathology workflows with generative AI-based virtually multiplexed tumour profiling. NAT MACH INTELL 2024; 6:1077-1093. [PMID: 39309216 PMCID: PMC11415301 DOI: 10.1038/s42256-024-00889-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 07/29/2024] [Indexed: 09/25/2024]
Abstract
Understanding the spatial heterogeneity of tumours and its links to disease initiation and progression is a cornerstone of cancer biology. Presently, histopathology workflows heavily rely on hematoxylin and eosin and serial immunohistochemistry staining, a cumbersome, tissue-exhaustive process that results in non-aligned tissue images. We propose the VirtualMultiplexer, a generative artificial intelligence toolkit that effectively synthesizes multiplexed immunohistochemistry images for several antibody markers (namely AR, NKX3.1, CD44, CD146, p53 and ERG) from only an input hematoxylin and eosin image. The VirtualMultiplexer captures biologically relevant staining patterns across tissue scales without requiring consecutive tissue sections, image registration or extensive expert annotations. Thorough qualitative and quantitative assessment indicates that the VirtualMultiplexer achieves rapid, robust and precise generation of virtually multiplexed imaging datasets of high staining quality that are indistinguishable from the real ones. The VirtualMultiplexer is successfully transferred across tissue scales and patient cohorts with no need for model fine-tuning. Crucially, the virtually multiplexed images enabled training a graph transformer that simultaneously learns from the joint spatial distribution of several proteins to predict clinically relevant endpoints. We observe that this multiplexed learning scheme was able to greatly improve clinical prediction, as corroborated across several downstream tasks, independent patient cohorts and cancer types. Our results showcase the clinical relevance of artificial intelligence-assisted multiplexed tumour imaging, accelerating histopathology workflows and cancer biology.
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Affiliation(s)
| | - Sofia Karkampouna
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Francesco Bonollo
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Eva Compérat
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Martina Radić
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Martin Spahn
- Department of Urology, Lindenhofspital Bern, Bern, Switzerland
- Department of Urology, University Duisburg-Essen, Essen, Germany
| | - Adriano Martinelli
- IBM Research Europe, Rüschlikon, Switzerland
- ETH Zürich, Zürich, Switzerland
- Biomedical Data Science Center, Lausanne University Hospital, Lausanne, Switzerland
| | - Martin Wartenberg
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Marianna Kruithof-de Julio
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Translational Organoid Resource, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Marianna Rapsomaniki
- IBM Research Europe, Rüschlikon, Switzerland
- Biomedical Data Science Center, Lausanne University Hospital, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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24
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Trapnell C. Revealing gene function with statistical inference at single-cell resolution. Nat Rev Genet 2024; 25:623-638. [PMID: 38951690 DOI: 10.1038/s41576-024-00750-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 07/03/2024]
Abstract
Single-cell and spatial molecular profiling assays have shown large gains in sensitivity, resolution and throughput. Applying these technologies to specimens from human and model organisms promises to comprehensively catalogue cell types, reveal their lineage origins in development and discern their contributions to disease pathogenesis. Moreover, rapidly dropping costs have made well-controlled perturbation experiments and cohort studies widely accessible, illuminating mechanisms that give rise to phenotypes at the scale of the cell, the tissue and the whole organism. Interpreting the coming flood of single-cell data, much of which will be spatially resolved, will place a tremendous burden on existing computational pipelines. However, statistical concepts, models, tools and algorithms can be repurposed to solve problems now arising in genetic and molecular biology studies of development and disease. Here, I review how the questions that recent technological innovations promise to answer can be addressed by the major classes of statistical tools.
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Affiliation(s)
- Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Seattle Hub for Synthetic Biology, Seattle, WA, USA.
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25
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Minne RL, Luo NY, Traynor AM, Huang M, DeTullio L, Godden J, Stoppler M, Kimple RJ, Baschnagel AM. Genomic and Immune Landscape Comparison of MET Exon 14 Skipping and MET-Amplified Non-small Cell Lung Cancer. Clin Lung Cancer 2024; 25:567-576.e1. [PMID: 38852006 DOI: 10.1016/j.cllc.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Mutation or amplification of the mesenchymal-epithelial transition (MET) tyrosine kinase receptor causes dysregulation of receptor function and stimulates tumor growth in non-small cell lung cancer (NSCLC) with the most common mutation being MET exon 14 (METex14). We sought to compare the genomic and immune landscape of MET-altered NSCLC with MET wild-type NSCLC. METHODS 18,047 NSCLC tumors were sequenced with Tempus xT assay. Tumors were categorized based on MET exon 14 (METex14) mutations; low MET amplification defined as a copy number gain (CNG) 6-9, high MET amplification defined as CNG ≥ 10, and MET other type mutations. Immuno-oncology (IO) biomarkers and the frequency of other somatic gene alterations were compared across MET-altered and MET wild-type groups. RESULTS 276 (1.53%) METex14, 138 (0.76%) high METamp, 63 (0.35%) low METamp, 27 (0.15%) MET other, and 17,543 (97%) MET wild-type were identified. Patients with any MET mutation including METex14 were older, while patients with METex14 were more frequently female and nonsmokers. MET gene expression was highest in METamp tumors. PD-L1 positivity rates were higher in MET-altered groups than MET wild-type. METex14 exhibited the lowest tumor mutational burden (TMB) and lowest neoantigen tumor burden (NTB). METamp exhibited the lowest proportion of CD4 T cells and the highest proportion of NK cells. There were significant differences in co-alterations between METamp and METex14. CONCLUSIONS METex14 tumors exhibited differences in IO biomarkers and the somatic landscape compared to non-METex14 NSCLC tumors. Variations in immune profiles can affect immunotherapy selection in MET-altered NSCLC and require further exploration.
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Affiliation(s)
- Rachel L Minne
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Natalie Y Luo
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Anne M Traynor
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | | | | | | | | | - Randall J Kimple
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Andrew M Baschnagel
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin.
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26
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Chen J, Larsson L, Swarbrick A, Lundeberg J. Spatial landscapes of cancers: insights and opportunities. Nat Rev Clin Oncol 2024; 21:660-674. [PMID: 39043872 DOI: 10.1038/s41571-024-00926-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2024] [Indexed: 07/25/2024]
Abstract
Solid tumours comprise many different cell types organized in spatially structured arrangements, with substantial intratumour and intertumour heterogeneity. Advances in spatial profiling technologies over the past decade hold promise to capture the complexity of these cellular architectures to build a holistic view of the intricate molecular mechanisms that shape the tumour ecosystem. Some of these mechanisms act at the cellular scale and are controlled by cell-autonomous programmes or communication between nearby cells, whereas other mechanisms result from coordinated efforts between large networks of cells and extracellular molecules organized into tissues and organs. In this Review we provide insights into the application of single-cell and spatial profiling tools, with a focus on spatially resolved transcriptomic tools developed to understand the cellular architecture of the tumour microenvironment and identify opportunities to use them to improve clinical management of cancers.
