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Logotheti S, Pavlopoulou A, Rudsari HK, Galow AM, Kafalı Y, Kyrodimos E, Giotakis AI, Marquardt S, Velalopoulou A, Verginadis II, Koumenis C, Stiewe T, Zoidakis J, Balasingham I, David R, Georgakilas AG. Intercellular pathways of cancer treatment-related cardiotoxicity and their therapeutic implications: the paradigm of radiotherapy. Pharmacol Ther 2024; 260:108670. [PMID: 38823489 DOI: 10.1016/j.pharmthera.2024.108670] [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: 11/11/2023] [Revised: 05/16/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024]
Abstract
Advances in cancer therapeutics have improved patient survival rates. However, cancer survivors may suffer from adverse events either at the time of therapy or later in life. Cardiovascular diseases (CVD) represent a clinically important, but mechanistically understudied complication, which interfere with the continuation of best-possible care, induce life-threatening risks, and/or lead to long-term morbidity. These concerns are exacerbated by the fact that targeted therapies and immunotherapies are frequently combined with radiotherapy, which induces durable inflammatory and immunogenic responses, thereby providing a fertile ground for the development of CVDs. Stressed and dying irradiated cells produce 'danger' signals including, but not limited to, major histocompatibility complexes, cell-adhesion molecules, proinflammatory cytokines, and damage-associated molecular patterns. These factors activate intercellular signaling pathways which have potentially detrimental effects on the heart tissue homeostasis. Herein, we present the clinical crosstalk between cancer and heart diseases, describe how it is potentiated by cancer therapies, and highlight the multifactorial nature of the underlying mechanisms. We particularly focus on radiotherapy, as a case known to often induce cardiovascular complications even decades after treatment. We provide evidence that the secretome of irradiated tumors entails factors that exert systemic, remote effects on the cardiac tissue, potentially predisposing it to CVDs. We suggest how diverse disciplines can utilize pertinent state-of-the-art methods in feasible experimental workflows, to shed light on the molecular mechanisms of radiotherapy-related cardiotoxicity at the organismal level and untangle the desirable immunogenic properties of cancer therapies from their detrimental effects on heart tissue. Results of such highly collaborative efforts hold promise to be translated to next-generation regimens that maximize tumor control, minimize cardiovascular complications, and support quality of life in cancer survivors.
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Affiliation(s)
- Stella Logotheti
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780, Athens, Greece; Biomedical Physics in Radiation Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | | | - Anne-Marie Galow
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Yağmur Kafalı
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Efthymios Kyrodimos
- First Department of Otorhinolaryngology, Head and Neck Surgery, Hippocrateion General Hospital Athens, National and Kapodistrian University of Athens, Athens, Greece
| | - Aris I Giotakis
- First Department of Otorhinolaryngology, Head and Neck Surgery, Hippocrateion General Hospital Athens, National and Kapodistrian University of Athens, Athens, Greece
| | - Stephan Marquardt
- Institute of Translational Medicine for Health Care Systems, Medical School Berlin, Hochschule Für Gesundheit Und Medizin, 14197 Berlin, Germany
| | - Anastasia Velalopoulou
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ioannis I Verginadis
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Constantinos Koumenis
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Philipps-University, 35043 Marburg, Germany; German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), 35043 Marburg, Germany; Genomics Core Facility, Philipps-University, 35043 Marburg, Germany; Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
| | - Jerome Zoidakis
- Department of Biotechnology, Biomedical Research Foundation, Academy of Athens, Athens, Greece; Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Robert David
- Department of Cardiac Surgery, Rostock University Medical Center, 18057 Rostock, Germany; Department of Life, Light & Matter, Interdisciplinary Faculty, Rostock University, 18059 Rostock, Germany
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780, Athens, Greece.
