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Venrooij KR, de Bondt L, Bonger KM. Mutually Orthogonal Bioorthogonal Reactions: Selective Chemistries for Labeling Multiple Biomolecules Simultaneously. Top Curr Chem (Cham) 2024; 382:24. [PMID: 38971884 PMCID: PMC11227474 DOI: 10.1007/s41061-024-00467-8] [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: 12/19/2023] [Accepted: 05/13/2024] [Indexed: 07/08/2024]
Abstract
Bioorthogonal click chemistry has played a transformative role in many research fields, including chemistry, biology, and medicine. Click reactions are crucial to produce increasingly complex bioconjugates, to visualize and manipulate biomolecules in living systems and for various applications in bioengineering and drug delivery. As biological (model) systems grow more complex, researchers have an increasing need for using multiple orthogonal click reactions simultaneously. In this review, we will introduce the most common bioorthogonal reactions and discuss their orthogonal use on the basis of their mechanism and electronic or steric tuning. We provide an overview of strategies to create reaction orthogonality and show recent examples of mutual orthogonal chemistry used for simultaneous biomolecule labeling. We end by discussing some considerations for the type of chemistry needed for labeling biomolecules in a system of choice.
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Affiliation(s)
- Kevin R Venrooij
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Lucienne de Bondt
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Kimberly M Bonger
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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2
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Reynolds DE, Sun Y, Wang X, Vallapureddy P, Lim J, Pan M, Fernandez Del Castillo A, Carlson JCT, Sellmyer MA, Nasrallah M, Binder Z, O'Rourke DM, Ming G, Song H, Ko J. Live Organoid Cyclic Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309289. [PMID: 38326078 PMCID: PMC11005682 DOI: 10.1002/advs.202309289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/07/2024] [Indexed: 02/09/2024]
Abstract
Organoids are becoming increasingly relevant in biology and medicine for their physiological complexity and accuracy in modeling human disease. To fully assess their biological profile while preserving their spatial information, spatiotemporal imaging tools are warranted. While previously developed imaging techniques, such as four-dimensional (4D) live imaging and light-sheet imaging have yielded important clinical insights, these technologies lack the combination of cyclic and multiplexed analysis. To address these challenges, bioorthogonal click chemistry is applied to display the first demonstration of multiplexed cyclic imaging of live and fixed patient-derived glioblastoma tumor organoids. This technology exploits bioorthogonal click chemistry to quench fluorescent signals from the surface and intracellular of labeled cells across multiple cycles, allowing for more accurate and efficient molecular profiling of their complex phenotypes. Herein, the versatility of this technology is demonstrated for the screening of glioblastoma markers in patient-derived human glioblastoma organoids while conserving their viability. It is anticipated that the findings and applications of this work can be broadly translated into investigating physiological developments in other organoid systems.
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Affiliation(s)
- David E. Reynolds
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Yusha Sun
- Department of NeuroscienceMahoney Institute for NeurosciencesPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Xin Wang
- Department of NeuroscienceMahoney Institute for NeurosciencesPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Phoebe Vallapureddy
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Jianhua Lim
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Menghan Pan
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Andres Fernandez Del Castillo
- Department of Biochemistry & Molecular BiophysicsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Jonathan C. T. Carlson
- Center for Systems BiologyMassachusetts General HospitalBostonMA02114USA
- Department of MedicineMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
| | - Mark A. Sellmyer
- Department of RadiologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - MacLean Nasrallah
- GBM Translational Center of ExcellenceAbramson Cancer CenterUniversity of PennsylvaniaPhiladelphiaPA19104USA
- Department of Pathology and Laboratory MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Zev Binder
- GBM Translational Center of ExcellenceAbramson Cancer CenterUniversity of PennsylvaniaPhiladelphiaPA19104USA
- Center for Cellular ImmunotherapiesUniversity of PennsylvaniaPhiladelphiaPA19104USA
- Department of NeurosurgeryPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Donald M. O'Rourke
- GBM Translational Center of ExcellenceAbramson Cancer CenterUniversity of PennsylvaniaPhiladelphiaPA19104USA
- Center for Cellular ImmunotherapiesUniversity of PennsylvaniaPhiladelphiaPA19104USA
- Department of NeurosurgeryPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Guo‐li Ming
- Department of NeuroscienceMahoney Institute for NeurosciencesPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