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Affiliation(s)
- Julia Chen
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Department of Medical Oncology, St George Hospital, Sydney, New South Wales, Australia
| | - Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
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27
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Ubogu EE, Conner JA, Wang Y, Yadav D, Saunders TL. Development of a major histocompatibility complex class II conditional knockout mouse to study cell-specific and time-dependent adaptive immune responses in peripheral nerves. Muscle Nerve 2024; 70:420-433. [PMID: 38922958 DOI: 10.1002/mus.28193] [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: 06/05/2023] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
INTRODUCTION/AIMS The precise relationship between molecular mimicry and tissue-specific autoimmunity is unknown. Major histocompatibility complex (MHC) class II antigen presenting cell-CD4+ T-cell receptor complex interactions are necessary for adaptive immunity. This study aimed to determine the role of endoneurial endothelial cell MHC class II in autoimmune polyneuropathy. METHODS Cryopreserved Guillain-Barré syndrome (GBS) patient sural nerve biopsies and sciatic nerves from the severe murine experimental autoimmune neuritis (sm-EAN) GBS model were studied. Cultured conditional ready MHC Class II antigen A-alpha chain (H2-Aa) embryonic stem cells were used to generate H2-Aaflox/+ C57BL/6 mice. Mice were backcrossed and intercrossed to the SJL background to generate H2-Aaflox/flox SJL mice, bred with hemizygous Tamoxifen-inducible von Willebrand factor Cre recombinase (vWF-iCre/+) SJL mice to generate H2-Aaflox/flox; vWF-iCre/+ mice to study microvascular endothelial cell adaptive immune responses. Sm-EAN was induced in Tamoxifen-treated H2-Aaflox/flox; vWF-iCre/+, H2-Aaflox/flox; +/+, H2-Aa+/+; vWF-iCre/+ and untreated H2-Aaflox/flox; vWF-iCre/+ adult female SJL mice. Neurobehavioral, electrophysiological and histopathological assessments were performed at predefined time points. RESULTS Endoneurial endothelial cell MHC class II expression was observed in normal and inflamed human and mouse peripheral nerves. Tamoxifen-treated H2-Aaflox/flox; vWF-iCre/+ mice were resistant to sm-EAN despite extensive MHC class II expression in lymphoid and non-lymphoid tissues. DISCUSSION A conditional MHC class II knockout mouse to study cell- and time-dependent adaptive immune responses in vivo was developed. Initial studies show microvascular endothelial cell MHC class II expression is necessary for peripheral nerve specific autoimmunity, as advocated by human in vitro adaptive immunity and ex vivo transplant rejection studies.
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Affiliation(s)
- Eroboghene E Ubogu
- Neuromuscular Immunopathology Research Laboratory, Division of Neuromuscular Disease, Department of Neurology, University of Alabama, Birmingham, Alabama, USA
| | - Jeremy A Conner
- Neuromuscular Immunopathology Research Laboratory, Division of Neuromuscular Disease, Department of Neurology, University of Alabama, Birmingham, Alabama, USA
| | - Yimin Wang
- Neuromuscular Immunopathology Research Laboratory, Division of Neuromuscular Disease, Department of Neurology, University of Alabama, Birmingham, Alabama, USA
| | - Dinesh Yadav
- Neuromuscular Immunopathology Research Laboratory, Division of Neuromuscular Disease, Department of Neurology, University of Alabama, Birmingham, Alabama, USA
| | - Thomas L Saunders
- Transgenic Animal Model Core, University of Michigan, Ann Arbor, Michigan, USA
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28
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Kurikawa Y, Koyama-Honda I, Tamura N, Koike S, Mizushima N. Organelle landscape analysis using a multiparametric particle-based method. PLoS Biol 2024; 22:e3002777. [PMID: 39288101 PMCID: PMC11407678 DOI: 10.1371/journal.pbio.3002777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/30/2024] [Indexed: 09/19/2024] Open
Abstract
Organelles have unique structures and molecular compositions for their functions and have been classified accordingly. However, many organelles are heterogeneous and in the process of maturation and differentiation. Because traditional methods have a limited number of parameters and spatial resolution, they struggle to capture the heterogeneous landscapes of organelles. Here, we present a method for multiparametric particle-based analysis of organelles. After disrupting cells, fluorescence microscopy images of organelle particles labeled with 6 to 8 different organelle markers were obtained, and their multidimensional data were represented in two-dimensional uniform manifold approximation and projection (UMAP) spaces. This method enabled visualization of landscapes of 7 major organelles as well as the transitional states of endocytic organelles directed to the recycling and degradation pathways. Furthermore, endoplasmic reticulum-mitochondria contact sites were detected in these maps. Our proposed method successfully detects a wide array of organelles simultaneously, enabling the analysis of heterogeneous organelle landscapes.
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Affiliation(s)
- Yoshitaka Kurikawa
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ikuko Koyama-Honda
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Norito Tamura
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seiichi Koike
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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29
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Kondo A, McGrady M, Nallapothula D, Ali H, Trevino AE, Lam A, Preska R, D'Angio HB, Wu Z, Lopez LN, Badhesha HK, Vargas CR, Ramesh A, Wiegley N, Han SS, Dall'Era M, Jen KY, Mayer AT, Afkarian M. Spatial proteomics of human diabetic kidney disease, from health to class III. Diabetologia 2024; 67:1962-1979. [PMID: 39037603 DOI: 10.1007/s00125-024-06210-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/30/2024] [Indexed: 07/23/2024]
Abstract
AIMS/HYPOTHESIS Diabetic kidney disease (DKD) is the leading cause of chronic and end-stage kidney disease in the USA and worldwide. Animal models have taught us much about DKD mechanisms, but translation of this knowledge into treatments for human disease has been slowed by the lag in our molecular understanding of human DKD. METHODS Using our Spatial TissuE Proteomics (STEP) pipeline (comprising curated human kidney tissues, multiplexed immunofluorescence and powerful analysis tools), we imaged and analysed the expression of 21 proteins in 23 tissue sections from individuals with diabetes and healthy kidneys (n=5), compared to those with DKDIIA, IIA-B and IIB (n=2 each) and DKDIII (n=1). RESULTS These analyses revealed the existence of 11 cellular clusters (kidney compartments/cell types): podocytes, glomerular endothelial cells, proximal tubules, distal nephron, peritubular capillaries, blood vessels (endothelial cells and vascular smooth muscle cells), macrophages, myeloid cells, other CD45+ inflammatory cells, basement membrane and the interstitium. DKD progression was associated with co-localised increases in inflammatory cells and collagen IV deposition, with concomitant loss of native proteins of each nephron segment. Cell-type frequency and neighbourhood analyses highlighted a significant increase in inflammatory cells and their adjacency to tubular and αSMA+ (α-smooth muscle actin-positive) cells in DKD. Finally, DKD progression showed marked regional variability within single tissue sections, as well as inter-individual variability within each DKD class. CONCLUSIONS/INTERPRETATION Using the STEP pipeline, we found alterations in protein expression, cellular phenotypic composition and microenvironment structure with DKD progression, demonstrating the power of this pipeline to reveal the pathophysiology of human DKD.
