1
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Campbell K, Naire S, Kuiper JH. A mathematical model of signalling molecule-mediated processes during regeneration of osteochondral defects after chondrocyte implantation. J Theor Biol 2024; 592:111874. [PMID: 38908475 DOI: 10.1016/j.jtbi.2024.111874] [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: 10/12/2023] [Revised: 04/12/2024] [Accepted: 06/06/2024] [Indexed: 06/24/2024]
Abstract
Treating bone-cartilage defects is a fundamental clinical problem. The ability of damaged cartilage to self-repair is limited due to its avascularity. Left untreated, these defects can lead to osteoarthritis. Details of osteochondral defect repair are elusive, but animal models indicate healing occurs via an endochondral ossification-like process, similar to that in the growth plate. In the growth plate, the signalling molecules parathyroid hormone-related protein (PTHrP) and Indian Hedgehog (Ihh) form a feedback loop regulating chondrocyte hypertrophy, with Ihh inducing and PTHrP suppressing hypertrophy. To better understand this repair process and to explore the regulatory role of signalling molecules on the regeneration process, we formulate a reaction-diffusion mathematical model of osteochondral defect regeneration after chondrocyte implantation. The drivers of healing are assumed to be chondrocytes and osteoblasts, and their interaction via signalling molecules. We model cell proliferation, migration and chondrocyte hypertrophy, and matrix production and conversion, spatially and temporally. We further model nutrient and signalling molecule diffusion and their interaction with the cells. We consider the PTHrP-Ihh feedback loop as the backbone mechanisms but the model is flexible to incorporate extra signalling mechanisms if needed. Our mathematical model is able to represent repair of osteochondral defects, starting with cartilage formation throughout the defect. This is followed by chondrocyte hypertrophy, matrix calcification and bone formation deep inside the defect, while cartilage at the surface is maintained and eventually separated from the deeper bone by a thin layer of calcified cartilage. The complete process requires around 48 months. A key highlight of the model demonstrates that the PTHrP-Ihh loop alone is insufficient and an extra mechanism is required to initiate chondrocyte hypertrophy, represented by a critical cartilage density. A parameter sensitivity study reveals that the timing of the repair process crucially depends on parameters, such as the critical cartilage density, and those describing the actions of PTHrP to suppress hypertrophy, such as its diffusion coefficient, threshold concentration and degradation rate.
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Affiliation(s)
- Kelly Campbell
- School of Computing and Mathematics, Keele University, Keele, ST5 5BG, UK
| | - Shailesh Naire
- School of Computing and Mathematics, Keele University, Keele, ST5 5BG, UK
| | - Jan Herman Kuiper
- School of Pharmacy and Bioengineering, Keele University, Keele, ST5 5BG, UK; Robert Jones and Agnes Hunt Orthopaedic & District Hospital NHS Trust, Oswestry, SY10 7AG, UK.
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2
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Wu D, Datta S. TWCOM: an R package for inference of cell-cell communication on spatially resolved transcriptomics data. BIOINFORMATICS ADVANCES 2024; 4:vbae101. [PMID: 39040219 PMCID: PMC11262461 DOI: 10.1093/bioadv/vbae101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/16/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
Summary The inference of cell-cell communication is important, as it unveils the intricate cellular behaviors at the molecular level, providing crucial insights essential for understanding complex biological processes and informing targeted interventions in various pathological contexts. Here, we present TWCOM, an R package that implements a Tweedie distribution-based model for accurate cell-cell communication inference. Operating under a generalized additive model framework, TWCOM adeptly handles both single-cell resolution and spot-based spatially resolved transcriptomics data, providing a versatile tool for robust biological sample analysis. Availability and implementation The R package TWCOM is available at https://github.com/dongyuanwu/TWCOM. Comprehensive documentation is included with the package.
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Affiliation(s)
- Dongyuan Wu
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, United States
| | - Susmita Datta
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, United States
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3
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Zhang L, Chen M, Wang Z, Zhong M, Chen H, Li T, Wang L, Zhao Z, Zhang XB, Ke G, Liu Y, Tan W. Spatiotemporal Regulation of Cell Fate in Living Systems Using Photoactivatable Artificial DNA Membraneless Organelles. ACS CENTRAL SCIENCE 2024; 10:1201-1210. [PMID: 38947212 PMCID: PMC11212128 DOI: 10.1021/acscentsci.4c00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/17/2024] [Accepted: 05/08/2024] [Indexed: 07/02/2024]
Abstract
Coacervates formed by liquid-liquid phase separation emerge as important biomimetic models for studying the dynamic behaviors of membraneless organelles and synchronously motivating the creation of smart architectures with the regulation of cell fate. Despite continuous progress, it remains challenging to balance the trade-offs among structural stability, versatility, and molecular communication for regulation of cell fate and systemic investigation in a complex physiological system. Herein, we present a self-stabilizing and fastener-bound gain-of-function methodology to create a new type of synthetic DNA membraneless organelle (MO) with high stability and controlled bioactivity on the basis of DNA coacervates. Specifically, long single-strand DNA generated by rolling circle amplification (RCA) is selected as the scaffold that assembles into membraneless coacervates via phase separation. Intriguingly, the as-formed DNA MO can recruit RCA byproducts and other components to achieve self-stabilization, nanoscale condensation, and function encoding. As a proof of concept, photoactivatable DNA MO is constructed and successfully employed for time-dependent accumulation and spatiotemporal management of cancer in a mouse model. This study offers new, important insights into synthetic membraneless organelles for the basic understanding and manipulation of important life processes.
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Affiliation(s)
- Lili Zhang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Mei Chen
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Materials Science and Engineering, Aptamer
Engineering Center of Hunan Province, Hunan
University, Changsha, Hunan 410082, China
| | - Zhiqiang Wang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Minjuan Zhong
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Hong Chen
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Ting Li
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Linlin Wang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Zhihui Zhao
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Xiao-Bing Zhang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Guoliang Ke
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Yanlan Liu
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute
of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University
School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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4
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Wang X, Yuan W. Nuclei-level prior knowledge constrained multiple instance learning for breast histopathology whole slide image classification. iScience 2024; 27:109826. [PMID: 38832012 PMCID: PMC11145340 DOI: 10.1016/j.isci.2024.109826] [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: 01/22/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
New breast cancer cases have surpassed lung cancer, becoming the world's most prevalent cancer. Despite advancing medical image analysis, deep learning's lack of interpretability limits its adoption among pathologists. Hence, a nuclei-level prior knowledge constrained multiple instance learning (MIL) (NPKC-MIL) for breast whole slide image (WSI) classification is proposed. NPKC-MIL primarily involves the following steps: Initially, employing the transfer learning to extract patch-level features and aggregate them into slide-level features through attention pooling. Subsequently, abstract the extracted nuclei as nodes, establish nucleus topology using the K-NN (K-Nearest Neighbors, K-NN) algorithm, and create handcrafted features for nodes. Finally, combine patch-level deep learning features with nuclei-level handcrafted features to fine-tune classification results generated by slide-level deep learning features. The experimental results demonstrate that NPKC-MIL outperforms current comparable deep learning models. NPKC-MIL expands the analytical dimension of WSI classification tasks and integrates prior knowledge into deep learning models to improve interpretability.
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Affiliation(s)
- Xunping Wang
- School of Remote Sensing and Information Engineering, Wuhan University, 129 Luoyu Road, Wuhan 430079, China
| | - Wei Yuan
- Co-Creation Center for Disaster Resilience, International Research Institute of Disaster Science, Tohoku University, Aoba 468-1, Aramaki, Aoba-ku, Sendai 980-8572, Japan
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5
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Royan MR, Hodne K, Nourizadeh-Lillabadi R, Weltzien FA, Henkel C, Fontaine R. Day length regulates gonadotrope proliferation and reproduction via an intra-pituitary pathway in the model vertebrate Oryzias latipes. Commun Biol 2024; 7:388. [PMID: 38553567 PMCID: PMC10980775 DOI: 10.1038/s42003-024-06059-y] [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: 06/22/2023] [Accepted: 03/16/2024] [Indexed: 04/01/2024] Open
Abstract
In seasonally breeding mammals and birds, the production of the hormones that regulate reproduction (gonadotropins) is controlled by a complex pituitary-brain-pituitary pathway. Indeed, the pituitary thyroid-stimulating hormone (TSH) regulates gonadotropin expression in pituitary gonadotropes, via dio2-expressing tanycytes, hypothalamic Kisspeptin, RFamide-related peptide, and gonadotropin-releasing hormone neurons. However, in fish, how seasonal environmental signals influence gonadotropins remains unclear. In addition, the seasonal regulation of gonadotrope (gonadotropin-producing cell) proliferation in the pituitary is, to the best of our knowledge, not elucidated in any vertebrate group. Here, we show that in the vertebrate model Japanese medaka (Oryzias latipes), a long day seasonally breeding fish, photoperiod (daylength) not only regulates hormone production by the gonadotropes but also their proliferation. We also reveal an intra-pituitary pathway that regulates gonadotrope cell number and hormone production. In this pathway, Tsh regulates gonadotropes via folliculostellate cells within the pituitary. This study suggests the existence of an alternative regulatory mechanism of seasonal gonadotropin production in fish.
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Affiliation(s)
- Muhammad Rahmad Royan
- Department of Preclinical Science and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Kjetil Hodne
- Department of Preclinical Science and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Rasoul Nourizadeh-Lillabadi
- Department of Preclinical Science and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Finn-Arne Weltzien
- Department of Preclinical Science and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Christiaan Henkel
- Department of Preclinical Science and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Romain Fontaine
- Department of Preclinical Science and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway.
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6
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Baghdassarian HM, Lewis NE. Resource allocation in mammalian systems. Biotechnol Adv 2024; 71:108305. [PMID: 38215956 PMCID: PMC11182366 DOI: 10.1016/j.biotechadv.2023.108305] [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: 08/03/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024]
Abstract
Cells execute biological functions to support phenotypes such as growth, migration, and secretion. Complementarily, each function of a cell has resource costs that constrain phenotype. Resource allocation by a cell allows it to manage these costs and optimize their phenotypes. In fact, the management of resource constraints (e.g., nutrient availability, bioenergetic capacity, and macromolecular machinery production) shape activity and ultimately impact phenotype. In mammalian systems, quantification of resource allocation provides important insights into higher-order multicellular functions; it shapes intercellular interactions and relays environmental cues for tissues to coordinate individual cells to overcome resource constraints and achieve population-level behavior. Furthermore, these constraints, objectives, and phenotypes are context-dependent, with cells adapting their behavior according to their microenvironment, resulting in distinct steady-states. This review will highlight the biological insights gained from probing resource allocation in mammalian cells and tissues.
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Affiliation(s)
- Hratch M Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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7
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Alzoubi I, Zhang L, Zheng Y, Loh C, Wang X, Graeber MB. PathoGraph: An Attention-Based Graph Neural Network Capable of Prognostication Based on CD276 Labelling of Malignant Glioma Cells. Cancers (Basel) 2024; 16:750. [PMID: 38398141 PMCID: PMC10886785 DOI: 10.3390/cancers16040750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Computerized methods have been developed that allow quantitative morphological analyses of whole slide images (WSIs), e.g., of immunohistochemical stains. The latter are attractive because they can provide high-resolution data on the distribution of proteins in tissue. However, many immunohistochemical results are complex because the protein of interest occurs in multiple locations (in different cells and also extracellularly). We have recently established an artificial intelligence framework, PathoFusion which utilises a bifocal convolutional neural network (BCNN) model for detecting and counting arbitrarily definable morphological structures. We have now complemented this model by adding an attention-based graph neural network (abGCN) for the advanced analysis and automated interpretation of such data. Classical convolutional neural network (CNN) models suffer from limitations when handling global information. In contrast, our abGCN is capable of creating a graph representation of cellular detail from entire WSIs. This abGCN method combines attention learning with visualisation techniques that pinpoint the location of informative cells and highlight cell-cell interactions. We have analysed cellular labelling for CD276, a protein of great interest in cancer immunology and a potential marker of malignant glioma cells/putative glioma stem cells (GSCs). We are especially interested in the relationship between CD276 expression and prognosis. The graphs permit predicting individual patient survival on the basis of GSC community features. Our experiments lay a foundation for the use of the BCNN-abGCN tool chain in automated diagnostic prognostication using immunohistochemically labelled histological slides, but the method is essentially generic and potentially a widely usable tool in medical research and AI based healthcare applications.
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Affiliation(s)
- Islam Alzoubi
- School of Computer Science, The University of Sydney, J12/1 Cleveland St, Darlington, Sydney, NSW 2008, Australia; (I.A.); (L.Z.)
| | - Lin Zhang
- School of Computer Science, The University of Sydney, J12/1 Cleveland St, Darlington, Sydney, NSW 2008, Australia; (I.A.); (L.Z.)
| | - Yuqi Zheng
- Ken Parker Brain Tumour Research Laboratories, Brain and Mind Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2050, Australia; (Y.Z.); (C.L.)
| | - Christina Loh
- Ken Parker Brain Tumour Research Laboratories, Brain and Mind Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2050, Australia; (Y.Z.); (C.L.)
| | - Xiuying Wang
- School of Computer Science, The University of Sydney, J12/1 Cleveland St, Darlington, Sydney, NSW 2008, Australia; (I.A.); (L.Z.)
| | - Manuel B. Graeber
- Ken Parker Brain Tumour Research Laboratories, Brain and Mind Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2050, Australia; (Y.Z.); (C.L.)
