1
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Jogdeo CM, Siddhanta K, Das A, Ding L, Panja S, Kumari N, Oupický D. Beyond Lipids: Exploring Advances in Polymeric Gene Delivery in the Lipid Nanoparticles Era. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2404608. [PMID: 38842816 DOI: 10.1002/adma.202404608] [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: 03/29/2024] [Revised: 05/23/2024] [Indexed: 06/07/2024]
Abstract
The recent success of gene therapy during the COVID-19 pandemic has underscored the importance of effective and safe delivery systems. Complementing lipid-based delivery systems, polymers present a promising alternative for gene delivery. Significant advances have been made in the recent past, with multiple clinical trials progressing beyond phase I and several companies actively working on polymeric delivery systems which provides assurance that polymeric carriers can soon achieve clinical translation. The massive advantage of structural tunability and vast chemical space of polymers is being actively leveraged to mitigate shortcomings of traditional polycationic polymers and improve the translatability of delivery systems. Tailored polymeric approaches for diverse nucleic acids and for specific subcellular targets are now being designed to improve therapeutic efficacy. This review describes the recent advances in polymer design for improved gene delivery by polyplexes and covalent polymer-nucleic acid conjugates. The review also offers a brief note on novel computational techniques for improved polymer design. The review concludes with an overview of the current state of polymeric gene therapies in the clinic as well as future directions on their translation to the clinic.
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Affiliation(s)
- Chinmay M Jogdeo
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kasturi Siddhanta
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ashish Das
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ling Ding
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Sudipta Panja
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Neha Kumari
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - David Oupický
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
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2
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Lin Q, Takebayashi K, Torigoe N, Liu B, Namula Z, Hirata M, Nagahara M, Tanihara F, Otoi T. Evaluation of culture methods and chemical reagent combinations on CRISPR/Cas9 gene editing systems by lipofection in pig zygotes. In Vitro Cell Dev Biol Anim 2024; 60:725-731. [PMID: 38664280 DOI: 10.1007/s11626-024-00908-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/04/2024] [Indexed: 08/03/2024]
Abstract
The delivery of CRISPR/Cas ribonucleoprotein (RNP) complexes is gaining attention owing to its high cleavage efficiency and reduced off-target effects. Although RNPs can be delivered into porcine zygotes via electroporation with relatively high efficiency, lipofection-mediated transfection appears to be versatile because of its ease of use, low cost, and adaptation to high-throughput systems. However, this system requires improvements in terms of embryo development and mutation rates. Therefore, this study elucidated the effects of culture methods and reagent combinations on the CRISPR/Cas9 gene editing systems by using three lipofection reagents: Lipofectamine™ CRISPRMAX™ Cas9 Transfection Reagent (CM), Lipofectamine™ 2000 Transfection Reagent (LP), and jetCRISPR™ RNP Transfection Reagent (Jet). Porcine zona pellucida-free zygotes were incubated for 5 h with Cas9, a guide RNA targeting CD163, and the above lipofection reagents. When examining the effect of culture methods using 4-well (multiple embryo culture) and 25-well plates (single embryo culture) on the efficiency of CM-mediated zygote transfection, the culture of embryos in 25-well plates significantly increased the blastocyst formation rate; however, there was no difference in mutation rates between the 4-well and 25-well plates. When assessing the effects of individual or combined reagents on the efficiency of zygote transfection, the mutation rate was significantly lower for individual LP compared to individual CM- and Jet-mediated transfections. Moreover, combinations of lipofection transfection reagents did not significantly increase the mutation rate or mutation efficiency.