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Affiliation(s)
| | | | | | - Hira Ali
- Enable Medicine, Menlo Park, CA, USA
| | | | - Amy Lam
- Enable Medicine, Menlo Park, CA, USA
| | | | | | | | - Lauren N Lopez
- Division of Nephrology, University of California, Davis, CA, USA
| | | | - Chenoa R Vargas
- Division of Nephrology, University of California, Davis, CA, USA
| | | | - Nasim Wiegley
- Division of Nephrology, University of California, Davis, CA, USA
| | - Seung Seok Han
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Marc Dall'Era
- Department of Urologic Surgery, University of California-Davis Medical Center, Sacramento, CA, USA
| | - Kuang-Yu Jen
- Department of Pathology and Laboratory Medicine, University of California- Davis, Sacramento, CA, USA
| | | | - Maryam Afkarian
- Division of Nephrology, University of California, Davis, CA, USA.
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30
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Kochetov B, Bell PD, Garcia PS, Shalaby AS, Raphael R, Raymond B, Leibowitz BJ, Schoedel K, Brand RM, Brand RE, Yu J, Zhang L, Diergaarde B, Schoen RE, Singhi A, Uttam S. UNSEG: unsupervised segmentation of cells and their nuclei in complex tissue samples. Commun Biol 2024; 7:1062. [PMID: 39215205 PMCID: PMC11364851 DOI: 10.1038/s42003-024-06714-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Abstract
Multiplexed imaging technologies have made it possible to interrogate complex tissue microenvironments at sub-cellular resolution within their native spatial context. However, proper quantification of this complexity requires the ability to easily and accurately segment cells into their sub-cellular compartments. Within the supervised learning paradigm, deep learning-based segmentation methods demonstrating human level performance have emerged. However, limited work has been done in developing such generalist methods within the unsupervised context. Here we present an easy-to-use unsupervised segmentation (UNSEG) method that achieves deep learning level performance without requiring any training data via leveraging a Bayesian-like framework, and nucleus and cell membrane markers. We show that UNSEG is internally consistent and better at generalizing to the complexity of tissue morphology than current deep learning methods, allowing it to unambiguously identify the cytoplasmic compartment of a cell, and localize molecules to their correct sub-cellular compartment. We also introduce a perturbed watershed algorithm for stably and automatically segmenting a cluster of cell nuclei into individual nuclei that increases the accuracy of classical watershed. Finally, we demonstrate the efficacy of UNSEG on a high-quality annotated gastrointestinal tissue dataset we have generated, on publicly available datasets, and in a range of practical scenarios.
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Affiliation(s)
- Bogdan Kochetov
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Phoenix D Bell
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
- Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Paulo S Garcia
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Akram S Shalaby
- University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH, USA
| | - Rebecca Raphael
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Benjamin Raymond
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brian J Leibowitz
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Karen Schoedel
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rhonda M Brand
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Magee Womens Research Institute, Pittsburgh, PA, USA
| | - Randall E Brand
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jian Yu
- Department of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lin Zhang
- Department of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Brenda Diergaarde
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert E Schoen
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aatur Singhi
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shikhar Uttam
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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31
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Bialy N, Alber F, Andrews B, Angelo M, Beliveau B, Bintu L, Boettiger A, Boehm U, Brown CM, Maina MB, Chambers JJ, Cimini BA, Eliceiri K, Errington R, Faklaris O, Gaudreault N, Germain RN, Goscinski W, Grunwald D, Halter M, Hanein D, Hickey JW, Lacoste J, Laude A, Lundberg E, Ma J, Malacrida L, Moore J, Nelson G, Neumann EK, Nitschke R, Onami S, Pimentel JA, Plant AL, Radtke AJ, Sabata B, Schapiro D, Schöneberg J, Spraggins JM, Sudar D, Vierdag WMAM, Volkmann N, Wählby C, Wang SS, Yaniv Z, Strambio-De-Castillia C. Harmonizing the Generation and Pre-publication Stewardship of FAIR bioimage data. ARXIV 2024:arXiv:2401.13022v5. [PMID: 38351940 PMCID: PMC10862930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health. For this potential to be realized, quality-assured bioimage data must be shared among labs at a global scale to be compared, pooled, and reanalyzed, thus unleashing untold potential beyond the original purpose for which the data was generated. There are two broad sets of requirements to enable bioimage data sharing in the life sciences. One set of requirements is articulated in the companion White Paper entitled "Enabling Global Image Data Sharing in the Life Sciences," which is published in parallel and addresses the need to build the cyberinfrastructure for sharing bioimage data (arXiv:2401.13023 [q-bio.OT], https://doi.org/10.48550/arXiv.2401.13023). Here, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse bioimage data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made generating community standard practices for imaging Quality Control (QC) and metadata (Faklaris et al., 2022; Hammer et al., 2021; Huisman et al., 2021; Microscopy Australia, 2016; Montero Llopis et al., 2021; Rigano et al., 2021; Sarkans et al., 2021). We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges and democratize access to common practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.
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Affiliation(s)
- Nikki Bialy
- Morgridge Institute for Research, Madison, USA
| | | | | | | | | | | | | | | | | | | | | | - Beth A Cimini
- Broad Institute of MIT and Harvard, Imaging Platform, Cambridge, USA
| | - Kevin Eliceiri
- Morgridge Institute for Research, Madison, USA
- University of Wisconsin-Madison, Madison, USA
| | | | | | | | - Ronald N Germain
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | - Michael Halter
- National Institute of Standards and Technology, Gaithersburg, USA
| | | | | | | | - Alex Laude
- Newcastle University, Newcastle upon Tyne, UK
| | - Emma Lundberg
- Stanford University, Palo Alto, USA
- SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jian Ma
- Carnegie Mellon University, Pittsburgh, USA
| | - Leonel Malacrida
- Institut Pasteur de Montevideo, & Universidad de la República, Montevideo, Uruguay
| | - Josh Moore
- German BioImaging-Gesellschaft für Mikroskopie und Bildanalyse e.V., Constance, Germany
| | - Glyn Nelson
- Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Anne L Plant
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Andrea J Radtke
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | | | | | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, USA
| | | | | | | | | | - Ziv Yaniv
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
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32
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Wang Y, Liu X, Zeng Y, Saka S, Xie W, Goldaracena I, Kohman R, Yin P, Church G. Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions. Nucleic Acids Res 2024; 52:e71. [PMID: 38966983 PMCID: PMC11347153 DOI: 10.1093/nar/gkae592] [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: 07/25/2023] [Revised: 05/23/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Antibodies have long served as vital tools in biological and clinical laboratories for the specific detection of proteins. Conventional methods employ fluorophore or horseradish peroxidase-conjugated antibodies to detect signals. More recently, DNA-conjugated antibodies have emerged as a promising technology, capitalizing on the programmability and amplification capabilities of DNA to enable highly multiplexed and ultrasensitive protein detection. However, the nonspecific binding of DNA-conjugated antibodies has impeded the widespread adoption of this approach. Here, we present a novel DNA-conjugated antibody staining protocol that addresses these challenges and demonstrates superior performance in suppressing nonspecific signals compared to previously published protocols. We further extend the utility of DNA-conjugated antibodies for signal-amplified in situ protein imaging through the hybridization chain reaction (HCR) and design a novel HCR DNA pair to expand the HCR hairpin pool from the previously published 5 pairs to 13, allowing for flexible hairpin selection and higher multiplexing. Finally, we demonstrate highly multiplexed in situ protein imaging using these techniques in both cultured cells and tissue sections.
