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Chen J, Zhou M, Wu W, Zhang J, Li Y, Li D. STimage-1K4M: A histopathology image-gene expression dataset for spatial transcriptomics. ARXIV 2024:arXiv:2406.06393v2. [PMID: 38947920 PMCID: PMC11213178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1,149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with 15,000 - 30,000 dimensional gene expressions. With 4,293,195 pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.
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Affiliation(s)
| | | | - Wenrong Wu
- University of North Carolina at Chapel Hill
| | | | - Yun Li
- University of North Carolina at Chapel Hill
| | - Didong Li
- University of North Carolina at Chapel Hill
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Cau MF, Ferraresso F, Seadler M, Badior K, Zhang Y, Ketelboeter LM, Rodriguez GG, Chen T, Ferraresso M, Wietrzny A, Robertson M, Haugen A, Cullis PR, de Moya M, Dyer M, Kastrup CJ. siRNA-mediated reduction of a circulating protein in swine using lipid nanoparticles. Mol Ther Methods Clin Dev 2024; 32:101258. [PMID: 38779336 PMCID: PMC11109470 DOI: 10.1016/j.omtm.2024.101258] [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: 10/31/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024]
Abstract
Genetic manipulation of animal models is a fundamental research tool in biology and medicine but is challenging in large animals. In rodents, models can be readily developed by knocking out genes in embryonic stem cells or by knocking down genes through in vivo delivery of nucleic acids. Swine are a preferred animal model for studying the cardiovascular and immune systems, but there are limited strategies for genetic manipulation. Lipid nanoparticles (LNPs) efficiently deliver small interfering RNA (siRNA) to knock down circulating proteins, but swine are sensitive to LNP-induced complement activation-related pseudoallergy (CARPA). We hypothesized that appropriately administering optimized siRNA-LNPs could knock down circulating levels of plasminogen, a blood protein synthesized in the liver. siRNA-LNPs against plasminogen (siPLG) reduced plasma plasminogen protein and hepatic plasminogen mRNA levels to below 5% of baseline values. Functional assays showed that reducing plasminogen levels modulated systemic blood coagulation. Clinical signs of CARPA were not observed, and occasional mild and transient hepatotoxicity was present in siPLG-treated animals at 5 h post-infusion, which returned to baseline by 7 days. These findings advance siRNA-LNPs in swine models, enabling genetic engineering of blood and hepatic proteins, which can likely expand to proteins in other tissues in the future.
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Affiliation(s)
- Massimo F. Cau
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Francesca Ferraresso
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Versiti Blood Research Institute, Milwaukee, WI 53226, USA
| | - Monica Seadler
- Versiti Blood Research Institute, Milwaukee, WI 53226, USA
- Department of Surgery, Division of Trauma and Acute Care Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Youjie Zhang
- Versiti Blood Research Institute, Milwaukee, WI 53226, USA
| | | | | | - Taylor Chen
- Versiti Blood Research Institute, Milwaukee, WI 53226, USA
| | | | | | - Madelaine Robertson
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Amber Haugen
- Versiti Blood Research Institute, Milwaukee, WI 53226, USA
| | - Pieter R. Cullis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Marc de Moya
- Department of Surgery, Division of Trauma and Acute Care Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mitchell Dyer
- Versiti Blood Research Institute, Milwaukee, WI 53226, USA
- Department of Surgery, Division of Vascular and Endovascular Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christian J. Kastrup
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Versiti Blood Research Institute, Milwaukee, WI 53226, USA
- Department of Surgery, Division of Trauma and Acute Care Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Departments of Biochemistry, Biomedical Engineering, and Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Li M, Jin M, Yang H. Remodelers of the vascular microenvironment: The effect of biopolymeric hydrogels on vascular diseases. Int J Biol Macromol 2024; 264:130764. [PMID: 38462100 DOI: 10.1016/j.ijbiomac.2024.130764] [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: 12/19/2023] [Revised: 01/31/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
Vascular disease is the leading health problem worldwide. Vascular microenvironment encompasses diverse cell types, including those within the vascular wall, blood cells, stromal cells, and immune cells. Initiation of the inflammatory state of the vascular microenvironment and changes in its mechanics can profoundly affect vascular homeostasis. Biomedical materials play a crucial role in modern medicine, hydrogels, characterized by their high-water content, have been increasingly utilized as a three-dimensional interaction network. In recent times, the remarkable progress in utilizing hydrogels and understanding vascular microenvironment have enabled the treatment of vascular diseases. In this review, we give an emphasis on the utilization of hydrogels and their advantages in the various vascular diseases including atherosclerosis, aneurysm, vascular ulcers of the lower limbs and myocardial infarction. Further, we highlight the importance and advantages of hydrogels as artificial microenvironments.
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Affiliation(s)
- Minhao Li
- School of Intelligent Medicine, China Medical University, No.77, Puhe Road, Shenyang 110122, Liaoning Province, China
| | - Meiqi Jin
- School of Intelligent Medicine, China Medical University, No.77, Puhe Road, Shenyang 110122, Liaoning Province, China
| | - Huazhe Yang
- School of Intelligent Medicine, China Medical University, No.77, Puhe Road, Shenyang 110122, Liaoning Province, China.