- University of Sydney Association of Professors (USAP), University of Sydney, Sydney, NSW 2006, Australia
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8
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Hagos YB, Lecat CS, Patel D, Mikolajczak A, Castillo SP, Lyon EJ, Foster K, Tran TA, Lee LS, Rodriguez-Justo M, Yong KL, Yuan Y. Deep Learning Enables Spatial Mapping of the Mosaic Microenvironment of Myeloma Bone Marrow Trephine Biopsies. Cancer Res 2024; 84:493-508. [PMID: 37963212 PMCID: PMC10831337 DOI: 10.1158/0008-5472.can-22-2654] [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: 09/02/2022] [Revised: 12/18/2022] [Accepted: 11/07/2023] [Indexed: 11/16/2023]
Abstract
Bone marrow trephine biopsy is crucial for the diagnosis of multiple myeloma. However, the complexity of bone marrow cellular, morphologic, and spatial architecture preserved in trephine samples hinders comprehensive evaluation. To dissect the diverse cellular communities and mosaic tissue habitats, we developed a superpixel-inspired deep learning method (MoSaicNet) that adapts to complex tissue architectures and a cell imbalance aware deep learning pipeline (AwareNet) to enable accurate detection and classification of rare cell types in multiplex immunohistochemistry images. MoSaicNet and AwareNet achieved an AUC of >0.98 for tissue and cellular classification on separate test datasets. Application of MoSaicNet and AwareNet enabled investigation of bone heterogeneity and thickness as well as spatial histology analysis of bone marrow trephine samples from monoclonal gammopathies of undetermined significance (MGUS) and from paired newly diagnosed and posttreatment multiple myeloma. The most significant difference between MGUS and newly diagnosed multiple myeloma (NDMM) samples was not related to cell density but to spatial heterogeneity, with reduced spatial proximity of BLIMP1+ tumor cells to CD8+ cells in MGUS compared with NDMM samples. Following treatment of patients with multiple myeloma, there was a reduction in the density of BLIMP1+ tumor cells, effector CD8+ T cells, and regulatory T cells, indicative of an altered immune microenvironment. Finally, bone heterogeneity decreased following treatment of patients with multiple myeloma. In summary, deep learning-based spatial mapping of bone marrow trephine biopsies can provide insights into the cellular topography of the myeloma marrow microenvironment and complement aspirate-based techniques. SIGNIFICANCE Spatial analysis of bone marrow trephine biopsies using histology, deep learning, and tailored algorithms reveals the bone marrow architectural heterogeneity and evolution during myeloma progression and treatment.
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Affiliation(s)
- Yeman Brhane Hagos
- Centre for Evolution and Cancer and Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Catherine S.Y. Lecat
- Research Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Dominic Patel
- Research Department of Pathology, University College London Cancer Institute, London, United Kingdom
| | - Anna Mikolajczak
- Research Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Simon P. Castillo
- Centre for Evolution and Cancer and Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Emma J. Lyon
- Research Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Kane Foster
- Research Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Thien-An Tran
- Research Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Lydia S.H. Lee
- Research Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Manuel Rodriguez-Justo
- Research Department of Pathology, University College London Cancer Institute, London, United Kingdom
| | - Kwee L. Yong
- Research Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Yinyin Yuan
- Centre for Evolution and Cancer and Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Centre for Molecular Pathology, Royal Marsden Hospital, London, United Kingdom
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9
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Jiang L, Khawaja H, Tahsin S, Clarkson TA, Miranti CK, Zohar Y. Microfluidic-based human prostate-cancer-on-chip. Front Bioeng Biotechnol 2024; 12:1302223. [PMID: 38322789 PMCID: PMC10844564 DOI: 10.3389/fbioe.2024.1302223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024] Open
Abstract
Lack of adequate models significantly hinders advances in prostate cancer treatment, where resistance to androgen-deprivation therapies and bone metastasis remain as major challenges. Current in vitro models fail to faithfully mimic the complex prostate physiology. In vivo animal models can shed light on the oncogenes involved in prostate cancer development and progression; however, the animal prostate gland is fundamentally different from that of human, and the underlying genetic mechanisms are different. To address this problem, we developed the first in vitro microfluidic human Prostate-Cancer-on-Chip (PCoC) model, where human prostate cancer and stromal fibroblast cells were co-cultivated in two channels separated by a porous membrane under culture medium flow. The established microenvironment enables soluble signaling factors secreted by each culture to locally diffuse through the membrane pores affecting the neighboring culture. We particularly explored the conversion of the stromal fibroblasts into cancer-associated fibroblasts (CAFs) due to the interaction between the 2 cell types. Immunofluorescence microscopy revealed that tumor cells induced CAF biomarkers, αSMA and COL1A1, in stromal fibroblasts. The stromal CAF conversion level was observed to increase along the flow direction in response to diffusion agents, consistent with simulations of solute concentration gradients. The tumor cells also downregulated androgen receptor (AR) expression in stromal fibroblasts, while an adequate level of stromal AR expression is maintained in normal prostate homeostasis. We further investigated tumor invasion into the stroma, an early step in the metastatic cascade, in devices featuring a serpentine channel with orthogonal channel segments overlaying a straight channel and separated by an 8 µm-pore membrane. Both tumor cells and stromal CAFs were observed to cross over into their neighboring channel, and the stroma's role seemed to be proactive in promoting cell invasion. As control, normal epithelial cells neither induced CAF conversion nor promoted cell invasion. In summary, the developed PCoC model allows spatiotemporal analysis of the tumor-stroma dynamic interactions, due to bi-directional signaling and physical contact, recapitulating tissue-level multicellular responses associated with prostate cancer in vivo. Hence, it can serve as an in vitro model to dissect mechanisms in human prostate cancer development and seek advanced therapeutic strategies.
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Affiliation(s)
- Linan Jiang
- Department of Aerospace and Mechanical Engineering, Tucson, AZ, United States
| | - Hunain Khawaja
- Cancer Biology Graduate Interdisciplinary Program, Tucson, AZ, United States
| | - Shekha Tahsin
- Cancer Biology Graduate Interdisciplinary Program, Tucson, AZ, United States
| | | | - Cindy K Miranti
- Department of Molecular and Cellular Biology, Tucson, AZ, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Yitshak Zohar
- Department of Aerospace and Mechanical Engineering, Tucson, AZ, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
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10
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Lingam M. Information Transmission via Molecular Communication in Astrobiological Environments. ASTROBIOLOGY 2024; 24:84-99. [PMID: 38109216 DOI: 10.1089/ast.2023.0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The ubiquity of information transmission via molecular communication between cells is comprehensively documented on Earth; this phenomenon might even have played a vital role in the origin(s) and early evolution of life. Motivated by these considerations, a simple model for molecular communication entailing the diffusion of signaling molecules from transmitter to receiver is elucidated. The channel capacity C (maximal rate of information transmission) and an optimistic heuristic estimate of the actual information transmission rate ℐ are derived for this communication system; the two quantities, especially the latter, are demonstrated to be broadly consistent with laboratory experiments and more sophisticated theoretical models. The channel capacity exhibits a potentially weak dependence on environmental parameters, whereas the actual information transmission rate may scale with the intercellular distance d as ℐ ∝ d-4 and could vary substantially across settings. These two variables are roughly calculated for diverse astrobiological environments, ranging from Earth's upper oceans (C ∼ 3.1 × 103 bits/s; ℐ ∼ 4.7 × 10-2 bits/s) and deep sea hydrothermal vents (C ∼ 4.2 × 103 bits/s; ℐ ∼ 1.2 × 10-1 bits/s) to the hydrocarbon lakes and seas of Titan (C ∼ 3.8 × 103 bits/s; ℐ ∼ 2.6 × 10-1 bits/s).
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Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Sciences, Florida Institute of Technology, Melbourne, Florida, USA
- Department of Physics, The University of Texas at Austin, Austin, Texas, USA
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11
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Zhao S, Chen DP, Fu T, Yang JC, Ma D, Zhu XZ, Wang XX, Jiao YP, Jin X, Xiao Y, Xiao WX, Zhang HY, Lv H, Madabhushi A, Yang WT, Jiang YZ, Xu J, Shao ZM. Single-cell morphological and topological atlas reveals the ecosystem diversity of human breast cancer. Nat Commun 2023; 14:6796. [PMID: 37880211 PMCID: PMC10600153 DOI: 10.1038/s41467-023-42504-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
Digital pathology allows computerized analysis of tumor ecosystem using whole slide images (WSIs). Here, we present single-cell morphological and topological profiling (sc-MTOP) to characterize tumor ecosystem by extracting the features of nuclear morphology and intercellular spatial relationship for individual cells. We construct a single-cell atlas comprising 410 million cells from 637 breast cancer WSIs and dissect the phenotypic diversity within tumor, inflammatory and stroma cells respectively. Spatially-resolved analysis identifies recurrent micro-ecological modules representing locoregional multicellular structures and reveals four breast cancer ecotypes correlating with distinct molecular features and patient prognosis. Further analysis with multiomics data uncovers clinically relevant ecosystem features. High abundance of locally-aggregated inflammatory cells indicates immune-activated tumor microenvironment and favorable immunotherapy response in triple-negative breast cancers. Morphological intratumor heterogeneity of tumor nuclei correlates with cell cycle pathway activation and CDK inhibitors responsiveness in hormone receptor-positive cases. sc-MTOP enables using WSIs to characterize tumor ecosystems at the single-cell level.
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Affiliation(s)
- Shen Zhao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - De-Pin Chen
- Institute for Artificial Intelligence in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China
| | - Tong Fu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jing-Cheng Yang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, China
| | - Ding Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiu-Zhi Zhu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiang-Xue Wang
- Institute for Artificial Intelligence in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China
| | - Yi-Ping Jiao
- Institute for Artificial Intelligence in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xi Jin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wen-Xuan Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hu-Yunlong Zhang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hong Lv
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Anant Madabhushi
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Atlanta Veterans Affairs Medical Center, Atlanta, GA, USA
| | - Wen-Tao Yang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Jun Xu
- Institute for Artificial Intelligence in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
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Zhang H, AbdulJabbar K, Grunewald T, Akarca AU, Hagos Y, Sobhani F, Lecat CSY, Patel D, Lee L, Rodriguez-Justo M, Yong K, Ledermann JA, Le Quesne J, Hwang ES, Marafioti T, Yuan Y. Self-supervised deep learning for highly efficient spatial immunophenotyping. EBioMedicine 2023; 95:104769. [PMID: 37672979 PMCID: PMC10493897 DOI: 10.1016/j.ebiom.2023.104769] [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: 02/14/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Efficient biomarker discovery and clinical translation depend on the fast and accurate analytical output from crucial technologies such as multiplex imaging. However, reliable cell classification often requires extensive annotations. Label-efficient strategies are urgently needed to reveal diverse cell distribution and spatial interactions in large-scale multiplex datasets. METHODS This study proposed Self-supervised Learning for Antigen Detection (SANDI) for accurate cell phenotyping while mitigating the annotation burden. The model first learns intrinsic pairwise similarities in unlabelled cell images, followed by a classification step to map learnt features to cell labels using a small set of annotated references. We acquired four multiplex immunohistochemistry datasets and one imaging mass cytometry dataset, comprising 2825 to 15,258 single-cell images to train and test the model. FINDINGS With 1% annotations (18-114 cells), SANDI achieved weighted F1-scores ranging from 0.82 to 0.98 across the five datasets, which was comparable to the fully supervised classifier trained on 1828-11,459 annotated cells (-0.002 to -0.053 of averaged weighted F1-score, Wilcoxon rank-sum test, P = 0.31). Leveraging the immune checkpoint markers stained in ovarian cancer slides, SANDI-based cell identification reveals spatial expulsion between PD1-expressing T helper cells and T regulatory cells, suggesting an interplay between PD1 expression and T regulatory cell-mediated immunosuppression. INTERPRETATION By striking a fine balance between minimal expert guidance and the power of deep learning to learn similarity within abundant data, SANDI presents new opportunities for efficient, large-scale learning for histology multiplex imaging data. FUNDING This study was funded by the Royal Marsden/ICR National Institute of Health Research Biomedical Research Centre.