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Affiliation(s)
- Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Xiaoyu Liu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Yitian Zeng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Wenxin Xie
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Isabel Goldaracena
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Richie E Kohman
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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33
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White BS, de Reyniès A, Newman AM, Waterfall JJ, Lamb A, Petitprez F, Lin Y, Yu R, Guerrero-Gimenez ME, Domanskyi S, Monaco G, Chung V, Banerjee J, Derrick D, Valdeolivas A, Li H, Xiao X, Wang S, Zheng F, Yang W, Catania CA, Lang BJ, Bertus TJ, Piermarocchi C, Caruso FP, Ceccarelli M, Yu T, Guo X, Bletz J, Coller J, Maecker H, Duault C, Shokoohi V, Patel S, Liliental JE, Simon S, Saez-Rodriguez J, Heiser LM, Guinney J, Gentles AJ. Community assessment of methods to deconvolve cellular composition from bulk gene expression. Nat Commun 2024; 15:7362. [PMID: 39191725 PMCID: PMC11350143 DOI: 10.1038/s41467-024-50618-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 07/11/2024] [Indexed: 08/29/2024] Open
Abstract
We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression of tumor samples, through a community-wide DREAM Challenge. We assess six published and 22 community-contributed methods using in vitro and in silico transcriptional profiles of admixed cancer and healthy immune cells. Several published methods predict most cell types well, though they either were not trained to evaluate all functional CD8+ T cell states or do so with low accuracy. Several community-contributed methods address this gap, including a deep learning-based approach, whose strong performance establishes the applicability of this paradigm to deconvolution. Despite being developed largely using immune cells from healthy tissues, deconvolution methods predict levels of tumor-derived immune cells well. Our admixed and purified transcriptional profiles will be a valuable resource for developing deconvolution methods, including in response to common challenges we observe across methods, such as sensitive identification of functional CD4+ T cell states.
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Affiliation(s)
- Brian S White
- Sage Bionetworks, Seattle, WA, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Aurélien de Reyniès
- Centre de Recherche des Cordeliers, INSERM U1138, Université Paris Cité, Paris, France
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Joshua J Waterfall
- INSERM U830 and Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | | | - Florent Petitprez
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
- MRC Centre for Reproductive Health, the Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Yating Lin
- Xiamen University, Xiamen, Fujian, China
| | | | - Martin E Guerrero-Gimenez
- Institute of Biochemistry and Biotechnology, School of Medicine, National University of Cuyo, Mendoza, Argentina
| | | | - Gianni Monaco
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, AV, Italy
| | | | | | - Daniel Derrick
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alberto Valdeolivas
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Haojun Li
- Xiamen University, Xiamen, Fujian, China
| | - Xu Xiao
- Xiamen University, Xiamen, Fujian, China
| | - Shun Wang
- Department of Pathology, Cancer Hospital, Chinese Aacdemy of Medical Science, Beijing, China
| | | | | | - Carlos A Catania
- Laboratory of Intelligent Systems (LABSIN), Engineering School, National University of Cuyo, Mendoza, Argentina
| | - Benjamin J Lang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | | | - Francesca P Caruso
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, AV, Italy
| | - Michele Ceccarelli
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, AV, Italy
- Sylvester Comprehensive Cancer Center, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, Florida, USA
| | | | | | | | - John Coller
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA, USA
| | - Holden Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Caroline Duault
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Vida Shokoohi
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA, USA
| | - Shailja Patel
- Translational Applications Service Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Joanna E Liliental
- Translational Applications Service Center, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Laura M Heiser
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | | | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
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34
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Liu L, Chen A, Li Y, Mulder J, Heyn H, Xu X. Spatiotemporal omics for biology and medicine. Cell 2024; 187:4488-4519. [PMID: 39178830 DOI: 10.1016/j.cell.2024.07.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/05/2024] [Accepted: 07/23/2024] [Indexed: 08/26/2024]
Abstract
The completion of the Human Genome Project has provided a foundational blueprint for understanding human life. Nonetheless, understanding the intricate mechanisms through which our genetic blueprint is involved in disease or orchestrates development across temporal and spatial dimensions remains a profound scientific challenge. Recent breakthroughs in cellular omics technologies have paved new pathways for understanding the regulation of genomic elements and the relationship between gene expression, cellular functions, and cell fate determination. The advent of spatial omics technologies, encompassing both imaging and sequencing-based methodologies, has enabled a comprehensive understanding of biological processes from a cellular ecosystem perspective. This review offers an updated overview of how spatial omics has advanced our understanding of the translation of genetic information into cellular heterogeneity and tissue structural organization and their dynamic changes over time. It emphasizes the discovery of various biological phenomena, related to organ functionality, embryogenesis, species evolution, and the pathogenesis of diseases.
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Affiliation(s)
| | - Ao Chen
- BGI Research, Shenzhen 518083, China
| | | | - Jan Mulder
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Xun Xu
- BGI Research, Hangzhou 310030, China; BGI Research, Shenzhen 518083, China.
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35
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Yosofvand M, Edmiston SN, Smithy JW, Peng X, Kostrzewa CE, Lin B, Ehrich F, Reiner A, Miedema J, Moy AP, Orlow I, Postow MA, Panageas K, Seshan VE, Callahan MK, Thomas NE, Shen R. Spatial Immunophenotyping from Whole-Slide Multiplexed Tissue Imaging Using Convolutional Neural Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.16.608247. [PMID: 39229153 PMCID: PMC11370407 DOI: 10.1101/2024.08.16.608247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
The multiplexed immunofluorescence (mIF) platform enables biomarker discovery through the simultaneous detection of multiple markers on a single tissue slide, offering detailed insights into intratumor heterogeneity and the tumor-immune microenvironment at spatially resolved single cell resolution. However, current mIF image analyses are labor-intensive, requiring specialized pathology expertise which limits their scalability and clinical application. To address this challenge, we developed CellGate, a deep-learning (DL) computational pipeline that provides streamlined, end-to-end whole-slide mIF image analysis including nuclei detection, cell segmentation, cell classification, and combined immuno-phenotyping across stacked images. The model was trained on over 750,000 single cell images from 34 melanomas in a retrospective cohort of patients using whole tissue sections stained for CD3, CD8, CD68, CK-SOX10, PD-1, PD-L1, and FOXP3 with manual gating and extensive pathology review. When tested on new whole mIF slides, the model demonstrated high precision-recall AUC. Further validation on whole-slide mIF images of 9 primary melanomas from an independent cohort confirmed that CellGate can reproduce expert pathology analysis with high accuracy. We show that spatial immuno-phenotyping results using CellGate provide deep insights into the immune cell topography and differences in T cell functional states and interactions with tumor cells in patients with distinct histopathology and clinical characteristics. This pipeline offers a fully automated and parallelizable computing process with substantially improved consistency for cell type classification across images, potentially enabling high throughput whole-slide mIF tissue image analysis for large-scale clinical and research applications.