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Si Y, Zou J, Gao Y, Chuai G, Liu Q, Chen L. Foundation models in molecular biology. BIOPHYSICS REPORTS 2024; 10:135-151. [PMID: 39027316 PMCID: PMC11252241 DOI: 10.52601/bpr.2024.240006] [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: 01/23/2024] [Accepted: 03/04/2024] [Indexed: 07/20/2024] Open
Abstract
Determining correlations between molecules at various levels is an important topic in molecular biology. Large language models have demonstrated a remarkable ability to capture correlations from large amounts of data in the field of natural language processing as well as image generation, and correlations captured from data using large language models can also be applicable to solving a wide range of specific tasks, hence large language models are also referred to as foundation models. The massive amount of data that exists in the field of molecular biology provides an excellent basis for the development of foundation models, and the recent emergence of foundation models in the field of molecular biology has really pushed the entire field forward. We summarize the foundation models developed based on RNA sequence data, DNA sequence data, protein sequence data, single-cell transcriptome data, and spatial transcriptome data respectively, and further discuss the research directions for the development of foundation models in molecular biology.
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Affiliation(s)
- Yunda Si
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Jiawei Zou
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yicheng Gao
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China
| | - Guohui Chuai
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China
| | - Qi Liu
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China
| | - Luonan Chen
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
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Zhang S, Tang Q, Zhang X, Chen X. Proximitomics by Reactive Species. ACS CENTRAL SCIENCE 2024; 10:1135-1147. [PMID: 38947200 PMCID: PMC11212136 DOI: 10.1021/acscentsci.4c00373] [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: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 07/02/2024]
Abstract
The proximitome is defined as the entire collection of biomolecules spatially in the proximity of a biomolecule of interest. More broadly, the concept of the proximitome can be extended to the totality of cells proximal to a specific cell type. Since the spatial organization of biomolecules and cells is essential for almost all biological processes, proximitomics has recently emerged as an active area of scientific research. One of the growing strategies for proximitomics leverages reactive species-which are generated in situ and spatially confined, to chemically tag and capture proximal biomolecules and cells for systematic analysis. In this Outlook, we summarize different types of reactive species that have been exploited for proximitomics and discuss their pros and cons for specific applications. In addition, we discuss the current challenges and future directions of this exciting field.
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Affiliation(s)
- Shaoran Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Qi Tang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
| | - Xu Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Xing Chen
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
- Synthetic
and Functional Biomolecules Center, Peking
University, Beijing 100871, People’s
Republic of China
- Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry
of Education, Peking University, Beijing 100871, People’s Republic of China
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Zhao LX, Chen LL, Cheng D, Wu TY, Fan YG, Wang ZY. Potential Application Prospects of Biomolecule-Modified Two-Dimensional Chiral Nanomaterials in Biomedicine. ACS Biomater Sci Eng 2024; 10:2022-2040. [PMID: 38506625 DOI: 10.1021/acsbiomaterials.3c01871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Chirality, one of the most fundamental properties of natural molecules, plays a significant role in biochemical reactions. Nanomaterials with chiral characteristics have superior properties, such as catalytic properties, optoelectronic properties, and photothermal properties, which have significant potential for specific applications in nanomedicine. Biomolecular modifications such as nucleic acids, peptides, proteins, and polysaccharides are sources of chirality for nanomaterials with great potential for application in addition to intrinsic chirality, artificial macromolecules, and metals. Two-dimensional (2D) nanomaterials, as opposed to other dimensions, due to proper surface area, extensive modification sites, drug loading potential, and simplicity of preparation, are prepared and utilized in diagnostic applications, drug delivery research, and tumor therapy. Current advanced studies on 2D chiral nanomaterials for biomedicine are focused on novel chiral development, structural control, and materials sustainability applications. However, despite the advances in biomedical research, chiral 2D nanomaterials still confront challenges such as the difficulty of synthesis, quality control, batch preparation, chiral stability, and chiral recognition and selectivity. This review aims to provide a comprehensive overview of the origins, synthesis, applications, and challenges of 2D chiral nanomaterials with biomolecules as cargo and chiral modifications and highlight their potential roles in biomedicine.