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Affiliation(s)
- Hanyun Zhang
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Khalid AbdulJabbar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Tami Grunewald
- Department of Oncology, UCL Cancer Institute, University College London, London, UK
| | - Ayse U Akarca
- Department of Cellular Pathology, University College London Hospital, London, UK
| | - Yeman Hagos
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Faranak Sobhani
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Catherine S Y Lecat
- Research Department of Hematology, Cancer Institute, University College London, UK
| | - Dominic Patel
- Research Department of Hematology, Cancer Institute, University College London, UK
| | - Lydia Lee
- Research Department of Hematology, Cancer Institute, University College London, UK
| | | | - Kwee Yong
- Research Department of Hematology, Cancer Institute, University College London, UK
| | - Jonathan A Ledermann
- Department of Oncology, UCL Cancer Institute, University College London, London, UK
| | - John Le Quesne
- School of Cancer Sciences, University of Glasgow, Glasgow, UK; CRUK Beatson Institute, Garscube Estate, Glasgow, UK; Department of Histopathology, Queen Elizabeth University Hospital, Glasgow, UK
| | - E Shelley Hwang
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospital, London, UK
| | - Yinyin Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
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13
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Page DB, Broeckx G, Jahangir CA, Verbandt S, Gupta RR, Thagaard J, Khiroya R, Kos Z, Abduljabbar K, Acosta Haab G, Acs B, Akturk G, Almeida JS, Alvarado-Cabrero I, Azmoudeh-Ardalan F, Badve S, Baharun NB, Bellolio ER, Bheemaraju V, Blenman KR, Botinelly Mendonça Fujimoto L, Bouchmaa N, Burgues O, Cheang MCU, Ciompi F, Cooper LA, Coosemans A, Corredor G, Dantas Portela FL, Deman F, Demaria S, Dudgeon SN, Elghazawy M, Ely S, Fernandez-Martín C, Fineberg S, Fox SB, Gallagher WM, Giltnane JM, Gnjatic S, Gonzalez-Ericsson PI, Grigoriadis A, Halama N, Hanna MG, Harbhajanka A, Hardas A, Hart SN, Hartman J, Hewitt S, Hida AI, Horlings HM, Husain Z, Hytopoulos E, Irshad S, Janssen EA, Kahila M, Kataoka TR, Kawaguchi K, Kharidehal D, Khramtsov AI, Kiraz U, Kirtani P, Kodach LL, Korski K, Kovács A, Laenkholm AV, Lang-Schwarz C, Larsimont D, Lennerz JK, Lerousseau M, Li X, Ly A, Madabhushi A, Maley SK, Manur Narasimhamurthy V, Marks DK, McDonald ES, Mehrotra R, Michiels S, Minhas FUAA, Mittal S, Moore DA, Mushtaq S, Nighat H, Papathomas T, Penault-Llorca F, Perera RD, Pinard CJ, Pinto-Cardenas JC, Pruneri G, Pusztai L, Rahman A, Rajpoot NM, Rapoport BL, Rau TT, Reis-Filho JS, Ribeiro JM, Rimm D, Vincent-Salomon A, Salto-Tellez M, Saltz J, Sayed S, Siziopikou KP, Sotiriou C, Stenzinger A, Sughayer MA, Sur D, Symmans F, Tanaka S, Taxter T, Tejpar S, Teuwen J, Thompson EA, Tramm T, Tran WT, van der Laak J, van Diest PJ, Verghese GE, Viale G, Vieth M, Wahab N, Walter T, Waumans Y, Wen HY, Yang W, Yuan Y, Adams S, Bartlett JMS, Loibl S, Denkert C, Savas P, Loi S, Salgado R, Specht Stovgaard E. Spatial analyses of immune cell infiltration in cancer: current methods and future directions: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer. J Pathol 2023; 260:514-532. [PMID: 37608771 DOI: 10.1002/path.6165] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/19/2023] [Indexed: 08/24/2023]
Abstract
Modern histologic imaging platforms coupled with machine learning methods have provided new opportunities to map the spatial distribution of immune cells in the tumor microenvironment. However, there exists no standardized method for describing or analyzing spatial immune cell data, and most reported spatial analyses are rudimentary. In this review, we provide an overview of two approaches for reporting and analyzing spatial data (raster versus vector-based). We then provide a compendium of spatial immune cell metrics that have been reported in the literature, summarizing prognostic associations in the context of a variety of cancers. We conclude by discussing two well-described clinical biomarkers, the breast cancer stromal tumor infiltrating lymphocytes score and the colon cancer Immunoscore, and describe investigative opportunities to improve clinical utility of these spatial biomarkers. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- David B Page
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Glenn Broeckx
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
- Centre for Oncological Research (CORE), MIPPRO, Faculty of Medicine, Antwerp University, Antwerp, Belgium
| | - Chowdhury Arif Jahangir
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Sara Verbandt
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Rajarsi R Gupta
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Jeppe Thagaard
- Technical University of Denmark, Kongens Lyngby, Denmark
- Visiopharm A/S, Hørsholm, Denmark
| | - Reena Khiroya
- Department of Cellular Pathology, University College Hospital, London, UK
| | - Zuzana Kos
- Department of Pathology and Laboratory Medicine, BC Cancer Vancouver Centre, University of British Columbia, Vancouver, BC, Canada
| | - Khalid Abduljabbar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | | | - Balazs Acs
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Guray Akturk
- Translational Molecular Biomarkers, Merck & Co Inc, Kenilworth, NJ, USA
| | - Jonas S Almeida
- National Cancer Institute, Division of Cancer Epidemiology and Genetics (DCEG), Rockville, MD, USA
| | | | | | - Sunil Badve
- Pathology and Laboratory Medicine, Emory University School of Medicine, Emory University Winship Cancer Institute, Atlanta, GA, USA
| | | | - Enrique R Bellolio
- Departamento de Anatomía Patológica, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | | | - Kim Rm Blenman
- Internal Medicine Section of Medical Oncology and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Computer Science, Yale School of Engineering and Applied Science, New Haven, CT, USA
| | | | - Najat Bouchmaa
- Institute of Biological Sciences, Faculty of Medical Sciences, Mohammed VI Polytechnic University (UM6P), Ben-Guerir, Morocco
| | - Octavio Burgues
- Pathology Department, Hospital Cliníco Universitario de Valencia/Incliva, Valencia, Spain
| | - Maggie Chon U Cheang
- Head of Integrative Genomics Analysis in Clinical Trials, ICR-CTSU, Division of Clinical Studies, Institute of Cancer Research, London, UK
| | - Francesco Ciompi
- Radboud University Medical Center, Department of Pathology, Nijmegen, The Netherlands
| | - Lee Ad Cooper
- Department of Pathology, Northwestern Feinberg School of Medicine, Chicago, IL, USA
| | - An Coosemans
- Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, KU Leuven, Leuven, Belgium
| | - Germán Corredor
- Biomedical Engineering Department, Emory University, Atlanta, GA, USA
| | | | - Frederik Deman
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Department of Pathology, Weill Cornell Medicine, New York, NY, USA
| | - Sarah N Dudgeon
- Conputational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Mahmoud Elghazawy
- University of Surrey, Guildford, UK
- Ain Shams University, Cairo, Egypt
| | - Scott Ely
- Translational Pathology, Translational Sciences and Diagnostics/Translational Medicine/R&D, Bristol Myers Squibb, Princeton, NJ, USA
| | - Claudio Fernandez-Martín
- Instituto Universitario de Investigación en Tecnología Centrada en el Ser Humano, HUMAN-tech, Universitat Politècnica de València, Valencia, Spain
| | - Susan Fineberg
- Montefiore Medical Center and the Albert Einstein College of Medicine, New York, NY, USA
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | | | - Sacha Gnjatic
- Department of Oncological Sciences, Medicine Hem/Onc, and Pathology, Tisch Cancer Institute - Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Anita Grigoriadis
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Niels Halama
- Translational Immunotherapy, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Alexandros Hardas
- Pathobiology & Population Sciences, The Royal Veterinary College, London, UK
| | - Steven N Hart
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Johan Hartman
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Stephen Hewitt
- Department of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Akira I Hida
- Department of Pathology, Matsuyama Shimin Hospital, Matsuyama, Japan
| | - Hugo M Horlings
- Division of Pathology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | | | | | - Sheeba Irshad
- King's College London & Guy's & St Thomas' NHS Trust, London, UK
| | - Emiel Am Janssen
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
| | - Mohamed Kahila
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Kosuke Kawaguchi
- Department of Breast Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Durga Kharidehal
- Department of Pathology, Narayana Medical College, Nellore, India
| | - Andrey I Khramtsov
- Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Umay Kiraz
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
| | - Pawan Kirtani
- Department of Histopathology, Aakash Healthcare Super Speciality Hospital, New Delhi, India
| | - Liudmila L Kodach
- Department of Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Konstanty Korski
- Data, Analytics and Imaging, Product Development, F.Hoffmann-La Roche AG, Basel, Switzerland
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anne-Vibeke Laenkholm
- Surgical Pathology, Zealand University Hospital, Roskilde, Denmark
- Surgical Pathology, University of Copenhagen, Copenhagen, Denmark
| | - Corinna Lang-Schwarz
- Institute of Pathology, Klinikum Bayreuth GmbH, Friedrich-Alexander-University Erlangen-Nuremberg, Bayreuth, Germany
| | - Denis Larsimont
- Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Jochen K Lennerz
- Center for Integrated Diagnostics, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Marvin Lerousseau
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, Paris, France
- Institut Curie, PSL University, Paris, France
- INSERM, U900, Paris, France
| | - Xiaoxian Li
- Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Amy Ly
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Anant Madabhushi
- Biomedical Engineering, Radiology and Imaging Sciences, Biomedical Informatics, Pathology, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Sai K Maley
- NRG Oncology/NSABP Foundation, Pittsburgh, PA, USA
| | | | - Douglas K Marks
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Elizabeth S McDonald
- Breast Cancer Translational Research Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Ravi Mehrotra
- Indian Cancer Genome Atlas, Pune, India
- Centre for Health, Innovation and Policy Foundation, Noida, India
| | - Stefan Michiels
- Office of Biostatistics and Epidemiology, Gustave Roussy, Oncostat U1018, Inserm, University Paris-Saclay, Ligue Contre le Cancer labeled Team, Villejuif, France
| | - Fayyaz Ul Amir Afsar Minhas
- Tissue Image Analytics Centre, Warwick Cancer Research Centre, PathLAKE Consortium, Department of Computer Science, University of Warwick, Coventry, UK
| | - Shachi Mittal
- Department of Chemical Engineering, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - David A Moore
- CRUK Lung Cancer Centre of Excellence, UCLH, London, UK
| | - Shamim Mushtaq
- Department of Biochemistry, Ziauddin University, Karachi, Pakistan
| | - Hussain Nighat
- Pathology and Laboratory Medicine, All India Institute of Medical Sciences, Raipur, India
| | - Thomas Papathomas
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
- Department of Clinical Pathology, Drammen Sykehus, Vestre Viken HF, Drammen, Norway
| | - Frederique Penault-Llorca
- Centre Jean Perrin, INSERM U1240, Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Rashindrie D Perera
- School of Electrical, Mechanical and Infrastructure Engineering, University of Melbourne, Melbourne, VIC, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Christopher J Pinard
- Radiogenomics Laboratory, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
- Department of Oncology, Lakeshore Animal Health Partners, Mississauga, ON, Canada
- Centre for Advancing Responsible and Ethical Artificial Intelligence (CARE-AI), University of Guelph, Guelph, ON, Canada
| | | | - Giancarlo Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Faculty of Medicine and Surgery, University of Milan, Milan, Italy
| | - Lajos Pusztai
- Yale Cancer Center, New Haven, CT, USA
- Department of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Arman Rahman
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | | | - Bernardo Leon Rapoport
- The Medical Oncology Centre of Rosebank, Johannesburg, South Africa
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Tilman T Rau
- Institute of Pathology, University Hospital Düsseldorf and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Jorge S Reis-Filho
- Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joana M Ribeiro
- Département de Médecine Oncologique, Institute Gustave Roussy, Villejuif, France
| | - David Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Anne Vincent-Salomon
- Department of Diagnostic and Theranostic Medicine, Institut Curie, University Paris-Sciences et Lettres, Paris, France
| | - Manuel Salto-Tellez
- Integrated Pathology Unit, Institute of Cancer Research, London, UK
- Precision Medicine Centre, Queen's University Belfast, Belfast, UK
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook Medicine, New York, NY, USA
| | - Shahin Sayed
- Department of Pathology, Aga Khan University, Nairobi, Kenya
| | - Kalliopi P Siziopikou
- Department of Pathology, Section of Breast Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory J.-C. Heuson, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Medical Oncology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles, Brussels, Belgium
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Centers for Personalized Medicine (ZPM), Heidelberg, Germany
| | | | - Daniel Sur
- Department of Medical Oncology, University of Medicine and Pharmacy "Iuliu Hatieganu", Cluj-Napoca, Romania
| | - Fraser Symmans
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Sabine Tejpar
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jonas Teuwen
- AI for Oncology Lab, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Trine Tramm
- Pathology, and Institute of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - William T Tran
- Department of Radiation Oncology, University of Toronto and Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Jeroen van der Laak
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
- Johns Hopkins Oncology Center, Baltimore, MD, USA
| | - Gregory E Verghese
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Giuseppe Viale
- Department of Pathology, European Institute of Oncology & University of Milan, Milan, Italy
| | - Michael Vieth
- Institute of Pathology, Klinikum Bayreuth GmbH, Friedrich-Alexander-University Erlangen-Nuremberg, Bayreuth, Germany
| | - Noorul Wahab
- Tissue Image Analytics Centre, Department of Computer Science, University of Warwick, Coventry, UK
| | - Thomas Walter
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, Paris, France
- Institut Curie, PSL University, Paris, France
- INSERM, U900, Paris, France
| | | | - Hannah Y Wen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wentao Yang
- Fudan Medical University Shanghai Cancer Center, Shanghai, PR China
| | - Yinyin Yuan
- Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sylvia Adams
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, Manhattan, NY, USA
| | | | - Sibylle Loibl
- Department of Medicine and Research, German Breast Group, Neu-Isenburg, Germany
| | - Carsten Denkert
- Institut für Pathologie, Philipps-Universität Marburg und Universitätsklinikum Marburg, Marburg, Germany
| | - Peter Savas
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Sherene Loi
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Elisabeth Specht Stovgaard
- Department of Pathology, Herlev and Gentofte Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
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14
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Cheng C, Chen W, Jin H, Chen X. A Review of Single-Cell RNA-Seq Annotation, Integration, and Cell-Cell Communication. Cells 2023; 12:1970. [PMID: 37566049 PMCID: PMC10417635 DOI: 10.3390/cells12151970] [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: 06/13/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cellular biology at an unprecedented resolution, enabling the characterization of cellular heterogeneity, identification of rare but significant cell types, and exploration of cell-cell communications and interactions. Its broad applications span both basic and clinical research domains. In this comprehensive review, we survey the current landscape of scRNA-seq analysis methods and tools, focusing on count modeling, cell-type annotation, data integration, including spatial transcriptomics, and the inference of cell-cell communication. We review the challenges encountered in scRNA-seq analysis, including issues of sparsity or low expression, reliability of cell annotation, and assumptions in data integration, and discuss the potential impact of suboptimal clustering and differential expression analysis tools on downstream analyses, particularly in identifying cell subpopulations. Finally, we discuss recent advancements and future directions for enhancing scRNA-seq analysis. Specifically, we highlight the development of novel tools for annotating single-cell data, integrating and interpreting multimodal datasets covering transcriptomics, epigenomics, and proteomics, and inferring cellular communication networks. By elucidating the latest progress and innovation, we provide a comprehensive overview of the rapidly advancing field of scRNA-seq analysis.
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Affiliation(s)
- Changde Cheng
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (W.C.); (H.J.)
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (W.C.); (H.J.)
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
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15
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Verstraete N, Marku M, Domagala M, Arduin H, Bordenave J, Fournié JJ, Ysebaert L, Poupot M, Pancaldi V. An agent-based model of monocyte differentiation into tumour-associated macrophages in chronic lymphocytic leukemia. iScience 2023; 26:106897. [PMID: 37332613 PMCID: PMC10275988 DOI: 10.1016/j.isci.2023.106897] [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: 03/08/2022] [Revised: 12/07/2022] [Accepted: 05/12/2023] [Indexed: 06/20/2023] Open
Abstract
Monocyte-derived macrophages help maintain tissue homeostasis and defend the organism against pathogens. In tumors, recent studies have uncovered complex macrophage populations, including tumor-associated macrophages, which support tumorigenesis through cancer hallmarks such as immunosuppression, angiogenesis, or matrix remodeling. In the case of chronic lymphocytic leukemia, these macrophages are known as nurse-like cells (NLCs) and they protect leukemic cells from spontaneous apoptosis, contributing to their chemoresistance. We propose an agent-based model of monocyte differentiation into NLCs upon contact with leukemic B cells in vitro. We performed patient-specific model optimization using cultures of peripheral blood mononuclear cells from patients. Using our model, we were able to reproduce the temporal survival dynamics of cancer cells in a patient-specific manner and to identify patient groups related to distinct macrophage phenotypes. Our results show a potentially important role of phagocytosis in the polarization process of NLCs and in promoting cancer cells' enhanced survival.