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Wang W, Ye J, Xu L, Mo DG, Chen C, Li T, Yao HC. The effects of IGF-1 and IGFBP-2 treatments on the atherosclerosis in the aorta and the coronary arteries of the high cholesterol diet-fed rabbits. Int Immunopharmacol 2024; 127:111409. [PMID: 38118312 DOI: 10.1016/j.intimp.2023.111409] [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: 10/17/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 12/22/2023]
Abstract
Several studies have demonstrated suppression of aortic atherosclerosis by insulin like growth factor-1 (IGF-1) in hypercholesterolemic rabbits. Though a recent study has reported that IGF-1 exerts anti-atherogenic effects in coronary arteries, the mechanisms of IGF-1 in coronary arteries need to be further verified. Studies about insulin like growth factor binding protein-2 (IGFBP-2) in atherosclerosis are rarely. The objective of this study is to examine the effects of IGF-1 and IGFBP-2 on the atherosclerosis development in the aorta and coronary arteries of the high-cholesterol diet (HCD)-fed rabbits. New Zealand white rabbits were fed either normal chow (n = 5) or a diet containing 1.0 % cholesterol (n = 18) for 12 weeks. Cholesterol-fed rabbits were given IGF-1 or IGFBP-2 or saline intravenously (each n = 6) for 10 weeks. The results revealed that IGF-1 decreased total cholesterol (TC) and low-density lipoprotein (LDL) levels (p < 0.05), whereas IGFBP-2 did not. IGF-1 significantly attenuated atherosclerotic lesions and reduced accumulated macrophages within the coronary artery plaques, whereas IGFBP-2 deteriorated these changes. Moreover, IGF-1 reduced serum platelet-activating factor acetylhydrolase levels, C reactive protein (CRP), and inhibited the protein expression levels of tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6). IGFBP-2 elevated serum 8-hydroxy-2'-deoxyguanosine levels, CRP, and promoted the protein expression levels of TNF-α and IL-6. In conclusion, IGF-1 can substantially suppress plaque formation in coronary arteries with a marked inhibition of macrophage accumulation likely via its anti-inflammatory properties, whereas IGFBP-2 plays an opposite effect on atherosclerosis. The present study highlighted a theoretical basis for pharmacological treatment of atherosclerosis.
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Affiliation(s)
- Wei Wang
- Department of Cardiology, Liaocheng People's Hospital Affiliated to Shandong First Medical University, Liaocheng, Shandong 252000, China
| | - Jing Ye
- Department of Pathology, Liaocheng People's Hospital, Liaocheng, Shandong 252000, China
| | - Li Xu
- Stem Cell and Regenerative Medicine Laboratory, Liaocheng People's Hospital, Liaocheng 252000, PR China
| | - De-Gang Mo
- Department of Cardiology, Liaocheng People's Hospital Affiliated to Shandong First Medical University, Liaocheng, Shandong 252000, China
| | - Chen Chen
- Department of Urology, Liaocheng People's Hospital, Liaocheng 252000, PR China
| | - Tai Li
- Department of Nursing, Liaocheng Vocational & Technical College, Liaocheng 252000, China
| | - Heng-Chen Yao
- Department of Cardiology, Liaocheng People's Hospital Affiliated to Shandong First Medical University, Liaocheng, Shandong 252000, China; Department of Cardiology, Liaocheng People's Hospital, Shandong University, Jinan, Shandong 250012, China.
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Macvanin M, Gluvic Z, Radovanovic J, Essack M, Gao X, Isenovic ER. New insights on the cardiovascular effects of IGF-1. Front Endocrinol (Lausanne) 2023; 14:1142644. [PMID: 36843588 PMCID: PMC9947133 DOI: 10.3389/fendo.2023.1142644] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
INTRODUCTION Cardiovascular (CV) disorders are steadily increasing, making them the world's most prevalent health issue. New research highlights the importance of insulin-like growth factor 1 (IGF-1) for maintaining CV health. METHODS We searched PubMed and MEDLINE for English and non-English articles with English abstracts published between 1957 (when the first report on IGF-1 identification was published) and 2022. The top search terms were: IGF-1, cardiovascular disease, IGF-1 receptors, IGF-1 and microRNAs, therapeutic interventions with IGF-1, IGF-1 and diabetes, IGF-1 and cardiovascular disease. The search retrieved original peer-reviewed articles, which were further analyzed, focusing on the role of IGF-1 in pathophysiological conditions. We specifically focused on including the most recent findings published in the past five years. RESULTS IGF-1, an anabolic growth factor, regulates cell division, proliferation, and survival. In addition to its well-known growth-promoting and metabolic effects, there is mounting evidence that IGF-1 plays a specialized role in the complex activities that underpin CV function. IGF-1 promotes cardiac development and improves cardiac output, stroke volume, contractility, and ejection fraction. Furthermore, IGF-1 mediates many growth hormones (GH) actions. IGF-1 stimulates contractility and tissue remodeling in humans to improve heart function after myocardial infarction. IGF-1 also improves the lipid profile, lowers insulin levels, increases insulin sensitivity, and promotes glucose metabolism. These findings point to the intriguing medicinal potential of IGF-1. Human studies associate low serum levels of free or total IGF-1 with an increased risk of CV and cerebrovascular illness. Extensive human trials are being conducted to investigate the therapeutic efficacy and outcomes of IGF-1-related therapy. DISCUSSION We anticipate the development of novel IGF-1-related therapy with minimal side effects. This review discusses recent findings on the role of IGF-1 in the cardiovascular (CVD) system, including both normal and pathological conditions. We also discuss progress in therapeutic interventions aimed at targeting the IGF axis and provide insights into the epigenetic regulation of IGF-1 mediated by microRNAs.
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Affiliation(s)
- Mirjana Macvanin
- Department of Radiobiology and Molecular Genetics, VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
- *Correspondence: Mirjana Macvanin,
| | - Zoran Gluvic
- Clinic for Internal Medicine, Department of Endocrinology and Diabetes, Zemun Clinical Hospital, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jelena Radovanovic
- Department of Radiobiology and Molecular Genetics, VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Magbubah Essack
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Esma R. Isenovic
- Department of Radiobiology and Molecular Genetics, VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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