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Affiliation(s)
- Qingyi Lin
- Laboratory of Animal Reproduction, Bio-Innovation Research Center, Tokushima University, 2272-1 Ishii, Myozai-Gun, Tokushima, 779-3233, Japan
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, 779-3233, Japan
| | - Koki Takebayashi
- Laboratory of Animal Reproduction, Bio-Innovation Research Center, Tokushima University, 2272-1 Ishii, Myozai-Gun, Tokushima, 779-3233, Japan
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, 779-3233, Japan
| | - Nanaka Torigoe
- Laboratory of Animal Reproduction, Bio-Innovation Research Center, Tokushima University, 2272-1 Ishii, Myozai-Gun, Tokushima, 779-3233, Japan
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, 779-3233, Japan
| | - Bin Liu
- Laboratory of Animal Reproduction, Bio-Innovation Research Center, Tokushima University, 2272-1 Ishii, Myozai-Gun, Tokushima, 779-3233, Japan
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, 779-3233, Japan
| | - Zhao Namula
- Laboratory of Animal Reproduction, Bio-Innovation Research Center, Tokushima University, 2272-1 Ishii, Myozai-Gun, Tokushima, 779-3233, Japan
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Maki Hirata
- Laboratory of Animal Reproduction, Bio-Innovation Research Center, Tokushima University, 2272-1 Ishii, Myozai-Gun, Tokushima, 779-3233, Japan
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, 779-3233, Japan
| | - Megumi Nagahara
- Laboratory of Animal Reproduction, Bio-Innovation Research Center, Tokushima University, 2272-1 Ishii, Myozai-Gun, Tokushima, 779-3233, Japan
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, 779-3233, Japan
| | - Fuminori Tanihara
- Laboratory of Animal Reproduction, Bio-Innovation Research Center, Tokushima University, 2272-1 Ishii, Myozai-Gun, Tokushima, 779-3233, Japan
| | - Takeshige Otoi
- Laboratory of Animal Reproduction, Bio-Innovation Research Center, Tokushima University, 2272-1 Ishii, Myozai-Gun, Tokushima, 779-3233, Japan.
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, 779-3233, Japan.
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3
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Clothier GKK, Guimarães TR, Thompson SW, Howard SC, Muir BW, Moad G, Zetterlund PB. Streamlining the Generation of Advanced Polymer Materials Through the Marriage of Automation and Multiblock Copolymer Synthesis in Emulsion. Angew Chem Int Ed Engl 2024; 63:e202320154. [PMID: 38400586 DOI: 10.1002/anie.202320154] [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: 01/08/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 02/25/2024]
Abstract
Synthetic polymers are of paramount importance in modern life - an incredibly wide range of polymeric materials possessing an impressive variety of properties have been developed to date. The recent emergence of artificial intelligence and automation presents a great opportunity to significantly speed up discovery and development of the next generation of advanced polymeric materials. We have focused on the high-throughput automated synthesis of multiblock copolymers that comprise three or more distinct polymer segments of different monomer composition bonded in linear sequence. The present work has exploited automation to prepare high molar mass multiblock copolymers (typically>100,000 g mol-1) using reversible addition-fragmentation chain transfer (RAFT) polymerization in aqueous emulsion. A variety of original multiblock copolymers have been synthesised via a Chemspeed robot, exemplified by a multiblock copolymer comprising thirteen constituent blocks. Moreover, libraries of copolymers of randomized monomer compositions (acrylates, acrylamides, methacrylates, and styrenes), block orders, and block lengths were also generated, thereby demonstrating the robustness of our synthetic approach. One multiblock copolymer contained all four monomer families listed in the pool, which is unprecedented in the literature. The present work demonstrates that automation has the power to render complex and laborious syntheses of such unprecedented materials not just possible, but facile and straightforward, thus representing the way forward to the next generation of complex macromolecular architectures.