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Affiliation(s)
- Nina Verstraete
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Malvina Marku
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Marcin Domagala
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Hélène Arduin
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Julie Bordenave
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Jean-Jacques Fournié
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Loïc Ysebaert
- Service d’Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, 31330 Toulouse, France
| | - Mary Poupot
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Vera Pancaldi
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Barcelona Supercomputing Center, Carrer de Jordi Girona, 29, 31, 08034 Barcelona, Spain
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16
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Zhu D, Trinh P, Liu E, Yang F. Cell-Cell Interactions Enhance Cartilage Zonal Development in 3D Gradient Hydrogels. ACS Biomater Sci Eng 2023; 9:831-843. [PMID: 36629329 DOI: 10.1021/acsbiomaterials.2c00469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cartilage tissue is characterized by zonal organization with gradual transitions of biochemical and mechanical cues from superficial to deep zones. We previously reported that 3D gradient hydrogels made of polyethylene glycol and chondroitin sulfate can induce zonal-specific responses of chondrocytes, resulting in zonal cartilage formation that mimics native tissues. While the role of cell-matrix interactions has been studied extensively, how cell-cell interactions across different zones influence cartilage zonal development remains unknown. The goal of this study is to harness gradient hydrogels as a tool to elucidate the role of cell-cell interactions in driving cartilage zonal development. When encapsulated in intact gradient hydrogels, chondrocytes exhibited strong zonal-specific responses that mimic native cartilage zonal organization. However, the separate culture of each zone of gradient hydrogels resulted in a significant decrease in cell proliferation and cartilage matrix deposition across all zones, while the trend of zonal dependence remains. Unexpectedly, mixing the coculture of all five zones of hydrogels in the same culture well largely abolished the zonal differences, with all zones behaving similarly to the softest zone. These results suggest that paracrine signal exchange among cells in different zones is essential in driving cartilage zonal development, and a spatial organization of zones is required for proper tissue zonal development. Intact, separate, or coculture groups resulted in distinct gene expression patterns in mechanosensing and cartilage-specific markers, suggesting that cell-cell interactions can also modulate mechanosensing. We further showed that 7 days of priming in intact gradient culture was sufficient to instruct the cells to complete the zonal development, and the separate or mixed coculture after 7 days of intact culture had minimal effects on cartilage formation. This study highlights the important role of cell-cell interactions in driving cartilage zonal development and validates gradient hydrogels as a useful tool to elucidate the role of cell-matrix and cell-cell interactions in driving zonal development during tissue morphogenesis and regeneration.
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Affiliation(s)
- Danqing Zhu
- Department of Bioengineering, Stanford University, Palo Alto, California 94305, United States
| | - Pavin Trinh
- Department of Bioengineering, Stanford University, Palo Alto, California 94305, United States
| | - Elisa Liu
- Department of Bioengineering, Stanford University, Palo Alto, California 94305, United States
| | - Fan Yang
- Department of Bioengineering, Stanford University, Palo Alto, California 94305, United States.,Department of Orthopaedic Surgery, Stanford University, Palo Alto, California 94305, United States
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17
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Alzoubi I, Bao G, Zheng Y, Wang X, Graeber MB. Artificial intelligence techniques for neuropathological diagnostics and research. Neuropathology 2022. [PMID: 36443935 DOI: 10.1111/neup.12880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/17/2022] [Accepted: 10/23/2022] [Indexed: 12/03/2022]
Abstract
Artificial intelligence (AI) research began in theoretical neurophysiology, and the resulting classical paper on the McCulloch-Pitts mathematical neuron was written in a psychiatry department almost 80 years ago. However, the application of AI in digital neuropathology is still in its infancy. Rapid progress is now being made, which prompted this article. Human brain diseases represent distinct system states that fall outside the normal spectrum. Many differ not only in functional but also in structural terms, and the morphology of abnormal nervous tissue forms the traditional basis of neuropathological disease classifications. However, only a few countries have the medical specialty of neuropathology, and, given the sheer number of newly developed histological tools that can be applied to the study of brain diseases, a tremendous shortage of qualified hands and eyes at the microscope is obvious. Similarly, in neuroanatomy, human observers no longer have the capacity to process the vast amounts of connectomics data. Therefore, it is reasonable to assume that advances in AI technology and, especially, whole-slide image (WSI) analysis will greatly aid neuropathological practice. In this paper, we discuss machine learning (ML) techniques that are important for understanding WSI analysis, such as traditional ML and deep learning, introduce a recently developed neuropathological AI termed PathoFusion, and present thoughts on some of the challenges that must be overcome before the full potential of AI in digital neuropathology can be realized.
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Affiliation(s)
- Islam Alzoubi
- School of Computer Science The University of Sydney Sydney New South Wales Australia
| | - Guoqing Bao
- School of Computer Science The University of Sydney Sydney New South Wales Australia
| | - Yuqi Zheng
- Ken Parker Brain Tumour Research Laboratories Brain and Mind Centre, Faculty of Medicine and Health, University of Sydney Camperdown New South Wales Australia
| | - Xiuying Wang
- School of Computer Science The University of Sydney Sydney New South Wales Australia
| | - Manuel B. Graeber
- Ken Parker Brain Tumour Research Laboratories Brain and Mind Centre, Faculty of Medicine and Health, University of Sydney Camperdown New South Wales Australia
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18
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Benchaprathanphorn K, Sakulaue P, Siriwatwechakul W, Muangman P, Chinaroonchai K, Namviriyachote N, Viravaidya-Pasuwat K. Expansion of fibroblast cell sheets using a modified MEEK micrografting technique for wound healing applications. Sci Rep 2022; 12:18541. [PMID: 36329229 PMCID: PMC9633782 DOI: 10.1038/s41598-022-21913-x] [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: 03/02/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022] Open
Abstract
Cell sheet engineering, a scaffold-free approach to fabricate functional tissue constructs from several cell monolayers, has shown promise in tissue regeneration and wound healing. Unfortunately, these cell sheets are often too small to provide sufficient wound area coverage. In this study, we describe a process to enlarge cell sheets using MEEK micrografting, a technique extensively used to expand skin autografts for large burn treatments. Human dermal fibroblast cell sheets were placed on MEEK's prefolded gauze without any use of adhesive, cut along the premarked lines and stretched out at various expansion ratios (1:3, 1:6 and 1:9), resulting in regular distribution of many square islands of fibroblasts at a much larger surface area. The cellular processes essential for wound healing, including reattachment, proliferation, and migration, of the fibroblasts on expanded MEEK gauze were superior to those on nylon dressing which served as a control. The optimal expansion ratio with the highest migration rate was 1:6, possibly due to the activation of chemical signals caused by mechanical stretching and an effective intercellular communication distance. Therefore, the combination of cell sheet engineering with the MEEK micrografting technique could provide high quality cells with a large coverage area, which would be particularly beneficial in wound care applications.
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Affiliation(s)
- Kanokaon Benchaprathanphorn
- grid.412151.20000 0000 8921 9789Biological Engineering Program, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok, 10140 Thailand
| | - Phongphot Sakulaue
- grid.412434.40000 0004 1937 1127School of Bio-Chemical Engineering and Technology, Sirindhorn International Institute of Technology, Thammasat University, Khlong Luang, 12120 Pathumthani Thailand
| | - Wanwipa Siriwatwechakul
- grid.412434.40000 0004 1937 1127School of Bio-Chemical Engineering and Technology, Sirindhorn International Institute of Technology, Thammasat University, Khlong Luang, 12120 Pathumthani Thailand
| | - Pornprom Muangman
- grid.416009.aTrauma Division, Department of Surgery, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700 Thailand
| | - Kusuma Chinaroonchai
- grid.416009.aTrauma Division, Department of Surgery, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700 Thailand
| | - Nantaporn Namviriyachote
- grid.416009.aTrauma Division, Department of Surgery, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700 Thailand
| | - Kwanchanok Viravaidya-Pasuwat
- grid.412151.20000 0000 8921 9789Biological Engineering Program, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok, 10140 Thailand ,grid.412151.20000 0000 8921 9789Department of Chemical Engineering, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok, 10140 Thailand ,grid.412151.20000 0000 8921 9789Biological Engineering and Chemical Engineering Department, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok, 10140 Thailand
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19
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Armingol E, Ghaddar A, Joshi CJ, Baghdassarian H, Shamie I, Chan J, Her HL, Berhanu S, Dar A, Rodriguez-Armstrong F, Yang O, O’Rourke EJ, Lewis NE. Inferring a spatial code of cell-cell interactions across a whole animal body. PLoS Comput Biol 2022; 18:e1010715. [PMID: 36395331 PMCID: PMC9714814 DOI: 10.1371/journal.pcbi.1010715] [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: 04/01/2022] [Revised: 12/01/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022] Open
Abstract
Cell-cell interactions shape cellular function and ultimately organismal phenotype. Interacting cells can sense their mutual distance using combinations of ligand-receptor pairs, suggesting the existence of a spatial code, i.e., signals encoding spatial properties of cellular organization. However, this code driving and sustaining the spatial organization of cells remains to be elucidated. Here we present a computational framework to infer the spatial code underlying cell-cell interactions from the transcriptomes of the cell types across the whole body of a multicellular organism. As core of this framework, we introduce our tool cell2cell, which uses the coexpression of ligand-receptor pairs to compute the potential for intercellular interactions, and we test it across the Caenorhabditis elegans' body. Leveraging a 3D atlas of C. elegans' cells, we also implement a genetic algorithm to identify the ligand-receptor pairs most informative of the spatial organization of cells across the whole body. Validating the spatial code extracted with this strategy, the resulting intercellular distances are negatively correlated with the inferred cell-cell interactions. Furthermore, for selected cell-cell and ligand-receptor pairs, we experimentally confirm the communicatory behavior inferred with cell2cell and the genetic algorithm. Thus, our framework helps identify a code that predicts the spatial organization of cells across a whole-animal body.
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Affiliation(s)
- Erick Armingol
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Abbas Ghaddar
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Chintan J. Joshi
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Hratch Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Isaac Shamie
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Jason Chan
- Poway High School, Poway, California, United States of America
| | - Hsuan-Lin Her
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America
| | - Samuel Berhanu
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Anushka Dar
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | | | - Olivia Yang
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Eyleen J. O’Rourke
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Cell Biology, School of Medicine of University of Virginia, Charlottesville, Virginia, United States of America
| | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
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20
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Fang S, Chen B, Zhang Y, Sun H, Liu L, Liu S, Li Y, Xu X. Computational Approaches and Challenges in Spatial Transcriptomics. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022:S1672-0229(22)00129-2. [PMID: 36252814 PMCID: PMC10372921 DOI: 10.1016/j.gpb.2022.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 09/08/2022] [Accepted: 10/09/2022] [Indexed: 01/19/2023]
Abstract
The development of spatial transcriptomics (ST) technologies has transformed genetic research from a single-cell data level to a two-dimensional spatial coordinate system and facilitated the study of the composition and function of various cell subsets in different environments and organs. The large-scale data generated by these ST technologies, which contain spatial gene expression information, have elicited the need for spatially resolved approaches to meet the requirements of computational and biological data interpretation. These requirements include dealing with the explosive growth of data to determine the cell-level and gene-level expression, correcting the inner batch effect and loss of expression to improve the data quality, conducting efficient interpretation and in-depth knowledge mining both at the single-cell and tissue-wide levels, and conducting multi-omics integration analysis to provide an extensible framework toward the in-depth understanding of biological processes. However, algorithms designed specifically for ST technologies to meet these requirements are still in their infancy. Here, we review computational approaches to these problems in light of corresponding issues and challenges, and present forward-looking insights into algorithm development.
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21
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Martin NG, Malacrino S, Wojciechowska M, Campo L, Jones H, Wedge DC, Holmes C, Sirinukunwattana K, Sailem H, Verrill C, Rittscher J. A Graph Based Neural Network Approach to Immune Profiling of Multiplexed Tissue Samples. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2022; 2022:3063-3067. [PMID: 36085678 DOI: 10.1109/embc48229.2022.9871251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Multiplexed immunofluorescence provides an un-precedented opportunity for studying specific cell-to-cell and cell microenvironment interactions. We employ graph neural networks to combine features obtained from tissue morphology with measurements of protein expression to profile the tumour microenvironment associated with different tumour stages. Our framework presents a new approach to analysing and processing these complex multi-dimensional datasets that overcomes some of the key challenges in analysing these data and opens up the opportunity to abstract biologically meaningful interactions.
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22
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Neutrophil and natural killer cell imbalances prevent muscle stem cell-mediated regeneration following murine volumetric muscle loss. Proc Natl Acad Sci U S A 2022; 119:e2111445119. [PMID: 35377804 PMCID: PMC9169656 DOI: 10.1073/pnas.2111445119] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Skeletal muscle is one of the largest tissues in the body and can regenerate when damaged through a population of resident muscle stem cells. A type of muscle trauma called volumetric muscle loss overwhelms the regenerative capacity of muscle stem cells and engenders fibrotic supplantation. A comparison of muscle injuries resulting in regeneration or fibrosis revealed that intercellular communication between neutrophils and natural killer cells impacts muscle stem cell-mediated repair. Perturbation of neutrophil–natural killer cell interactions resulted in a variation of healing outcomes and suggested that immunomodulatory interventions can be effective to prevent aberrant healing outcomes. Volumetric muscle loss (VML) overwhelms the innate regenerative capacity of mammalian skeletal muscle (SkM), leading to numerous disabilities and reduced quality of life. Immune cells are critical responders to muscle injury and guide tissue resident stem cell– and progenitor-mediated myogenic repair. However, how immune cell infiltration and intercellular communication networks with muscle stem cells are altered following VML and drive pathological outcomes remains underexplored. Herein, we contrast the cellular and molecular mechanisms of VML injuries that result in the fibrotic degeneration or regeneration of SkM. Following degenerative VML injuries, we observed the heightened infiltration of natural killer (NK) cells as well as the persistence of neutrophils beyond 2 wk postinjury. Functional validation of NK cells revealed an antagonistic role in neutrophil accumulation in part via inducing apoptosis and CCR1-mediated chemotaxis. The persistent infiltration of neutrophils in degenerative VML injuries was found to contribute to impairments in muscle stem cell regenerative function, which was also attenuated by transforming growth factor beta 1 (TGFβ1). Blocking TGFβ signaling reduced neutrophil accumulation and fibrosis and improved muscle-specific force. Collectively, these results enhance our understanding of immune cell–stem cell cross talk that drives regenerative dysfunction and provide further insight into possible avenues for fibrotic therapy exploration.