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36
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Wu Z, Kondo A, McGrady M, Baker EAG, Chidester B, Wu E, Rahim MK, Bracey NA, Charu V, Cho RJ, Cheng JB, Afkarian M, Zou J, Mayer AT, Trevino AE. Discovery and generalization of tissue structures from spatial omics data. CELL REPORTS METHODS 2024; 4:100838. [PMID: 39127044 PMCID: PMC11384092 DOI: 10.1016/j.crmeth.2024.100838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/15/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024]
Abstract
Tissues are organized into anatomical and functional units at different scales. New technologies for high-dimensional molecular profiling in situ have enabled the characterization of structure-function relationships in increasing molecular detail. However, it remains a challenge to consistently identify key functional units across experiments, tissues, and disease contexts, a task that demands extensive manual annotation. Here, we present spatial cellular graph partitioning (SCGP), a flexible method for the unsupervised annotation of tissue structures. We further present a reference-query extension pipeline, SCGP-Extension, that generalizes reference tissue structure labels to previously unseen samples, performing data integration and tissue structure discovery. Our experiments demonstrate reliable, robust partitioning of spatial data in a wide variety of contexts and best-in-class accuracy in identifying expertly annotated structures. Downstream analysis on SCGP-identified tissue structures reveals disease-relevant insights regarding diabetic kidney disease, skin disorder, and neoplastic diseases, underscoring its potential to drive biological insight and discovery from spatial datasets.
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Affiliation(s)
- Zhenqin Wu
- Enable Medicine, Menlo Park, CA 94025, USA.
| | | | | | | | | | - Eric Wu
- Enable Medicine, Menlo Park, CA 94025, USA; Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | | | - Nathan A Bracey
- Institute of Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Vivek Charu
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Department of Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Maryam Afkarian
- Division of Nephrology, Department of Medicine, University of California, Davis, Davis, CA 95618, USA
| | - James Zou
- Enable Medicine, Menlo Park, CA 94025, USA; Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
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37
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Liu B, Hu S, Wang X. Applications of single-cell technologies in drug discovery for tumor treatment. iScience 2024; 27:110486. [PMID: 39171294 PMCID: PMC11338156 DOI: 10.1016/j.isci.2024.110486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024] Open
Abstract
Single-cell technologies have been known as advanced and powerful tools to study tumor biological systems at the single-cell resolution and are playing increasingly critical roles in multiple stages of drug discovery and development. Specifically, single-cell technologies can promote the discovery of drug targets, help high-throughput screening at single-cell level, and contribute to pharmacokinetic studies of anti-tumor drugs. Emerging single-cell analysis technologies have been developed to further integrating multidimensional single-cell molecular features, expanding the scale of single-cell data, profiling phenotypic impact of genes in single cell, and providing full-length coverage single-cell sequencing. In this review, we systematically summarized the applications of single-cell technologies in various sections of drug discovery for tumor treatment, including target identification, high-throughput drug screening, and pharmacokinetic evaluation and highlighted emerging single-cell technologies in providing in-depth understanding of tumor biology. Single-cell-technology-based drug discovery is expected to further optimize therapeutic strategies and improve clinical outcomes of tumor patients.
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Affiliation(s)
- Bingyu Liu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, China
| | - Shunfeng Hu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, China
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, China
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China
- Taishan Scholars Program of Shandong Province, Jinan, Shandong 250021, China
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38
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Holman DR, Rubin SJS, Ferenc M, Holman EA, Koron AN, Daniel R, Boland BS, Nolan GP, Chang JT, Rogalla S. Automated spatial omics landscape analysis approach reveals novel tissue architectures in ulcerative colitis. Sci Rep 2024; 14:18934. [PMID: 39147769 PMCID: PMC11327370 DOI: 10.1038/s41598-024-68397-5] [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: 02/18/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024] Open
Abstract
The utility of spatial omics in leveraging cellular interactions in normal and diseased states for precision medicine is hampered by a lack of strategies for matching disease states with spatial heterogeneity-guided cellular annotations. Here we use a spatial context-dependent approach that matches spatial pattern detection to cell annotation. Using this approach in existing datasets from ulcerative colitis patient colonic biopsies, we identified architectural complexities and associated difficult-to-detect rare cell types in ulcerative colitis germinal-center B cell follicles. Our approach deepens our understanding of health and disease pathogenesis, illustrates a strategy for automating nested architecture detection for highly multiplexed spatial biology data, and informs precision diagnosis and therapeutic strategies.
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Affiliation(s)
- Derek R Holman
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Samuel J S Rubin
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Mariusz Ferenc
- Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Warsaw, Poland
| | - Elizabeth A Holman
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Alexander N Koron
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Robel Daniel
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - John T Chang
- Division of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Stephan Rogalla
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA.
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39
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Wiedenmann M, Barch M, Chang PS, Giltnane J, Risom T, Zijlstra A. An Immunofluorescence-Guided Segmentation Model in Hematoxylin and Eosin Images Is Enabled by Tissue Artifact Correction Using a Cycle-Consistent Generative Adversarial Network. Mod Pathol 2024; 37:100591. [PMID: 39147031 DOI: 10.1016/j.modpat.2024.100591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/01/2024] [Indexed: 08/17/2024]
Abstract
Despite recent advances, the adoption of computer vision methods into clinical and commercial applications has been hampered by the limited availability of accurate ground truth tissue annotations required to train robust supervised models. Generating such ground truth can be accelerated by annotating tissue molecularly using immunofluorescence (IF) staining and mapping these annotations to a post-IF hematoxylin and eosin (H&E) (terminal H&E) stain. Mapping the annotations between IF and terminal H&E increases both the scale and accuracy by which ground truth could be generated. However, discrepancies between terminal H&E and conventional H&E caused by IF tissue processing have limited this implementation. We sought to overcome this challenge and achieve compatibility between these parallel modalities using synthetic image generation, in which a cycle-consistent generative adversarial network was applied to transfer the appearance of conventional H&E such that it emulates terminal H&E. These synthetic emulations allowed us to train a deep learning model for the segmentation of epithelium in terminal H&E that could be validated against the IF staining of epithelial-based cytokeratins. The combination of this segmentation model with the cycle-consistent generative adversarial network stain transfer model enabled performative epithelium segmentation in conventional H&E images. The approach demonstrates that the training of accurate segmentation models for the breadth of conventional H&E data can be executed free of human expert annotations by leveraging molecular annotation strategies such as IF, so long as the tissue impacts of the molecular annotation protocol are captured by generative models that can be deployed prior to the segmentation process.