- Department of Cell and Developmental BiologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
- Department of PsychiatryPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
- Institute for Regenerative MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Hongjun Song
- Department of NeuroscienceMahoney Institute for NeurosciencesPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
- GBM Translational Center of ExcellenceAbramson Cancer CenterUniversity of PennsylvaniaPhiladelphiaPA19104USA
- Department of Cell and Developmental BiologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
- Department of PsychiatryPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
- The Epigenetics InstitutePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Jina Ko
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPA19104USA
- Department of Pathology and Laboratory MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
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Yang W, Liu R, Yin X, Wu K, Yan Z, Wang X, Fan G, Tang Z, Li Y, Jiang H. Novel Near-Infrared Fluorescence Probe for Bioimaging and Evaluating Superoxide Anion Fluctuations in Ferroptosis-Mediated Epilepsy. Anal Chem 2023; 95:12240-12246. [PMID: 37556358 DOI: 10.1021/acs.analchem.3c00852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Ferroptosis is an iron-regulated, caspase-mediated pathway of cell death that is associated with the excessive aggregation of lipid-reactive oxygen species and is extensively involved in the evolution of many diseases, including epilepsy. The superoxide anion (O2•-), as the primary precursor of ROS, is closely related to ferroptosis-mediated epilepsy. Therefore, it is crucial to establish a highly effective and convenient method for the real-time dynamic monitoring of O2•- during the ferroptosis process in epilepsy for the diagnosis and therapy of ferroptosis-mediated epilepsy. Nevertheless, no probes for detecting O2•- in ferroptosis-mediated epilepsy have been reported. Herein, we systematically conceptualized and developed a novel near-infrared (NIR) fluorescence probe, NIR-FP, for accurately tracking the fluctuation of O2•- in ferroptosis-mediated epilepsy. The probe showed exceptional sensitivity and outstanding selectivity toward O2•-. In addition, the probe has been utilized effectively to bioimage and evaluate endogenous O2•- variations in three types of ferroptosis-mediated epilepsy models (the kainic acid-induced chronic epilepsy model, the pentylenetetrazole-induced acute epilepsy model, and the pilocarpine-induced status epilepticus model). The above applications illustrated that NIR-FP could serve as a reliable and suitable tool for guiding the accurate diagnosis and therapy of ferroptosis-mediated epilepsy.
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Affiliation(s)
- Wenjie Yang
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Ruixin Liu
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Xiaoyi Yin
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Ke Wu
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Zhi Yan
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Xiaoming Wang
- Experimental Center, Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Guanwei Fan
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
| | - Zhixin Tang
- Experimental Center, Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yunlun Li
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Haiqiang Jiang
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
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Venkatesan M, Zhang N, Marteau B, Yajima Y, De Zarate Garcia NO, Fang Z, Hu T, Cai S, Ford A, Olszewski H, Borst A, Coskun AF. Spatial subcellular organelle networks in single cells. Sci Rep 2023; 13:5374. [PMID: 37005468 PMCID: PMC10067843 DOI: 10.1038/s41598-023-32474-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: 04/27/2022] [Accepted: 03/28/2023] [Indexed: 04/04/2023] Open
Abstract
Organelles play important roles in human health and disease, such as maintaining homeostasis, regulating growth and aging, and generating energy. Organelle diversity in cells not only exists between cell types but also between individual cells. Therefore, studying the distribution of organelles at the single-cell level is important to understand cellular function. Mesenchymal stem cells are multipotent cells that have been explored as a therapeutic method for treating a variety of diseases. Studying how organelles are structured in these cells can answer questions about their characteristics and potential. Herein, rapid multiplexed immunofluorescence (RapMIF) was performed to understand the spatial organization of 10 organelle proteins and the interactions between them in the bone marrow (BM) and umbilical cord (UC) mesenchymal stem cells (MSCs). Spatial correlations, colocalization, clustering, statistical tests, texture, and morphological analyses were conducted at the single cell level, shedding light onto the interrelations between the organelles and comparisons of the two MSC subtypes. Such analytics toolsets indicated that UC MSCs exhibited higher organelle expression and spatially spread distribution of mitochondria accompanied by several other organelles compared to BM MSCs. This data-driven single-cell approach provided by rapid subcellular proteomic imaging enables personalized stem cell therapeutics.