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23
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Lummertz da Rocha E, Kubaczka C, Sugden WW, Najia MA, Jing R, Markel A, LeBlanc ZC, Dos Santos Peixoto R, Falchetti M, Collins JJ, North TE, Daley GQ. CellComm infers cellular crosstalk that drives haematopoietic stem and progenitor cell development. Nat Cell Biol 2022; 24:579-589. [PMID: 35414020 PMCID: PMC10123873 DOI: 10.1038/s41556-022-00884-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/01/2022] [Indexed: 01/05/2023]
Abstract
Intercellular communication orchestrates a multitude of physiologic and pathologic conditions. Algorithms to infer cell-cell communication and predict downstream signalling and regulatory networks are needed to illuminate mechanisms of stem cell differentiation and tissue development. Here, to fill this gap, we developed and applied CellComm to investigate how the aorta-gonad-mesonephros microenvironment dictates haematopoietic stem and progenitor cell emergence. We identified key microenvironmental signals and transcriptional networks that regulate haematopoietic development, including Stat3, Nr0b2, Ybx1 and App, and confirmed their roles using zebrafish, mouse and human models. Notably, CellComm revealed extensive crosstalk among signalling pathways and convergence on common transcriptional regulators, indicating a resilient developmental programme that ensures dynamic adaptation to changes in the embryonic environment. Our work provides an algorithm and data resource for the scientific community.
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Affiliation(s)
- Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Caroline Kubaczka
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Wade W Sugden
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
| | - Mohamad Ali Najia
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Health Sciences & Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ran Jing
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Arianna Markel
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zachary C LeBlanc
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
| | - Rafael Dos Santos Peixoto
- Undergraduate program in Automation and Control Engineering, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Marcelo Falchetti
- Graduate Program of Pharmacology, Center for Biological Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
| | - James J Collins
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Health Sciences & Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Trista E North
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA.
| | - George Q Daley
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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24
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Kim SJ, Byun H, Lee S, Kim E, Lee GM, Huh SJ, Joo J, Shin H. Spatially arranged encapsulation of stem cell spheroids within hydrogels for the regulation of spheroid fusion and cell migration. Acta Biomater 2022; 142:60-72. [PMID: 35085797 DOI: 10.1016/j.actbio.2022.01.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/09/2021] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
Mesenchymal stem cell spheroids have been encapsulated in hydrogels for various applications because spheroids demonstrate higher cell activity than individual cells in suspension. However, there is limited information on the effect of distance between spheroids (inter-spheroid distance) on fusion or migration in a hydrogel. In this study, we developed temperature-responsive hydrogels with surface microwell patterns to culture adipose-derived stem cell (ASC) spheroids and deliver them into a Matrigel for the investigation of the effect of inter-spheroid distance on spheroid behavior. The ASC spheroids were encapsulated successfully in a Matrigel, denoted as sandwich culture, with a specific inter-spheroid distance ranging from 100 to 400 µm. Interestingly, ASCs migrated from the host spheroid and formed a bridge-like structure between spheroids, denoted as a cellular bridge, only when the inter-spheroid distance was 200 µm. Thus, we performed a sandwich culture of human umbilical vein endothelial cells (HUVECs) and ASCs in co-cultured spheroids in the Matrigel to create a homogeneous endothelial cell network in the hydrogel. The HUVECs sprouted through the ASC cellular bridge and directly interacted with the adjacent spheroid when the inter-spheroid distance was 200 µm. Similar results were obtained from an in vivo study. Thus, our study suggests the appropriate inter-spheroid distance for effective spheroid encapsulation in a hydrogel. STATEMENT OF SIGNIFICANCE: Recently, spheroid-based 3D tissue culture techniques such as spheroid encapsulation or 3D printing are being intensively investigated for various purposes. However, there is limited research regarding the effect of the inter-spheroid distance on spheroid communication. Here, we demonstrate a spatially arranged spheroid encapsulation method within a Matrigel by using a temperature-responsive hydrogel. Human adipose-derived stem cell spheroids are encapsulated with a precisely controlled inter-spheroid distance from 100 to 400 µm and show different tendencies in cell migration and spheroid fusion. Our results suggest that the inter-spheroid distance affects spheroid communication, and thus, the inter-spheroid distance needs to be considered carefully according to the purpose.
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Affiliation(s)
- Se-Jeong Kim
- Department of Bioengineering, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea; BK21 FOUR, Education and Research Group for Biopharmaceutical Innovation Leader, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Hayeon Byun
- Department of Bioengineering, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea; BK21 FOUR, Education and Research Group for Biopharmaceutical Innovation Leader, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Sangmin Lee
- Department of Bioengineering, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea; BK21 FOUR, Education and Research Group for Biopharmaceutical Innovation Leader, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Eunhyung Kim
- Department of Bioengineering, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea; BK21 FOUR, Education and Research Group for Biopharmaceutical Innovation Leader, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Gyeong Min Lee
- Department of Bioengineering, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea; BK21 FOUR, Education and Research Group for Biopharmaceutical Innovation Leader, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Seung Jae Huh
- Department of Bioengineering, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea; BK21 FOUR, Education and Research Group for Biopharmaceutical Innovation Leader, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Jinmyoung Joo
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea.
| | - Heungsoo Shin
- Department of Bioengineering, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea; BK21 FOUR, Education and Research Group for Biopharmaceutical Innovation Leader, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea; Institute of Nano Science and Technology (INST), Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea.
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25
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Hussain S, Malik SI. Effects of tumor derived exosomes on T cells markers expression. BRAZ J BIOL 2022; 84:e250556. [PMID: 35137845 DOI: 10.1590/1519-6984.250556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 12/07/2021] [Indexed: 11/22/2022] Open
Abstract
Exosomes are 30-120nm bio particles transferred from donor to recipient cells leading to modification in their regulatory mechanisms depending upon the coded message in the form of loaded biomolecule. Cancer cells derived exosomes the true representatives of the parent cells have been found to modify the tumor surrounding/distinct regions and participate in metastasis, angiogenesis and immune suppression. Tis study was aimed to study the effects of tumor mice derived exosomes on the normal mice spleen isolated T cells by using co-culture experiments and flow cytometer analysis. We mainly focused on some of the T cells population and cytokines including IFN-γ, FOXP3+ regulatory T (Treg) cells and KI67 (proliferation marker). Overall results indicated random changes in different set of experiments, where the cancer derived exosomes reduced the IFN-γ expression in both CD4 and CD8 T cells, similarly the Treg cells were also found decreased in the presence of cancer exosomes. No significant changes were observed on the Ki67 marker expression. Such studies are helpful in understanding the role of cancer exosomes in immune cells suppression in tumor microenvironment. Cancer exosomes will need to be validated in vivo and in vitro on a molecular scale in detail for clinical applications.
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Affiliation(s)
- S Hussain
- Capital University of Science and Technology - CUST, Faculty of Health and Life Sciences, Department of Bioinformatics and Biosciences, Islamabad, Pakistan
| | - S I Malik
- Capital University of Science and Technology - CUST, Faculty of Health and Life Sciences, Department of Bioinformatics and Biosciences, Islamabad, Pakistan
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26
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Dos Santos FCA, Negre AFP, Rodríguez DAO, de Sousa GC, Rodrigues GA, Sanches BDA, Carvalho HF, Taboga SR, Biancardi MF. Female Prostate Development: Morphological Analysis of the Budding Dynamic. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:272-280. [PMID: 35039106 DOI: 10.1017/s1431927621014008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The presence of the prostate in female mammals has long been known. However, pieces of information related to its development are still lacking. The aim of this study was to explore the budding dynamic during the initial prostate development in female gerbils. Pregnant females were timed, the fetuses were euthanized, and the urogenital sinus was dissected out between the embryonic days 20 and 24 (E20-E24 groups). Newborn pups (1-day-old; P1 group) underwent the same procedures. The female prostate development was based on epithelial buds which arose far from the paraurethral mesenchyme (PAM). The epithelial buds reached the PAM at prenatal day 24, crossing a small gap in the smooth muscle layer between the periurethral mesenchyme (PEM) and the PAM. Steroid nuclear receptors such as the androgen receptor and estrogen receptor alpha were localized in the PEM through the urethral wall, although some epithelial labeling was also present in the urogenital sinus epithelium (UGE). P63-positive cells were found only in the UGE, becoming restricted to the basal compartment after the 23rd prenatal day. The results showed that the gerbil female prostate exhibits a distinct budding pattern as compared to the male prostate development.
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Affiliation(s)
- Fernanda C A Dos Santos
- Department of Histology, Embryology, and Cell Biology, Federal University of Goiás, Campus Samambaia, Goiânia, Goiás74690-900, Brazil
| | - Ana F P Negre
- Department of Histology, Embryology, and Cell Biology, Federal University of Goiás, Campus Samambaia, Goiânia, Goiás74690-900, Brazil
| | - Daniel A O Rodríguez
- Department of Structural and Functional Biology, State University of Campinas, Campinas, São Paulo13083-862, Brazil
| | - Géssica C de Sousa
- Department of Histology, Embryology, and Cell Biology, Federal University of Goiás, Campus Samambaia, Goiânia, Goiás74690-900, Brazil
| | - Giovanna A Rodrigues
- Department of Histology, Embryology, and Cell Biology, Federal University of Goiás, Campus Samambaia, Goiânia, Goiás74690-900, Brazil
| | - Bruno D A Sanches
- Department of Structural and Functional Biology, State University of Campinas, Campinas, São Paulo13083-862, Brazil
| | - Hernandes F Carvalho
- Department of Structural and Functional Biology, State University of Campinas, Campinas, São Paulo13083-862, Brazil
| | - Sebastião R Taboga
- Department of Biology, State University of São Paulo, São José do Rio Preto, São Paulo15054-000, Brazil
| | - Manoel F Biancardi
- Department of Histology, Embryology, and Cell Biology, Federal University of Goiás, Campus Samambaia, Goiânia, Goiás74690-900, Brazil
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27
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Proximity of immune and tumor cells underlies response to BRAF/MEK-targeted therapies in metastatic melanoma patients. NPJ Precis Oncol 2022; 6:6. [PMID: 35058553 PMCID: PMC8776860 DOI: 10.1038/s41698-021-00249-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/16/2021] [Indexed: 02/03/2023] Open
Abstract
Acquired resistance to BRAF/MEK-targeted therapy occurs in the majority of melanoma patients that harbor BRAF mutated tumors, leading to relapse or progression and the underlying mechanism is unclear in many cases. Using multiplex immunohistochemistry and spatial imaging analysis of paired tumor sections obtained from 11 melanoma patients prior to BRAF/MEK-targeted therapy and when the disease progressed on therapy, we observed a significant increase of tumor cellularity in the progressed tumors and the close association of SOX10+ melanoma cells with CD8+ T cells negatively correlated with patient's progression-free survival (PFS). In the TCGA-melanoma dataset (n = 445), tumor cellularity exhibited additive prognostic value in the immune score signature to predict overall survival in patients with early-stage melanoma. Moreover, tumor cellularity prognoses OS independent of immune score in patients with late-stage melanoma.
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28
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Maisel BA, Yi M, Peck AR, Sun Y, Hooke JA, Kovatich AJ, Shriver CD, Hu H, Nevalainen MT, Tanaka T, Simone N, Wang LL, Rui H, Chervoneva I. Spatial Metrics of Interaction between CD163-Positive Macrophages and Cancer Cells and Progression-Free Survival in Chemo-Treated Breast Cancer. Cancers (Basel) 2022; 14:308. [PMID: 35053472 PMCID: PMC8773496 DOI: 10.3390/cancers14020308] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 02/07/2023] Open
Abstract
Tumor-associated macrophages (TAMs) promote progression of breast cancer and other solid malignancies via immunosuppressive, pro-angiogenic and pro-metastatic effects. Tumor-promoting TAMs tend to express M2-like macrophage markers, including CD163. Histopathological assessments suggest that the density of CD163-positive TAMs within the tumor microenvironment is associated with reduced efficacy of chemotherapy and unfavorable prognosis. However, previous analyses have required research-oriented pathologists to visually enumerate CD163+ TAMs, which is both laborious and subjective and hampers clinical implementation. Objective, operator-independent image analysis methods to quantify TAM-associated information are needed. In addition, since M2-like TAMs exert local effects on cancer cells through direct juxtacrine cell-to-cell interactions, paracrine signaling, and metabolic factors, we hypothesized that spatial metrics of adjacency of M2-like TAMs to breast cancer cells will have further information value. Immunofluorescence histo-cytometry of CD163+ TAMs was performed retrospectively on tumor microarrays of 443 cases of invasive breast cancer from patients who subsequently received adjuvant chemotherapy. An objective and automated algorithm was developed to phenotype CD163+ TAMs and calculate their density within the tumor stroma and derive several spatial metrics of interaction with cancer cells. Shorter progression-free survival was associated with a high density of CD163+ TAMs, shorter median cancer-to-CD163+ nearest neighbor distance, and a high number of either directly adjacent CD163+ TAMs (within juxtacrine proximity <12 μm to cancer cells) or communicating CD163+ TAMs (within paracrine communication distance <250 μm to cancer cells) after multivariable adjustment for clinical and pathological risk factors and correction for optimistic bias due to dichotomization.