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Affiliation(s)
- Marcel Wiedenmann
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Mariya Barch
- Department of Research Pathology, Genentech Inc, South San Francisco, California
| | - Patrick S Chang
- Department of Research Pathology, Genentech Inc, South San Francisco, California
| | - Jennifer Giltnane
- Department of Research Pathology, Genentech Inc, South San Francisco, California
| | - Tyler Risom
- Department of Research Pathology, Genentech Inc, South San Francisco, California.
| | - Andries Zijlstra
- Department of Research Pathology, Genentech Inc, South San Francisco, California; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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40
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Zhang D, Rodríguez-Kirby LAR, Lin Y, Song M, Wang L, Wang L, Kanatani S, Jimenez-Beristain T, Dang Y, Zhong M, Kukanja P, Wang S, Chen XL, Gao F, Wang D, Xu H, Lou X, Liu Y, Chen J, Sestan N, Uhlén P, Kriegstein A, Zhao H, Castelo-Branco G, Fan R. Spatial dynamics of mammalian brain development and neuroinflammation by multimodal tri-omics mapping. RESEARCH SQUARE 2024:rs.3.rs-4814866. [PMID: 39184075 PMCID: PMC11343178 DOI: 10.21203/rs.3.rs-4814866/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
The ability to spatially map multiple layers of the omics information over different time points allows for exploring the mechanisms driving brain development, differentiation, arealization, and alterations in disease. Herein we developed and applied spatial tri-omic sequencing technologies, DBiT ARP-seq (spatial ATAC-RNA-Protein-seq) and DBiT CTRP-seq (spatial CUT&Tag-RNA-Protein-seq) together with multiplexed immunofluorescence imaging (CODEX) to map spatial dynamic remodeling in brain development and neuroinflammation. A spatiotemporal tri-omic atlas of the mouse brain was obtained at different stages from postnatal day P0 to P21, and compared to the regions of interest in the human developing brains. Specifically, in the cortical area, we discovered temporal persistence and spatial spreading of chromatin accessibility for the layer-defining transcription factors. In corpus callosum, we observed dynamic chromatin priming of myelin genes across the subregions. Together, it suggests a role for layer specific projection neurons to coordinate axonogenesis and myelination. We further mapped the brain of a lysolecithin (LPC) neuroinflammation mouse model and observed common molecular programs in development and neuroinflammation. Microglia, exhibiting both conserved and distinct programs for inflammation and resolution, are transiently activated not only at the core of the LPC lesion, but also at distal locations presumably through neuronal circuitry. Thus, this work unveiled common and differential mechanisms in brain development and neuroinflammation, resulting in a valuable data resource to investigate brain development, function and disease.
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Affiliation(s)
- Di Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- These authors contributed equally
| | - Leslie A Rubio Rodríguez-Kirby
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- These authors contributed equally
| | - Yingxin Lin
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mengyi Song
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Li Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Lijun Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Shigeaki Kanatani
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Tony Jimenez-Beristain
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yonglong Dang
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Mei Zhong
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Petra Kukanja
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Shaohui Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Xinyi Lisa Chen
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Fu Gao
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Dejiang Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Hang Xu
- Binformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xing Lou
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Yang Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Jinmiao Chen
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Binformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Per Uhlén
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Arnold Kriegstein
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06520, USA
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41
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Su J, Song Y, Zhu Z, Huang X, Fan J, Qiao J, Mao F. Cell-cell communication: new insights and clinical implications. Signal Transduct Target Ther 2024; 9:196. [PMID: 39107318 PMCID: PMC11382761 DOI: 10.1038/s41392-024-01888-z] [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: 12/29/2023] [Revised: 05/09/2024] [Accepted: 06/02/2024] [Indexed: 09/11/2024] Open
Abstract
Multicellular organisms are composed of diverse cell types that must coordinate their behaviors through communication. Cell-cell communication (CCC) is essential for growth, development, differentiation, tissue and organ formation, maintenance, and physiological regulation. Cells communicate through direct contact or at a distance using ligand-receptor interactions. So cellular communication encompasses two essential processes: cell signal conduction for generation and intercellular transmission of signals, and cell signal transduction for reception and procession of signals. Deciphering intercellular communication networks is critical for understanding cell differentiation, development, and metabolism. First, we comprehensively review the historical milestones in CCC studies, followed by a detailed description of the mechanisms of signal molecule transmission and the importance of the main signaling pathways they mediate in maintaining biological functions. Then we systematically introduce a series of human diseases caused by abnormalities in cell communication and their progress in clinical applications. Finally, we summarize various methods for monitoring cell interactions, including cell imaging, proximity-based chemical labeling, mechanical force analysis, downstream analysis strategies, and single-cell technologies. These methods aim to illustrate how biological functions depend on these interactions and the complexity of their regulatory signaling pathways to regulate crucial physiological processes, including tissue homeostasis, cell development, and immune responses in diseases. In addition, this review enhances our understanding of the biological processes that occur after cell-cell binding, highlighting its application in discovering new therapeutic targets and biomarkers related to precision medicine. This collective understanding provides a foundation for developing new targeted drugs and personalized treatments.
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Affiliation(s)
- Jimeng Su
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ying Song
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
| | - Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
| | - Xinyue Huang
- Biomedical Research Institute, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jibiao Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
- Cancer Center, Peking University Third Hospital, Beijing, China.
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42
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Bhushan V, Nita-Lazar A. Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology. J Proteome Res 2024; 23:2700-2722. [PMID: 38451675 PMCID: PMC11296931 DOI: 10.1021/acs.jproteome.3c00839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The mammalian cell is a complex entity, with membrane-bound and membrane-less organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches drive discrete biological processes and cell functions, thus maintaining cell equilibrium. Cellular processes such as signaling, growth, proliferation, motility, and programmed cell death require dynamic protein movements between cell compartments. Aberrant protein localization is associated with a wide range of diseases. Therefore, analyzing the subcellular proteome of the cell can provide a comprehensive overview of cellular biology. With recent advancements in mass spectrometry, imaging technology, computational tools, and deep machine learning algorithms, studies pertaining to subcellular protein localization and their dynamic distributions are gaining momentum. These studies reveal changing interaction networks because of "moonlighting proteins" and serve as a discovery tool for disease network mechanisms. Consequently, this review aims to provide a comprehensive repository for recent advancements in subcellular proteomics subcontexting methods, challenges, and future perspectives for method developers. In summary, subcellular proteomics is crucial to the understanding of the fundamental cellular mechanisms and the associated diseases.
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Affiliation(s)
- Vanya Bhushan
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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43
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Matusiak M, Hickey JW, van IJzendoorn DG, Lu G, Kidziński L, Zhu S, Colburg DR, Luca B, Phillips DJ, Brubaker SW, Charville GW, Shen J, Loh KM, Okwan-Duodu DK, Nolan GP, Newman AM, West RB, van de Rijn M. Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. Cancer Discov 2024; 14:1418-1439. [PMID: 38552005 PMCID: PMC11294822 DOI: 10.1158/2159-8290.cd-23-1300] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/23/2024] [Accepted: 03/26/2024] [Indexed: 08/03/2024]
Abstract
Tumor-associated macrophages are transcriptionally heterogeneous, but the spatial distribution and cell interactions that shape macrophage tissue roles remain poorly characterized. Here, we spatially resolve five distinct human macrophage populations in normal and malignant human breast and colon tissue and reveal their cellular associations. This spatial map reveals that distinct macrophage populations reside in spatially segregated micro-environmental niches with conserved cellular compositions that are repeated across healthy and diseased tissue. We show that IL4I1+ macrophages phagocytose dying cells in areas with high cell turnover and predict good outcome in colon cancer. In contrast, SPP1+ macrophages are enriched in hypoxic and necrotic tumor regions and portend worse outcome in colon cancer. A subset of FOLR2+ macrophages is embedded in plasma cell niches. NLRP3+ macrophages co-localize with neutrophils and activate an inflammasome in tumors. Our findings indicate that a limited number of unique human macrophage niches function as fundamental building blocks in tissue. Significance: This work broadens our understanding of the distinct roles different macrophage populations may exert on cancer growth and reveals potential predictive markers and macrophage population-specific therapy targets.