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Affiliation(s)
- Ling-Xiao Zhao
- Key Laboratory of Medical Cell Biology of Ministry of Education, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang 110122, China
| | - Li-Lin Chen
- Key Laboratory of Medical Cell Biology of Ministry of Education, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang 110122, China
| | - Di Cheng
- Dalian Gentalker Biological Technology Co., Ltd., Dalian 116699, China
| | - Ting-Yao Wu
- First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121000, China
| | - Yong-Gang Fan
- Key Laboratory of Medical Cell Biology of Ministry of Education, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang 110122, China
| | - Zhan-You Wang
- Key Laboratory of Medical Cell Biology of Ministry of Education, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang 110122, China
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Xu X, Yin K, Xu S, Wang Z, Wu R. Mass spectrometry-based methods for investigating the dynamics and organization of the surfaceome: exploring potential clinical implications. Expert Rev Proteomics 2024; 21:99-113. [PMID: 38300624 PMCID: PMC10928381 DOI: 10.1080/14789450.2024.2314148] [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: 11/22/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
INTRODUCTION Cell-surface proteins are extremely important for many cellular events, such as regulating cell-cell communication and cell-matrix interactions. Aberrant alterations in surface protein expression, modification (especially glycosylation), and interactions are directly related to human diseases. Systematic investigation of surface proteins advances our understanding of protein functions, cellular activities, and disease mechanisms, which will lead to identifying surface proteins as disease biomarkers and drug targets. AREAS COVERED In this review, we summarize mass spectrometry (MS)-based proteomics methods for global analysis of cell-surface proteins. Then, investigations of the dynamics of surface proteins are discussed. Furthermore, we summarize the studies for the surfaceome interaction networks. Additionally, biological applications of MS-based surfaceome analysis are included, particularly highlighting the significance in biomarker identification, drug development, and immunotherapies. EXPERT OPINION Modern MS-based proteomics provides an opportunity to systematically characterize proteins. However, due to the complexity of cell-surface proteins, the labor-intensive workflow, and the limit of clinical samples, comprehensive characterization of the surfaceome remains extraordinarily challenging, especially in clinical studies. Developing and optimizing surfaceome enrichment methods and utilizing automated sample preparation workflow can expand the applications of surfaceome analysis and deepen our understanding of the functions of cell-surface proteins.
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Affiliation(s)
- Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zeyu Wang
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Wright MH. Chemical biology tools for protein labelling: insights into cell-cell communication. Biochem J 2023; 480:1445-1457. [PMID: 37732646 PMCID: PMC10586760 DOI: 10.1042/bcj20220309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
Multicellular organisms require carefully orchestrated communication between and within cell types and tissues, and many unicellular organisms also sense their context and environment, sometimes coordinating their responses. This review highlights contributions from chemical biology in discovering and probing mechanisms of cell-cell communication. We focus on chemical tools for labelling proteins in a cellular context and how these can be applied to decipher the target receptor of a signalling molecule, label a receptor of interest in situ to understand its biology, provide a read-out of protein activity or interactions in downstream signalling pathways, or discover protein-protein interactions across cell-cell interfaces.
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Affiliation(s)
- Megan H. Wright
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
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Wang Y, Sun SK, Liu Y, Zhang Z. Advanced hitchhiking nanomaterials for biomedical applications. Theranostics 2023; 13:4781-4801. [PMID: 37771786 PMCID: PMC10526662 DOI: 10.7150/thno.88002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 09/30/2023] Open
Abstract
Hitchhiking, a recently developed bio-inspired cargo delivery system, has been harnessed for diverse applications. By leveraging the interactions between nanoparticles and circulatory cells or proteins, hitchhiking enables efficient navigation through the vasculature while evading immune system clearance. Moreover, it allows for targeted delivery of nutrients to tissues, surveillance of the immune system, and pathogen elimination. Various synthetic nanomaterials have been developed to facilitate hitchhiking with circulatory cells or proteins. By combining the advantages of synthetic nanomaterials and circulatory cells or proteins, hitchhiking nanomaterials demonstrate several advantages over conventional vectors, including enhanced circulatory stability and optimized therapeutic efficacy. This review provides an overview of general strategies for hitchhiking, choices of cells and proteins, and recent advances of hitchhiking nanomaterials for biomedical applications.
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Affiliation(s)
- Ying Wang
- School of Medical Imaging, Tianjin Medical University, Tianjin 300203, China
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin 300384, China
| | - Shao-Kai Sun
- School of Medical Imaging, Tianjin Medical University, Tianjin 300203, China
| | - Yang Liu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhanzhan Zhang
- School of Medical Imaging, Tianjin Medical University, Tianjin 300203, China
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin 300384, China
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