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Affiliation(s)
- Brenton A. Maisel
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA; (B.A.M.); (M.Y.)
| | - Misung Yi
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA; (B.A.M.); (M.Y.)
| | - Amy R. Peck
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (A.R.P.); (Y.S.); (M.T.N.)
| | - Yunguang Sun
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (A.R.P.); (Y.S.); (M.T.N.)
| | - Jeffrey A. Hooke
- John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (J.A.H.); (A.J.K.); (C.D.S.)
| | - Albert J. Kovatich
- John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (J.A.H.); (A.J.K.); (C.D.S.)
| | - Craig D. Shriver
- John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (J.A.H.); (A.J.K.); (C.D.S.)
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA;
| | - Marja T. Nevalainen
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (A.R.P.); (Y.S.); (M.T.N.)
| | - Takemi Tanaka
- Department of Pathology, University of Oklahoma Health Sciences Center, Stephenson Cancer Center, Oklahoma City, OK 73104, USA;
| | - Nicole Simone
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Li Lily Wang
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA;
| | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (A.R.P.); (Y.S.); (M.T.N.)
| | - Inna Chervoneva
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA; (B.A.M.); (M.Y.)
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29
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Pati P, Jaume G, Foncubierta-Rodríguez A, Feroce F, Anniciello AM, Scognamiglio G, Brancati N, Fiche M, Dubruc E, Riccio D, Di Bonito M, De Pietro G, Botti G, Thiran JP, Frucci M, Goksel O, Gabrani M. Hierarchical graph representations in digital pathology. Med Image Anal 2021; 75:102264. [PMID: 34781160 DOI: 10.1016/j.media.2021.102264] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 09/22/2021] [Accepted: 10/06/2021] [Indexed: 01/01/2023]
Abstract
Cancer diagnosis, prognosis, and therapy response predictions from tissue specimens highly depend on the phenotype and topological distribution of constituting histological entities. Thus, adequate tissue representations for encoding histological entities is imperative for computer aided cancer patient care. To this end, several approaches have leveraged cell-graphs, capturing the cell-microenvironment, to depict the tissue. These allow for utilizing graph theory and machine learning to map the tissue representation to tissue functionality, and quantify their relationship. Though cellular information is crucial, it is incomplete alone to comprehensively characterize complex tissue structure. We herein treat the tissue as a hierarchical composition of multiple types of histological entities from fine to coarse level, capturing multivariate tissue information at multiple levels. We propose a novel multi-level hierarchical entity-graph representation of tissue specimens to model the hierarchical compositions that encode histological entities as well as their intra- and inter-entity level interactions. Subsequently, a hierarchical graph neural network is proposed to operate on the hierarchical entity-graph and map the tissue structure to tissue functionality. Specifically, for input histology images, we utilize well-defined cells and tissue regions to build HierArchical Cell-to-Tissue (HACT) graph representations, and devise HACT-Net, a message passing graph neural network, to classify the HACT representations. As part of this work, we introduce the BReAst Carcinoma Subtyping (BRACS) dataset, a large cohort of Haematoxylin & Eosin stained breast tumor regions-of-interest, to evaluate and benchmark our proposed methodology against pathologists and state-of-the-art computer-aided diagnostic approaches. Through comparative assessment and ablation studies, our proposed method is demonstrated to yield superior classification results compared to alternative methods as well as individual pathologists. The code, data, and models can be accessed at https://github.com/histocartography/hact-net.
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Affiliation(s)
- Pushpak Pati
- IBM Zurich Research Lab, Zurich, Switzerland; Computer-Assisted Applications in Medicine, ETH Zurich, Zurich, Switzerland.
| | - Guillaume Jaume
- IBM Zurich Research Lab, Zurich, Switzerland; Signal Processing Laboratory 5, EPFL, Lausanne, Switzerland
| | | | - Florinda Feroce
- National Cancer Institute - IRCCS-Fondazione Pascale, Naples, Italy
| | | | | | - Nadia Brancati
- Institute for High Performance Computing and Networking - CNR, Naples, Italy
| | - Maryse Fiche
- Aurigen- Centre de Pathologie, Lausanne, Switzerland
| | | | - Daniel Riccio
- Institute for High Performance Computing and Networking - CNR, Naples, Italy
| | | | - Giuseppe De Pietro
- Institute for High Performance Computing and Networking - CNR, Naples, Italy
| | - Gerardo Botti
- National Cancer Institute - IRCCS-Fondazione Pascale, Naples, Italy
| | | | - Maria Frucci
- Institute for High Performance Computing and Networking - CNR, Naples, Italy
| | - Orcun Goksel
- Computer-Assisted Applications in Medicine, ETH Zurich, Zurich, Switzerland; Department of Information Technology, Uppsala University, Sweden
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30
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Maffeis V, Belluati A, Craciun I, Wu D, Novak S, Schoenenberger CA, Palivan CG. Clustering of catalytic nanocompartments for enhancing an extracellular non-native cascade reaction. Chem Sci 2021; 12:12274-12285. [PMID: 34603657 PMCID: PMC8480338 DOI: 10.1039/d1sc04267j] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/14/2021] [Indexed: 01/10/2023] Open
Abstract
Compartmentalization is fundamental in nature, where the spatial segregation of biochemical reactions within and between cells ensures optimal conditions for the regulation of cascade reactions. While the distance between compartments or their interaction are essential parameters supporting the efficiency of bio-reactions, so far they have not been exploited to regulate cascade reactions between bioinspired catalytic nanocompartments. Here, we generate individual catalytic nanocompartments (CNCs) by encapsulating within polymersomes or attaching to their surface enzymes involved in a cascade reaction and then, tether the polymersomes together into clusters. By conjugating complementary DNA strands to the polymersomes' surface, DNA hybridization drove the clusterization process of enzyme-loaded polymersomes and controlled the distance between the respective catalytic nanocompartments. Owing to the close proximity of CNCs within clusters and the overall stability of the cluster architecture, the cascade reaction between spatially segregated enzymes was significantly more efficient than when the catalytic nanocompartments were not linked together by DNA duplexes. Additionally, residual DNA single strands that were not engaged in clustering, allowed for an interaction of the clusters with the cell surface as evidenced by A549 cells, where clusters decorating the surface endowed the cells with a non-native enzymatic cascade. The self-organization into clusters of catalytic nanocompartments confining different enzymes of a cascade reaction allows for a distance control of the reaction spaces which opens new avenues for highly efficient applications in domains such as catalysis or nanomedicine.
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Affiliation(s)
- Viviana Maffeis
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland .,NCCR-Molecular Systems Engineering BPR 1095, Mattenstrasse 24a CH-4058 Basel Switzerland
| | - Andrea Belluati
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland
| | - Ioana Craciun
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland
| | - Dalin Wu
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland
| | - Samantha Novak
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland .,NCCR-Molecular Systems Engineering BPR 1095, Mattenstrasse 24a CH-4058 Basel Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland .,NCCR-Molecular Systems Engineering BPR 1095, Mattenstrasse 24a CH-4058 Basel Switzerland
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31
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Furman SA, Stern AM, Uttam S, Taylor DL, Pullara F, Chennubhotla SC. In situ functional cell phenotyping reveals microdomain networks in colorectal cancer recurrence. CELL REPORTS METHODS 2021; 1:100072. [PMID: 34888541 PMCID: PMC8653984 DOI: 10.1016/j.crmeth.2021.100072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/14/2021] [Accepted: 08/09/2021] [Indexed: 04/21/2023]
Abstract
Tumors are dynamic ecosystems comprising localized niches (microdomains), possessing distinct compositions and spatial configurations of cancer and non-cancer cell populations. Microdomain-specific network signaling coevolves with a continuum of cell states and functional plasticity associated with disease progression and therapeutic responses. We present LEAPH, an unsupervised machine learning algorithm for identifying cell phenotypes, which applies recursive steps of probabilistic clustering and spatial regularization to derive functional phenotypes (FPs) along a continuum. Combining LEAPH with pointwise mutual information and network biology analyses enables the discovery of outcome-associated microdomains visualized as distinct spatial configurations of heterogeneous FPs. Utilization of an immunofluorescence-based (51 biomarkers) image dataset of colorectal carcinoma primary tumors (n = 213) revealed microdomain-specific network dysregulation supporting cancer stem cell maintenance and immunosuppression that associated selectively with the recurrence phenotype. LEAPH enables an explainable artificial intelligence platform providing insights into pathophysiological mechanisms and novel drug targets to inform personalized therapeutic strategies.
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Affiliation(s)
- Samantha A. Furman
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Andrew M. Stern
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Shikhar Uttam
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - D. Lansing Taylor
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- SpIntellx, Inc., 2425 Sidney Street, Pittsburgh, PA 15203, USA
| | - Filippo Pullara
- SpIntellx, Inc., 2425 Sidney Street, Pittsburgh, PA 15203, USA
| | - S. Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- SpIntellx, Inc., 2425 Sidney Street, Pittsburgh, PA 15203, USA
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32
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Yamada S, Yassin MA, Weigel T, Schmitz T, Hansmann J, Mustafa K. Surface activation with oxygen plasma promotes osteogenesis with enhanced extracellular matrix formation in three-dimensional microporous scaffolds. J Biomed Mater Res A 2021; 109:1560-1574. [PMID: 33675166 DOI: 10.1002/jbm.a.37151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 02/03/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022]
Abstract
Various types of synthetic polyesters have been developed as biomaterials for tissue engineering. These materials commonly possess biodegradability, biocompatibility, and formability, which are preferable properties for bone regeneration. The major challenge of using synthetic polyesters is the result of low cell affinity due to their hydrophobic nature, which hinders efficient cell seeding and active cell dynamics. To improve wettability, plasma treatment is widely used in industry. Here, we performed surface activation with oxygen plasma to hydrophobic copolymers, poly(l-lactide-co-trimethylene carbonate), which were shaped in 2D films and 3D microporous scaffolds, and then we evaluated the resulting surface properties and the cellular responses of rat bone marrow stem cells (rBMSC) to the material. Using scanning electron microscopy and Fourier-transform infrared spectroscopy, we demonstrated that short-term plasma treatment increased nanotopographical surface roughness and wettability with minimal change in surface chemistry. On treated surfaces, initial cell adhesion and elongation were significantly promoted, and seeding efficiency was improved. In an osteoinductive environment, rBMSC on plasma-treated scaffolds exhibited accelerated osteogenic differentiation with osteogenic markers including RUNX2, osterix, bone sialoprotein, and osteocalcin upregulated, and a greater amount of collagen matrix and mineral deposition were found. This study shows the utility of plasma surface activation for polymeric scaffolds in bone tissue engineering.
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Affiliation(s)
- Shuntaro Yamada
- Department of Clinical Dentistry, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Mohammed A Yassin
- Department of Clinical Dentistry, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Tobias Weigel
- Chair of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Würzburg, Würzburg, Germany
- Translational Center Regenerative Therapies, Fraunhofer Institute for Silicate Research (ISC), Würzburg, Germany
| | - Tobias Schmitz
- Chair of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Würzburg, Würzburg, Germany
| | - Jan Hansmann
- Chair of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Würzburg, Würzburg, Germany
- Translational Center Regenerative Therapies, Fraunhofer Institute for Silicate Research (ISC), Würzburg, Germany
- Department Electrical Engineering, University for Applied Sciences Würzburg/Schweinfurt, Schweinfurt, Germany
| | - Kamal Mustafa
- Department of Clinical Dentistry, Faculty of Medicine, University of Bergen, Bergen, Norway
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33
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Krenn V, Bosone C, Burkard TR, Spanier J, Kalinke U, Calistri A, Salata C, Rilo Christoff R, Pestana Garcez P, Mirazimi A, Knoblich JA. Organoid modeling of Zika and herpes simplex virus 1 infections reveals virus-specific responses leading to microcephaly. Cell Stem Cell 2021; 28:1362-1379.e7. [PMID: 33838105 PMCID: PMC7611471 DOI: 10.1016/j.stem.2021.03.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 12/07/2020] [Accepted: 03/04/2021] [Indexed: 02/07/2023]
Abstract
Viral infection in early pregnancy is a major cause of microcephaly. However, how distinct viruses impair human brain development remains poorly understood. Here we use human brain organoids to study the mechanisms underlying microcephaly caused by Zika virus (ZIKV) and herpes simplex virus (HSV-1). We find that both viruses efficiently replicate in brain organoids and attenuate their growth by causing cell death. However, transcriptional profiling reveals that ZIKV and HSV-1 elicit distinct cellular responses and that HSV-1 uniquely impairs neuroepithelial identity. Furthermore, we demonstrate that, although both viruses fail to potently induce the type I interferon system, the organoid defects caused by their infection can be rescued by distinct type I interferons. These phenotypes are not seen in 2D cultures, highlighting the superiority of brain organoids in modeling viral infections. These results uncover virus-specific mechanisms and complex cellular immune defenses associated with virus-induced microcephaly.
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Affiliation(s)
- Veronica Krenn
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Camilla Bosone
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Julia Spanier
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Helmholtz Centre for Infection Research, Braunschweig, and the Hanover Medical School, Hanover 30625, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Helmholtz Centre for Infection Research, Braunschweig, and the Hanover Medical School, Hanover 30625, Germany; Cluster of Excellence - Resolving Infection Susceptibility (RESIST), Hanover Medical School, Hanover 30625, Germany
| | - Arianna Calistri
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Raissa Rilo Christoff
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Patricia Pestana Garcez
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Ali Mirazimi
- Department of Laboratory Medicine (LABMED), Karolinska Institute, Stockholm 17177, Sweden; National Veterinary Institute, Uppsala 75189, Sweden
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria; Medical University of Vienna, Vienna 1030, Austria.