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Affiliation(s)
| | - John W. Hickey
- Department of Pathology, Stanford University, Stanford, California.
| | | | - Guolan Lu
- Department of Pathology, Stanford University, Stanford, California.
| | - Lukasz Kidziński
- Department of Bioengineering, Stanford University, Stanford, California.
| | - Shirley Zhu
- Department of Pathology, Stanford University, Stanford, California.
| | | | - Bogdan Luca
- Department of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California.
- Department of Biomedical Data Science, Stanford University, Stanford, California.
| | | | - Sky W. Brubaker
- Department of Microbiology and Immunology, Stanford University, Stanford, California.
| | | | - Jeanne Shen
- Department of Pathology, Stanford University, Stanford, California.
| | - Kyle M. Loh
- Department of Developmental Biology, Stanford University, Stanford, California.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.
| | | | - Garry P. Nolan
- Department of Pathology, Stanford University, Stanford, California.
| | - Aaron M. Newman
- Department of Biomedical Data Science, Stanford University, Stanford, California.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.
- Stanford Cancer Institute, Stanford University, Stanford, California.
| | - Robert B. West
- Department of Pathology, Stanford University, Stanford, California.
| | - Matt van de Rijn
- Department of Pathology, Stanford University, Stanford, California.
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44
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Tao Y, Feng F, Luo X, Reihsmann CV, Hopkirk AL, Cartailler JP, Brissova M, Parker SCJ, Saunders DC, Liu J. CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images. PLoS Comput Biol 2024; 20:e1012344. [PMID: 39196899 PMCID: PMC11355562 DOI: 10.1371/journal.pcbi.1012344] [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: 02/04/2024] [Accepted: 07/22/2024] [Indexed: 08/30/2024] Open
Abstract
Recent studies show that cellular neighborhoods play an important role in evolving biological events such as cancer and diabetes. Therefore, it is critical to accurately and efficiently identify cellular neighborhoods from spatially-resolved single-cell transcriptomic data or single-cell resolution tissue imaging data. In this work, we develop CNTools, a computational toolbox for end-to-end cellular neighborhood analysis on annotated cell images, comprising both the identification and analysis steps. It includes state-of-the-art cellular neighborhood identification methods and post-identification smoothing techniques, with our newly proposed Cellular Neighbor Embedding (CNE) method and Naive Smoothing technique, as well as several established downstream analysis approaches. We applied CNTools on three real-world CODEX datasets and evaluated identification methods with smoothing techniques quantitatively and qualitatively. It shows that CNE with Naive Smoothing overall outperformed other methods and revealed more convincing biological insights. We also provided suggestions on how to choose proper identification methods and smoothing techniques according to input data.
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Affiliation(s)
- Yicheng Tao
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Fan Feng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Xin Luo
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Conrad V. Reihsmann
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Alexander L. Hopkirk
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jean-Philippe Cartailler
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Marcela Brissova
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Stephen C. J. Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Diane C. Saunders
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jie Liu
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
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45
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Polak R, Zhang ET, Kuo CJ. Cancer organoids 2.0: modelling the complexity of the tumour immune microenvironment. Nat Rev Cancer 2024; 24:523-539. [PMID: 38977835 DOI: 10.1038/s41568-024-00706-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/09/2024] [Indexed: 07/10/2024]
Abstract
The development of neoplasia involves a complex and continuous interplay between malignantly transformed cells and the tumour microenvironment (TME). Cancer immunotherapies targeting the immune TME have been increasingly validated in clinical trials but response rates vary substantially between tumour histologies and are often transient, idiosyncratic and confounded by resistance. Faithful experimental models of the patient-specific tumour immune microenvironment, capable of recapitulating tumour biology and immunotherapy effects, would greatly improve patient selection, target identification and definition of resistance mechanisms for immuno-oncology therapeutics. In this Review, we discuss currently available and rapidly evolving 3D tumour organoid models that capture important immune features of the TME. We highlight diverse opportunities for organoid-based investigations of tumour immunity, drug development and precision medicine.
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Affiliation(s)
- Roel Polak
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Elisa T Zhang
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA.
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46
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Deen AJ, Thorsson J, O’Roberts EM, Panshikar P, Ullman T, Krantz D, Oses C, Stadler C. Making Multiplexed Imaging Flexible: Combining Essential Markers With Established Antibody Panels. J Histochem Cytochem 2024; 72:517-544. [PMID: 39215640 PMCID: PMC11421402 DOI: 10.1369/00221554241274856] [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: 03/19/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
Multiplexed immunofluorescence (IF) can be achieved using different commercially available platforms, often making use of conjugated antibodies detected in iterative cycles. A growing portfolio of pre-conjugated antibodies is offered by the providers, as well as the possibility for in-house conjugation. For many conjugation methods and kits, there are limitations in which antibodies can be used, and conjugation results are sometimes irreproducible. The conjugation process can limit or slow down the progress of studies requiring conjugation of essential markers needed for a given project. Here, we demonstrate a protocol combining manual indirect immunofluorescence (IF) of primary antibodies, followed by antibody elution and staining with multiplexed panels of commercially pre-conjugated antibodies on the PhenoCycler platform. We present detailed protocols for applying the workflow on fresh frozen and formalin fixed paraffin embedded tissue sections. We also provide a ready to use workflow for coregistration of the images and demonstrate this for two examples.
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Affiliation(s)
- Ashik Jawahar Deen
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Johan Thorsson
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Eleanor M. O’Roberts
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Pranauti Panshikar
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Tony Ullman
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - David Krantz
- Department of Oncology-Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Carolina Oses
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Charlotte Stadler
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
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47
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Ma X, Lembersky D, Kim ES, Becich MJ, Testa JR, Bruno TC, Osmanbeyoglu HU. Spatial Landscape of Malignant Pleural and Peritoneal Mesothelioma Tumor Immune Microenvironments. CANCER RESEARCH COMMUNICATIONS 2024; 4:2133-2146. [PMID: 38994676 PMCID: PMC11328914 DOI: 10.1158/2767-9764.crc-23-0524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/15/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Immunotherapies have demonstrated limited clinical efficacy in malignant mesothelioma treatment. We conducted multiplex immunofluorescence analyses on tissue microarrays (n = 3) from patients with malignant pleural mesothelioma (MPM, n = 88) and malignant peritoneal mesothelioma (MPeM, n = 25). Our study aimed to elucidate spatial distributions of key immune cell populations and their association with lymphocyte activation gene 3 (LAG3), BRCA1-associated protein 1 (BAP1), neurofibromatosis type 2 (NF2), and methylthioadenosine phosphorylase (MTAP), with MTAP serving as a cyclin-dependent kinase inhibitor 2A/2B (CDKN2A/B) surrogate marker. Additionally, we examined the relationship between the spatial distribution of major immune cell types and prognosis and clinical characteristics of patients with malignant mesothelioma. We observed a higher degree of interaction between immune cells and tumor cells in MPM compared with MPeM. Notably, within MPM tumors, we detected a significantly increased interaction between tumor cells and CD8+ T cells in tumors with low BAP1 expression compared with those with high BAP1 expression. To support the broader research community, we have developed The Human Spatial Atlas of Malignant Mesothelioma, containing hematoxylin and eosin and multiplex immunofluorescence images with corresponding metadata. SIGNIFICANCE Considering the limited therapeutic options available to patients with malignant mesothelioma, there is substantial translational potential in understanding the correlation between the spatial architecture of the malignant mesothelioma tumor immune microenvironment and tumor biology. Our investigation reveals critical cell-cell interactions that may influence the immune response against malignant mesothelioma tumors, potentially contributing to the differential behaviors observed in MPM and MPeM. These findings represent a valuable resource for the malignant mesothelioma cancer research community.