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Affiliation(s)
- Mythreye Venkatesan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Nicholas Zhang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA
| | - Benoit Marteau
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Yukina Yajima
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Nerea Ortiz De Zarate Garcia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Departamento de Bioingenieria e Ingenieria Aeroespacial, Universidad Carlos III de Madrid, Getafe, Spain
| | - Zhou Fang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Thomas Hu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shuangyi Cai
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Adam Ford
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Harrison Olszewski
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Andrew Borst
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Ahmet F Coskun
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
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Lugani S, Halabi EA, Oh J, Kohler R, Peterson H, Breakefield XO, Chiocca EAA, Miller MA, Garris C, Weissleder R. Dual Immunostimulatory Pathway Agonism through a Synthetic Nanocarrier Triggers Robust Anti-Tumor Immunity in Murine Glioblastoma. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208782. [PMID: 36427266 PMCID: PMC10197197 DOI: 10.1002/adma.202208782] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/07/2022] [Indexed: 05/21/2023]
Abstract
Myeloid cells are abundant, create a highly immunosuppressive environment in glioblastoma (GBM), and thus contribute to poor immunotherapy responses. Based on the hypothesis that small molecules can be used to stimulate myeloid cells to elicit anti-tumor effector functions, a synthetic nanoparticle approach is developed to deliver dual NF-kB pathway-inducing agents into these cells via systemic administration. Synthetic, cyclodextrin-adjuvant nanoconstructs (CANDI) with high affinity for tumor-associated myeloid cells are dually loaded with a TLR7 and 8 (Toll-like receptor, 7 and 8) agonist (R848) and a cIAP (cellular inhibitor of apoptosis protein) inhibitor (LCL-161) to dually activate these myeloid cells. Here CANDI is shown to: i) readily enter the GBM tumor microenvironment (TME) and accumulate at high concentrations, ii) is taken up by tumor-associated myeloid cells, iii) potently synergize payloads compared to monotherapy, iv) activate myeloid cells, v) fosters a "hot" TME with high levels of T effector cells, and vi) controls the growth of murine GBM as mono- and combination therapies with anti-PD1. Multi-pathway targeted myeloid stimulation via the CANDI platform can efficiently drive anti-tumor immunity in GBM.
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Affiliation(s)
- Sophie Lugani
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 672, 69120 Heidelberg
| | - Elias A. Halabi
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Juhyun Oh
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Rainer Kohler
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Hannah Peterson
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Xandra O. Breakefield
- Department of Radiology, Massachusetts General Hospital, and Harvard Medical School, Boston, MA
- Department of Neurology, Massachusetts General Hospital, and Harvard Medical School, Boston, MA
| | - E. Antonio A. Chiocca
- Department of Neurosurgery, Brigham and Women Hospital, and Harvard Medical School, Boston, MA
| | - Miles A. Miller
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Christopher Garris
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
- Department of Radiology, Massachusetts General Hospital, and Harvard Medical School, Boston, MA
- Department of Neurosurgery, Brigham and Women Hospital, and Harvard Medical School, Boston, MA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115
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Lucas K. Cycling, Fasting, Fishing, and Other Things: The Emerging World of Biocompatible Chemistries. Adv Biol (Weinh) 2023; 7:e2200178. [PMID: 36047616 DOI: 10.1002/adbi.202200178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/01/2022] [Indexed: 01/21/2023]
Abstract
New tools in the field of biocompatible chemistries are enabling researchers to probe immunological and genetic information with highly multiplexed capabilities. These bioorthogonal click chemistry reactions provide a platform for tumor and immune cell profiling for dozens of markers on the same cell sample simultaneously, providing a more complete snapshot of the disease.
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Affiliation(s)
- Kilean Lucas
- Harvard University, 7 Fuller Rd., Billerica, MA, 01821, USA
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Lucas K, Oh J, Hoelzl J, Weissleder R. Cellular point-of-care diagnostics using an inexpensive layer-stack microfluidic device. LAB ON A CHIP 2022; 22:2145-2154. [PMID: 35514273 PMCID: PMC9214713 DOI: 10.1039/d2lc00162d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cellular analyses are increasingly used to diagnose diseases at point-of-care and global healthcare settings. Some analyses are simple as they rely on chromogenic stains (blood counts, malaria) but others often require higher multiplexing to define and quantitate cell populations (cancer diagnosis, immunoprofiling). Simplifying the latter with inexpensive solutions represents a current bottleneck in designing start-end pipelines. Based on the hypothesis that novel film adhesives could be used to create inexpensive disposable devices, we tested a number of different designs and materials, to rapidly perform 12-15 channel single-cell imaging. Using an optimized passive pumping layer-stack microfluidic (PLASMIC) device (<1 $ in supplies) we show that rapid, inexpensive cellular analysis is feasible.
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Affiliation(s)
- Kilean Lucas
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA.
| | - Juhyun Oh
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA.
| | - Jan Hoelzl
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA.
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA.
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
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