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Secretome and Tunneling Nanotubes: A Multilevel Network for Long Range Intercellular Communication between Endothelial Cells and Distant Cells. Int J Mol Sci 2021; 22:ijms22157971. [PMID: 34360735 PMCID: PMC8347715 DOI: 10.3390/ijms22157971] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/14/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
As a cellular interface between the blood and tissues, the endothelial cell (EC) monolayer is involved in the control of key functions including vascular tone, permeability and homeostasis, leucocyte trafficking and hemostasis. EC regulatory functions require long-distance communications between ECs, circulating hematopoietic cells and other vascular cells for efficient adjusting thrombosis, angiogenesis, inflammation, infection and immunity. This intercellular crosstalk operates through the extracellular space and is orchestrated in part by the secretory pathway and the exocytosis of Weibel Palade Bodies (WPBs), secretory granules and extracellular vesicles (EVs). WPBs and secretory granules allow both immediate release and regulated exocytosis of messengers such as cytokines, chemokines, extracellular membrane proteins, coagulation or growth factors. The ectodomain shedding of transmembrane protein further provide the release of both receptor and ligands with key regulatory activities on target cells. Thin tubular membranous channels termed tunneling nanotubes (TNTs) may also connect EC with distant cells. EVs, in particular exosomes, and TNTs may contain and transfer different biomolecules (e.g., signaling mediators, proteins, lipids, and microRNAs) or pathogens and have emerged as a major triggers of horizontal intercellular transfer of information.
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Human NK cells prime inflammatory DC precursors to induce Tc17 differentiation. Blood Adv 2021; 4:3990-4006. [PMID: 32841340 DOI: 10.1182/bloodadvances.2020002084] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/14/2020] [Indexed: 12/27/2022] Open
Abstract
Adaptive immune responses are acknowledged to evolve from innate immunity. However, limited information exists regarding whether encounters between innate cells direct the generation of specialized T-cell subsets. We aim to understand how natural killer (NK) cells modulate cell-mediated immunity in humans. We found that human CD14+CD16- monocytes that differentiate into inflammatory dendritic cells (DCs) are shaped at the early stages of differentiation by cell-to-cell interactions with NK cells. Although a fraction of monocytes is eliminated by NK-cell-mediated cytotoxicity, the polarization of interferon-γ (IFN-γ) at the NKp30-stabilized synapses triggers a stable IFN-γ signature in surviving monocytes that persists after their differentiation into DCs. Notably, NK-cell-instructed DCs drive the priming of type 17 CD8+ T cells (Tc17) with the capacity to produce IFN-γ and interleukin-17A. Compared with healthy donors, this cellular network is impaired in patients with classical NK-cell deficiency driven by mutations in the GATA2 gene. Our findings reveal a previously unrecognized connection by which Tc17-mediated immunity might be regulated by NK-cell-mediated tuning of antigen-presenting cells.
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36
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The Mystery of Red Blood Cells Extracellular Vesicles in Sleep Apnea with Metabolic Dysfunction. Int J Mol Sci 2021; 22:ijms22094301. [PMID: 33919065 PMCID: PMC8122484 DOI: 10.3390/ijms22094301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
Sleep is very important for overall health and quality of life, while sleep disorder has been associated with several human diseases, namely cardiovascular, metabolic, cognitive, and cancer-related alterations. Obstructive sleep apnea (OSA) is the most common respiratory sleep-disordered breathing, which is caused by the recurrent collapse of the upper airway during sleep. OSA has emerged as a major public health problem and increasing evidence suggests that untreated OSA can lead to the development of various diseases including neurodegenerative diseases. In addition, OSA may lead to decreased blood oxygenation and fragmentation of the sleep cycle. The formation of free radicals or reactive oxygen species (ROS) can emerge and react with nitric oxide (NO) to produce peroxynitrite, thereby diminishing the bioavailability of NO. Hypoxia, the hallmark of OSA, refers to a decline of tissue oxygen saturation and affects several types of cells, playing cell-to-cell communication a vital role in the outcome of this interplay. Red blood cells (RBCs) are considered transporters of oxygen and nutrients to the tissues, and these RBCs are important interorgan communication systems with additional functions, including participation in the control of systemic NO metabolism, redox regulation, blood rheology, and viscosity. RBCs have been shown to induce endothelial dysfunction and increase cardiac injury. The mechanistic links between changes of RBC functional properties and cardiovascular are largely unknown. Extracellular vesicles (EVs) are secreted by most cell types and released in biological fluids both under physiological and pathological conditions. EVs are involved in intercellular communication by transferring complex cargoes including proteins, lipids, and nucleic acids from donor cells to recipient cells. Advancing our knowledge about mechanisms of RBC-EVs formation and their pathophysiological relevance may help to shed light on circulating EVs and to translate their application to clinical practice. We will focus on the potential use of RBC-EVs as valuable diagnostic and prognostic biomarkers and state-specific cargoes, and possibilities as therapeutic vehicles for drug and gene delivery. The use of RBC-EVs as a precision medicine for the diagnosis and treatment of the patient with sleep disorder will improve the prognosis and the quality of life in patients with cardiovascular disease (CVD).
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Serex L, Sharma K, Rizov V, Bertsch A, McKinney JD, Renaud P. Microfluidic-assisted bioprinting of tissues and organoids at high cell concentrations. Biofabrication 2021; 13. [DOI: 10.1088/1758-5090/abca80] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/13/2020] [Indexed: 02/06/2023]
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38
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Armingol E, Officer A, Harismendy O, Lewis NE. Deciphering cell-cell interactions and communication from gene expression. Nat Rev Genet 2021; 22:71-88. [PMID: 33168968 PMCID: PMC7649713 DOI: 10.1038/s41576-020-00292-x] [Citation(s) in RCA: 477] [Impact Index Per Article: 159.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 12/13/2022]
Abstract
Cell-cell interactions orchestrate organismal development, homeostasis and single-cell functions. When cells do not properly interact or improperly decode molecular messages, disease ensues. Thus, the identification and quantification of intercellular signalling pathways has become a common analysis performed across diverse disciplines. The expansion of protein-protein interaction databases and recent advances in RNA sequencing technologies have enabled routine analyses of intercellular signalling from gene expression measurements of bulk and single-cell data sets. In particular, ligand-receptor pairs can be used to infer intercellular communication from the coordinated expression of their cognate genes. In this Review, we highlight discoveries enabled by analyses of cell-cell interactions from transcriptomic data and review the methods and tools used in this context.
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Affiliation(s)
- Erick Armingol
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Adam Officer
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA
| | - Olivier Harismendy
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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39
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Insights into the mechanism of vascular endothelial cells on bone biology. Biosci Rep 2021; 41:227494. [PMID: 33403387 PMCID: PMC7816070 DOI: 10.1042/bsr20203258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/25/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
In the skeletal system, blood vessels not only function as a conduit system for transporting gases, nutrients, metabolic waste, or cells but also provide multifunctional signal molecules regulating bone development, regeneration, and remodeling. Endothelial cells (ECs) in bone tissues, unlike in other organ tissues, are in direct contact with the pericytes of blood vessels, resulting in a closer connection with peripheral connective tissues. Close-contact ECs contribute to osteogenesis and osteoclastogenesis by secreting various cytokines in the paracrine or juxtacrine pathways. An increasing number of studies have revealed that extracellular vesicles (EVs) derived from ECs can directly regulate maturation process of osteoblasts and osteoclasts. The different pathways focus on targets at different distances, forming the basis of the intimate spatial and temporal link between bone tissue and blood vessels. Here, we provide a systematic review to elaborate on the function of ECs in bone biology and its underlying mechanisms based on three aspects: paracrine, EVs, and juxtacrine. This review proposes the possibility of a therapeutic strategy targeting blood vessels, as an adjuvant treatment for bone disorders.
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40
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Belanger MC, Anbaei P, Dunn AF, Kinman AW, Pompano RR. Spatially Resolved Analytical Chemistry in Intact, Living Tissues. Anal Chem 2020; 92:15255-15262. [PMID: 33201681 PMCID: PMC7864589 DOI: 10.1021/acs.analchem.0c03625] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tissues are an exciting frontier for bioanalytical chemistry, one in which spatial distribution is just as important as total content. Intact tissue preserves the native cellular and molecular organization and the cell-cell contacts found in vivo. Live tissue, in particular, offers the potential to analyze dynamic events in a spatially resolved manner, leading to fundamental biological insights and translational discoveries. In this Perspective, we provide a tutorial on the four fundamental challenges for the bioanalytical chemist working in living tissue samples as well as best practices for mitigating them. The challenges include (i) the complexity of the sample matrix, which contributes myriad interfering species and causes nonspecific binding of reagents; (ii) hindered delivery and mixing; (iii) the need to maintain physiological conditions; and (iv) tissue reactivity. This framework is relevant to a variety of methods for spatially resolved chemical analysis, including optical imaging, inserted sensors and probes such as electrodes, and surface analyses such as sensing arrays. The discussion focuses primarily on ex vivo tissues, though many considerations are relevant in vivo as well. Our goal is to convey the exciting potential of analytical chemistry to contribute to understanding the functions of live, intact tissues.
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Affiliation(s)
- Maura C. Belanger
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
| | - Parastoo Anbaei
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
| | - Austin F. Dunn
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
| | - Andrew W.L. Kinman
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
| | - Rebecca R. Pompano
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
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41
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Yang S, Pieters PA, Joesaar A, Bögels BWA, Brouwers R, Myrgorodska I, Mann S, de Greef TFA. Light-Activated Signaling in DNA-Encoded Sender-Receiver Architectures. ACS NANO 2020; 14:15992-16002. [PMID: 33078948 PMCID: PMC7690052 DOI: 10.1021/acsnano.0c07537] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/14/2020] [Indexed: 05/22/2023]
Abstract
Collective decision making by living cells is facilitated by exchange of diffusible signals where sender cells release a chemical signal that is interpreted by receiver cells. A variety of nonliving artificial cell models have been developed in recent years that mimic various aspects of diffusion-based intercellular communication. However, localized secretion of diffusive signals from individual protocells, which is critical for mimicking biological sender-receiver systems, has remained challenging to control precisely. Here, we engineer light-responsive, DNA-encoded sender-receiver architectures, where protein-polymer microcapsules act as cell mimics and molecular communication occurs through diffusive DNA signals. We prepare spatial distributions of sender and receiver protocells using a microfluidic trapping array and set up a signaling gradient from a single sender cell using light, which activates surrounding receivers through DNA strand displacement. Our systematic analysis reveals how the effective signal range of a single sender is determined by various factors including the density and permeability of receivers, extracellular signal degradation, signal consumption, and catalytic regeneration. In addition, we construct a three-population configuration where two sender cells are embedded in a dense array of receivers that implement Boolean logic and investigate spatial integration of nonidentical input cues. The results offer a means for studying diffusion-based sender-receiver topologies and present a strategy to achieve the congruence of reaction-diffusion and positional information in chemical communication systems that have the potential to reconstitute collective cellular patterns.
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Affiliation(s)
- Shuo Yang
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Pascal A. Pieters
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Alex Joesaar
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Bas W. A. Bögels
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Rens Brouwers
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Iuliia Myrgorodska
- Centre
for Protolife Research and Max Planck Bristol Centre for Minimal Biology,
School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Stephen Mann
- Centre
for Protolife Research and Max Planck Bristol Centre for Minimal Biology,
School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Tom F. A. de Greef
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 MB, The Netherlands
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42
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Kindberg A, Hu JK, Bush JO. Forced to communicate: Integration of mechanical and biochemical signaling in morphogenesis. Curr Opin Cell Biol 2020; 66:59-68. [PMID: 32569947 PMCID: PMC7577940 DOI: 10.1016/j.ceb.2020.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/06/2020] [Accepted: 05/05/2020] [Indexed: 01/05/2023]
Abstract
Morphogenesis is a physical process that requires the generation of mechanical forces to achieve dynamic changes in cell position, tissue shape, and size as well as biochemical signals to coordinate these events. Mechanical forces are also used by the embryo to transmit detailed information across space and detected by target cells, leading to downstream changes in cellular properties and behaviors. Indeed, forces provide signaling information of complementary quality that can both synergize and diversify the functional outputs of biochemical signaling. Here, we discuss recent findings that reveal how mechanical signaling and biochemical signaling are integrated during morphogenesis and the possible context-specific advantages conferred by the interactions between these signaling mechanisms.
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Affiliation(s)
- Abigail Kindberg
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, USA; Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Jimmy K Hu
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA.
| | - Jeffrey O Bush
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, USA; Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA.
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43
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Abstract
Exosomes are cell-derived nano-sized, phospholipid vehicles that function to transport prodigious amounts of bioactive molecules to specific recipient tissues. Several hallmarks of cancer are impacted by this exosome-mediated cell-to-cell communication, including, remodeling the architecture of the extracellular matrix, endowing cancer cells with characteristics of drug resistance, or even modulating immune responses. Owing to their immunomodulatory potential and endogenous functionalities, exosomes may also be exploited in various innovative immunological approaches to activate adaptive and innate immune effector cells to mount an effective anticancer immunosurveillance. The review highlights the recent advances in state-of-the-art technologies and protocols for using exosomes as an effective and promising application for cancer immunotherapy.
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44
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AbdulJabbar K, Raza SEA, Rosenthal R, Jamal-Hanjani M, Veeriah S, Akarca A, Lund T, Moore DA, Salgado R, Al Bakir M, Zapata L, Hiley CT, Officer L, Sereno M, Smith CR, Loi S, Hackshaw A, Marafioti T, Quezada SA, McGranahan N, Le Quesne J, Swanton C, Yuan Y. Geospatial immune variability illuminates differential evolution of lung adenocarcinoma. Nat Med 2020; 26:1054-1062. [PMID: 32461698 PMCID: PMC7610840 DOI: 10.1038/s41591-020-0900-x] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/23/2020] [Indexed: 01/09/2023]
Abstract
Remarkable progress in molecular analyses has improved our understanding of the evolution of cancer cells toward immune escape1-5. However, the spatial configurations of immune and stromal cells, which may shed light on the evolution of immune escape across tumor geographical locations, remain unaddressed. We integrated multiregion exome and RNA-sequencing (RNA-seq) data with spatial histology mapped by deep learning in 100 patients with non-small cell lung cancer from the TRACERx cohort6. Cancer subclones derived from immune cold regions were more closely related in mutation space, diversifying more recently than subclones from immune hot regions. In TRACERx and in an independent multisample cohort of 970 patients with lung adenocarcinoma, tumors with more than one immune cold region had a higher risk of relapse, independently of tumor size, stage and number of samples per patient. In lung adenocarcinoma, but not lung squamous cell carcinoma, geometrical irregularity and complexity of the cancer-stromal cell interface significantly increased in tumor regions without disruption of antigen presentation. Decreased lymphocyte accumulation in adjacent stroma was observed in tumors with low clonal neoantigen burden. Collectively, immune geospatial variability elucidates tumor ecological constraints that may shape the emergence of immune-evading subclones and aggressive clinical phenotypes.