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Affiliation(s)
- Xiaojun Ma
- UPMC Hillman Cancer Center, Cancer Biology Program, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - David Lembersky
- UPMC Hillman Cancer Center, Cancer Biology Program, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Elena S Kim
- UPMC Hillman Cancer Center, Cancer Biology Program, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Michael J Becich
- UPMC Hillman Cancer Center, Cancer Biology Program, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Joseph R Testa
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Tullia C Bruno
- UPMC Hillman Cancer Center, Cancer Biology Program, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Hatice U Osmanbeyoglu
- UPMC Hillman Cancer Center, Cancer Biology Program, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Bioengineering, University of Pittsburgh School of Engineering, Pittsburgh, Pennsylvania
- Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania
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48
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Cesnik A, Schaffer LV, Gaur I, Jain M, Ideker T, Lundberg E. Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes. Annu Rev Biomed Data Sci 2024; 7:369-389. [PMID: 38748859 PMCID: PMC11343683 DOI: 10.1146/annurev-biodatasci-102423-113534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Abstract
While the primary sequences of human proteins have been cataloged for over a decade, determining how these are organized into a dynamic collection of multiprotein assemblies, with structures and functions spanning biological scales, is an ongoing venture. Systematic and data-driven analyses of these higher-order structures are emerging, facilitating the discovery and understanding of cellular phenotypes. At present, knowledge of protein localization and function has been primarily derived from manual annotation and curation in resources such as the Gene Ontology, which are biased toward richly annotated genes in the literature. Here, we envision a future powered by data-driven mapping of protein assemblies. These maps can capture and decode cellular functions through the integration of protein expression, localization, and interaction data across length scales and timescales. In this review, we focus on progress toward constructing integrated cell maps that accelerate the life sciences and translational research.
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Affiliation(s)
- Anthony Cesnik
- Department of Bioengineering, Stanford University, Stanford, California, USA;
| | - Leah V Schaffer
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Ishan Gaur
- Department of Bioengineering, Stanford University, Stanford, California, USA;
| | - Mayank Jain
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Trey Ideker
- Departments of Computer Science and Engineering and Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Emma Lundberg
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Pathology, Stanford University, Palo Alto, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA;
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49
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Oñate MK, Oon C, Bhattacharyya S, Low V, Chen C, Zhao X, Yan Z, Hang Y, Kim SK, Xia Z, Sherman MH. Stromal KITL/SCF promotes pancreas tissue homeostasis and restrains tumor progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.29.605485. [PMID: 39131374 PMCID: PMC11312444 DOI: 10.1101/2024.07.29.605485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Components of normal tissue architecture serve as barriers to tumor progression. Inflammatory and wound-healing programs are requisite features of solid tumorigenesis, wherein alterations to immune and non-immune stromal elements enable loss of homeostasis during tumor evolution. The precise mechanisms by which normal stromal cell states limit tissue plasticity and tumorigenesis, and which are lost during tumor progression, remain largely unknown. Here we show that healthy pancreatic mesenchyme expresses the paracrine signaling molecule KITL, also known as stem cell factor, and identify loss of stromal KITL during tumorigenesis as tumor-promoting. Genetic inhibition of mesenchymal KITL in the contexts of homeostasis, injury, and cancer together indicate a role for KITL signaling in maintenance of pancreas tissue architecture, such that loss of the stromal KITL pool increased tumor growth and reduced survival of tumor-bearing mice. Together, these findings implicate loss of mesenchymal KITL as a mechanism for establishing a tumor-permissive microenvironment.
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Affiliation(s)
- M. Kathrina Oñate
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Chet Oon
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Sohinee Bhattacharyya
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Vivien Low
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Canping Chen
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Xiaofan Zhao
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Ziqiao Yan
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Yan Hang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, California
| | - Seung K. Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, California
- Department of Medicine, Stanford University School of Medicine, Stanford, California
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Zheng Xia
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Mara H. Sherman
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon
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50
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Lun XK, Sheng K, Yu X, Lam CY, Gowri G, Serrata M, Zhai Y, Su H, Luan J, Kim Y, Ingber DE, Jackson HW, Yaffe MB, Yin P. Signal amplification by cyclic extension enables high-sensitivity single-cell mass cytometry. Nat Biotechnol 2024:10.1038/s41587-024-02316-x. [PMID: 39075149 DOI: 10.1038/s41587-024-02316-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/13/2024] [Indexed: 07/31/2024]
Abstract
Mass cytometry uses metal-isotope-tagged antibodies to label targets of interest, which enables simultaneous measurements of ~50 proteins or protein modifications in millions of single cells, but its sensitivity is limited. Here, we present a signal amplification technology, termed Amplification by Cyclic Extension (ACE), implementing thermal-cycling-based DNA in situ concatenation in combination with 3-cyanovinylcarbazole phosphoramidite-based DNA crosslinking to enable signal amplification simultaneously on >30 protein epitopes. We demonstrate the utility of ACE in low-abundance protein quantification with suspension mass cytometry to characterize molecular reprogramming during the epithelial-to-mesenchymal transition as well as the mesenchymal-to-epithelial transition. We show the capability of ACE to quantify the dynamics of signaling network responses in human T lymphocytes. We further present the application of ACE in imaging mass cytometry-based multiparametric tissue imaging to identify tissue compartments and profile spatial aspects related to pathological states in polycystic kidney tissues.
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Affiliation(s)
- Xiao-Kang Lun
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Kuanwei Sheng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Xueyang Yu
- Departments of Biology and Bioengineering, Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ching Yeung Lam
- Mount Sinai Health Systems and Department of Molecular Genetics, Lunenfeld Tanenbaum Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Gokul Gowri
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Matthew Serrata
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Yunhao Zhai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Hanquan Su
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Jingyi Luan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Youngeun Kim
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Materials Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Vascular Biology Program and Department of Surgery, Harvard Medical School and Boston Children's Hospital, Boston, MA, USA
| | - Hartland W Jackson
- Mount Sinai Health Systems and Department of Molecular Genetics, Lunenfeld Tanenbaum Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Michael B Yaffe
- Departments of Biology and Bioengineering, Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston, MA, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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