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Affiliation(s)
- Khalid AbdulJabbar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Shan E Ahmed Raza
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ayse Akarca
- Department of Cellular Pathology, University College London, University College Hospital, London, UK
| | - Tom Lund
- Translational Immune Oncology Group, Centre for Molecular Medicine, Royal Marsden Hospital NHS Trust, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London, University College Hospital, London, UK
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA-Ziekenhuizen, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Leah Officer
- MRC Toxicology Unit, University of Cambridge, Leicester, UK
| | - Marco Sereno
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | | | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Allan Hackshaw
- Cancer Research UK & University College London Cancer Trials Centre, University College London, London, UK
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London, University College Hospital, London, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
| | - John Le Quesne
- MRC Toxicology Unit, University of Cambridge, Leicester, UK.
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK.
- Glenfield Hospital, University Hospitals Leicester NHS Trust, Leicester, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Medical Oncology, University College London Hospitals NHS Foundation Trust, London, UK.
| | - Yinyin Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
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45
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Hannig J, Schäfer H, Ackermann J, Hebel M, Schäfer T, Döring C, Hartmann S, Hansmann ML, Koch I. Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma. PLoS Comput Biol 2020; 16:e1007516. [PMID: 31961873 PMCID: PMC6999891 DOI: 10.1371/journal.pcbi.1007516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 02/04/2020] [Accepted: 10/29/2019] [Indexed: 11/25/2022] Open
Abstract
In pathology, tissue images are evaluated using a light microscope, relying on the expertise and experience of pathologists. There is a great need for computational methods to quantify and standardize histological observations. Computational quantification methods become more and more essential to evaluate tissue images. In particular, the distribution of tumor cells and their microenvironment are of special interest. Here, we systematically investigated tumor cell properties and their spatial neighborhood relations by a new application of statistical analysis to whole slide images of Hodgkin lymphoma, a tumor arising in lymph nodes, and inflammation of lymph nodes called lymphadenitis. We considered properties of more than 400, 000 immunohistochemically stained, CD30-positive cells in 35 whole slide images of tissue sections from subtypes of the classical Hodgkin lymphoma, nodular sclerosis and mixed cellularity, as well as from lymphadenitis. We found that cells of specific morphology exhibited significantly favored and unfavored spatial neighborhood relations of cells in dependence of their morphology. This information is important to evaluate differences between Hodgkin lymph nodes infiltrated by tumor cells (Hodgkin lymphoma) and inflamed lymph nodes, concerning the neighborhood relations of cells and the sizes of cells. The quantification of neighborhood relations revealed new insights of relations of CD30-positive cells in different diagnosis cases. The approach is general and can easily be applied to whole slide image analysis of other tumor types. In pathology, histological diagnosis is still challenging, in particular, for tumor diseases. Pathologists diagnose the disease and its stage of development on the basis of evaluation and interpretation of images of tissue sections. The quantification of experimental data to support decisions of diagnosis and prognosis, applying bioinformatics methods, is an important issue. Here, we introduce a new, general approach to analyze tissue images of tumor and non-tumor patients and to evaluate the distribution of tumor cells in the tissue. Moreover, we consider neighborhood relations between immunostained cells of different cell morphology. We focus on a special type of lymph node tumor, the Hodgkin lymphoma, exploring the two main types of the classical Hodgkin lymphoma, the nodular sclerosis and the mixed cellularity, and the non-tumor case, the lymphadenitis, representing an inflammation of the lymph node. We considered more than 400, 000 cells immunohistochemically stained with CD30 in 35 whole slide images of tissue sections. We found that cells of specific morphology exhibited significant relations to cells of certain morphology as spatial nearest neighbor. We could show different neighborhood patterns of CD30-positive cells between tumor and non-tumor. The approach is general and can easily be applied to other tumor types.
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Affiliation(s)
- Jennifer Hannig
- KITE - Kompetenzzentrum für Informationstechnologie, Technische Hochschule Mittelhessen, Friedberg, Germany
| | - Hendrik Schäfer
- Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Jörg Ackermann
- Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Marie Hebel
- Institute of Biochemistry II, Johann Wolfgang Goethe-University, University Hospital Frankfurt am Main, Frankfurt am Main, Germany
| | - Tim Schäfer
- Department of Child and Adolescent Psychiatry, University Hospital Frankfurt am Main, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Claudia Döring
- Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Martin-Leo Hansmann
- Consultation and reference center for lymph node pathology at Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Ina Koch
- Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- * E-mail:
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46
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Presbitero A, Mancini E, Castiglione F, Krzhizhanovskaya VV, Quax R. Game of neutrophils: modeling the balance between apoptosis and necrosis. BMC Bioinformatics 2019; 20:475. [PMID: 31823711 PMCID: PMC6905093 DOI: 10.1186/s12859-019-3044-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/21/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Neutrophils are one of the key players in the human innate immune system (HIIS). In the event of an insult where the body is exposed to inflammation triggering moieties (ITMs), neutrophils are mobilized towards the site of insult and antagonize the inflammation. If the inflammation is cleared, neutrophils go into a programmed death called apoptosis. However, if the insult is intense or persistent, neutrophils take on a violent death pathway called necrosis, which involves the rupture of their cytoplasmic content into the surrounding tissue that causes local tissue damage, thus further aggravating inflammation. This seemingly paradoxical phenomenon fuels the inflammatory process by triggering the recruitment of additional neutrophils to the site of inflammation, aimed to contribute to the complete neutralization of severe inflammation. This delicate balance between the cost and benefit of the neutrophils' choice of death pathway has been optimized during the evolution of the innate immune system. The goal of our work is to understand how the tradeoff between the cost and benefit of the different death pathways of neutrophils, in response to various levels of insults, has been optimized over evolutionary time by using the concepts of evolutionary game theory. RESULTS We show that by using evolutionary game theory, we are able to formulate a game that predicts the percentage of necrosis and apoptosis when exposed to various levels of insults. CONCLUSION By adopting an evolutionary perspective, we identify the driving mechanisms leading to the delicate balance between apoptosis and necrosis in neutrophils' cell death in response to different insults. Using our simple model, we verify that indeed, the global cost of remaining ITMs is the driving mechanism that reproduces the percentage of necrosis and apoptosis observed in data and neutrophils need sufficient information of the overall inflammation to be able to pick a death pathway that presumably increases the survival of the organism.
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Affiliation(s)
- Alva Presbitero
- ITMO University, Saint Petersburg, Russian Federation.
- University of Amsterdam, Amsterdam, the Netherlands.
| | | | - Filippo Castiglione
- University of Amsterdam, Amsterdam, the Netherlands
- IAC- National Research Council of Italy, Rome, Italy
| | - Valeria V Krzhizhanovskaya
- ITMO University, Saint Petersburg, Russian Federation
- University of Amsterdam, Amsterdam, the Netherlands
| | - Rick Quax
- University of Amsterdam, Amsterdam, the Netherlands
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47
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Daneshpour H, Youk H. Modeling cell-cell communication for immune systems across space and time. ACTA ACUST UNITED AC 2019; 18:44-52. [PMID: 31922054 PMCID: PMC6941841 DOI: 10.1016/j.coisb.2019.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Communicating is crucial for cells to coordinate their behaviors. Immunological processes, involving diverse cytokines and cell types, are ideal for developing frameworks for modeling coordinated behaviors of cells. Here, we review recent studies that combine modeling and experiments to reveal how immune systems use autocrine, paracrine, and juxtacrine signals to achieve behaviors such as controlling population densities and hair regenerations. We explain that models are useful because one can computationally vary numerous parameters, in experimentally infeasible ways, to evaluate alternate immunological responses. For each model, we focus on the length-scales and time-scales involved and explain why integrating multiple length-scales and time-scales in a model remain challenging. We suggest promising modeling strategies for meeting this challenge and their practical consequences.
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Affiliation(s)
- Hirad Daneshpour
- Kavli Institute of Nanoscience, the Netherlands.,Department of Bionanoscience, Delft University of Technology, Delft, 2629HZ, the Netherlands
| | - Hyun Youk
- Kavli Institute of Nanoscience, the Netherlands.,Department of Bionanoscience, Delft University of Technology, Delft, 2629HZ, the Netherlands.,CIFAR, CIFAR Azrieli Global Scholars Program, Toronto, ON, M5G 1M1, Canada
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48
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Quantitative Histopathology of Stained Tissues using Color Spatial Light Interference Microscopy (cSLIM). Sci Rep 2019; 9:14679. [PMID: 31604963 PMCID: PMC6789107 DOI: 10.1038/s41598-019-50143-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/31/2019] [Indexed: 01/22/2023] Open
Abstract
Tissue biopsy evaluation in the clinic is in need of quantitative disease markers for diagnosis and, most importantly, prognosis. Among the new technologies, quantitative phase imaging (QPI) has demonstrated promise for histopathology because it reveals intrinsic tissue nanoarchitecture through the refractive index. However, a vast majority of past QPI investigations have relied on imaging unstained tissues, which disrupts the established specimen processing. Here we present color spatial light interference microscopy (cSLIM) as a new whole-slide imaging modality that performs interferometric imaging on stained tissue, with a color detector array. As a result, cSLIM yields in a single scan both the intrinsic tissue phase map and the standard color bright-field image, familiar to the pathologist. Our results on 196 breast cancer patients indicate that cSLIM can provide stain-independent prognostic information from the alignment of collagen fibers in the tumor microenvironment. The effects of staining on the tissue phase maps were corrected by a mathematical normalization. These characteristics are likely to reduce barriers to clinical translation for the new cSLIM technology.
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49
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Erbaş A, Olvera de la Cruz M, Marko JF. Receptor-Ligand Rebinding Kinetics in Confinement. Biophys J 2019; 116:1609-1624. [PMID: 31029377 PMCID: PMC6506716 DOI: 10.1016/j.bpj.2019.02.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 02/05/2019] [Accepted: 02/19/2019] [Indexed: 10/27/2022] Open
Abstract
Rebinding kinetics of molecular ligands plays a key role in the operation of biomachinery, from regulatory networks to protein transcription, and is also a key factor in design of drugs and high-precision biosensors. In this study, we investigate initial release and rebinding of ligands to their binding sites grafted on a planar surface, a situation commonly observed in single-molecule experiments and that occurs in vivo, e.g., during exocytosis. Via scaling arguments and molecular dynamic simulations, we analyze the dependence of nonequilibrium rebinding kinetics on two intrinsic length scales: the average separation distance between the binding sites and the total diffusible volume (i.e., height of the experimental reservoir in which diffusion takes place or average distance between receptor-bearing surfaces). We obtain time-dependent scaling laws for on rates and for the cumulative number of rebinding events. For diffusion-limited binding, the (rebinding) on rate decreases with time via multiple power-law regimes before the terminal steady-state (constant on-rate) regime. At intermediate times, when particle density has not yet become uniform throughout the diffusible volume, the cumulative number of rebindings exhibits a novel, to our knowledge, plateau behavior because of the three-dimensional escape process of ligands from binding sites. The duration of the plateau regime depends on the average separation distance between binding sites. After the three-dimensional diffusive escape process, a one-dimensional diffusive regime describes on rates. In the reaction-limited scenario, ligands with higher affinity to their binding sites (e.g., longer residence times) delay entry to the power-law regimes. Our results will be useful for extracting hidden timescales in experiments such as kinetic rate measurements for ligand-receptor interactions in microchannels, as well as for cell signaling via diffusing molecules.
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Affiliation(s)
- Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey.
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois; Department of Physics and Astronomy, Northwestern University, Evanston, Illinois; Department of Chemistry, Northwestern University, Evanston, Illinois
| | - John F Marko
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois; Department of Molecular Biosciences, Northwestern University, Evanston, Illinois.
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50
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Hanna SJ, McCoy-Simandle K, Leung E, Genna A, Condeelis J, Cox D. Tunneling nanotubes, a novel mode of tumor cell-macrophage communication in tumor cell invasion. J Cell Sci 2019; 132:jcs.223321. [PMID: 30659112 DOI: 10.1242/jcs.223321] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/28/2018] [Indexed: 12/18/2022] Open
Abstract
The interaction between tumor cells and macrophages is crucial in promoting tumor invasion and metastasis. In this study, we examined a novel mechanism of intercellular communication, namely membranous actin-based tunneling nanotubes (TNTs), that occurs between macrophages and tumor cells in the promotion of macrophage-dependent tumor cell invasion. The presence of heterotypic TNTs between macrophages and tumor cells induced invasive tumor cell morphology, which was dependent on EGF-EGFR signaling. Furthermore, reduction of a protein involved in TNT formation, M-Sec (TNFAIP2), in macrophages inhibited tumor cell elongation, blocked the ability of tumor cells to invade in 3D and reduced macrophage-dependent long-distance tumor cell streaming in vitro Using an in vivo zebrafish model that recreates macrophage-mediated tumor cell invasion, we observed TNT-mediated macrophage-dependent tumor cell invasion, distant metastatic foci and areas of metastatic spread. Overall, our studies support a role for TNTs as a novel means of interaction between tumor cells and macrophages that leads to tumor progression and metastasis.
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Affiliation(s)
- Samer J Hanna
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Gruss MRRC 306, Bronx, NY 10461, USA
| | - Kessler McCoy-Simandle
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Gruss MRRC 306, Bronx, NY 10461, USA
| | - Edison Leung
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Gruss MRRC 306, Bronx, NY 10461, USA
| | - Alessandro Genna
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Gruss MRRC 306, Bronx, NY 10461, USA
| | - John Condeelis
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Gruss MRRC 306, Bronx, NY 10461, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, 1300 Morris Park Ave, Gruss MRRC 306, Bronx, NY 10461, USA.,Integrated Imaging Program, Albert Einstein College of Medicine, 1300 Morris Park Ave, Gruss MRRC 306, Bronx, NY 10461, USA
| | - Dianne Cox
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Gruss MRRC 306, Bronx, NY 10461, USA .,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, 1300 Morris Park Ave, Gruss MRRC 306, Bronx, NY 10461, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Gruss MRRC 306, Bronx, NY 10461, USA
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