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Affiliation(s)
- Glenn K K Clothier
- Cluster for Advanced Macromolecular Design (CAMD), School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Thiago R Guimarães
- Laboratoire de Chimie des Polymères Organiques (LCPO), CNRS (UMR 5629), ENSCPB, Université de Bordeaux, 16 avenue Pey Berland, 33607, Pessac, France
| | - Steven W Thompson
- Cluster for Advanced Macromolecular Design (CAMD), School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Shaun C Howard
- CSIRO Manufacturing, Bag 10, Clayton South, VIC, 3169, Australia
| | - Benjamin W Muir
- CSIRO Manufacturing, Bag 10, Clayton South, VIC, 3169, Australia
| | - Graeme Moad
- CSIRO Manufacturing, Bag 10, Clayton South, VIC, 3169, Australia
| | - Per B Zetterlund
- Cluster for Advanced Macromolecular Design (CAMD), School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
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4
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Sekar RP, Lawson JL, Wright ARE, McGrath C, Schadeck C, Kumar P, Tay JW, Dragavon J, Kumar R. Poly(l-glutamic acid) augments the transfection performance of lipophilic polycations by overcoming tradeoffs among cytotoxicity, pDNA delivery efficiency, and serum stability. RSC APPLIED POLYMERS 2024; 2:701-718. [PMID: 39035825 PMCID: PMC11255917 DOI: 10.1039/d4lp00085d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 04/27/2024] [Indexed: 07/23/2024]
Abstract
Polycations are scalable and affordable nanocarriers for delivering therapeutic nucleic acids. Yet, cationicity-dependent tradeoffs between nucleic acid delivery efficiency, cytotoxicity, and serum stability hinder clinical translation. Typically, the most efficient polycationic vehicles also tend to be the most toxic. For lipophilic polycations-which recruit hydrophobic interactions in addition to electrostatic interactions to bind and deliver nucleic acids-extensive chemical or architectural modifications sometimes fail to resolve intractable toxicity-efficiency tradeoffs. Here, we employ a facile post-synthetic polyplex surface modification strategy wherein poly(l-glutamic acid) (PGA) rescues toxicity, inhibits hemolysis, and prevents serum inhibition of lipophilic polycation-mediated plasmid (pDNA) delivery. Importantly, the sequence in which polycations, pDNA, and PGA are combined dictates pDNA conformations and spatial distribution. Circular dichroism spectroscopy reveals that PGA must be added last to polyplexes assembled from lipophilic polycations and pDNA; else, PGA will disrupt polycation-mediated pDNA condensation. Although PGA did not mitigate toxicity caused by hydrophilic PEI-based polycations, PGA tripled the population of transfected viable cells for lipophilic polycations. Non-specific adsorption of serum proteins abrogated pDNA delivery mediated by lipophilic polycations; however, PGA-coated polyplexes proved more serum-tolerant than uncoated polyplexes. Despite lower cellular uptake than uncoated polyplexes, PGA-coated polyplexes were imported into nuclei at higher rates. PGA also silenced the hemolytic activity of lipophilic polycations. Our work provides fundamental insights into how polyanionic coatings such as PGA transform intermolecular interactions between lipophilic polycations, nucleic acids, and serum proteins, and facilitate gentle yet efficient transgene delivery.
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Affiliation(s)
- Ram Prasad Sekar
- Chemical and Biological Engineering, Colorado School of Mines Golden CO 80401 USA
| | | | - Aryelle R E Wright
- Quantitative Biosciences and Engineering, Colorado School of Mines Golden CO 80401 USA
| | - Caleb McGrath
- Quantitative Biosciences and Engineering, Colorado School of Mines Golden CO 80401 USA
| | - Cesar Schadeck
- Materials Science, Colorado School of Mines Golden CO 80401 USA
| | - Praveen Kumar
- Shared Instrumentation Facility, Colorado School of Mines Golden CO USA
| | - Jian Wei Tay
- BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
| | - Joseph Dragavon
- BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
| | - Ramya Kumar
- Chemical and Biological Engineering, Colorado School of Mines Golden CO 80401 USA
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5
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Leyden MC, Oviedo F, Saxena S, Kumar R, Le N, Reineke TM. Synergistic Polymer Blending Informs Efficient Terpolymer Design and Machine Learning Discerns Performance Trends for pDNA Delivery. Bioconjug Chem 2024; 35:897-911. [PMID: 38924453 DOI: 10.1021/acs.bioconjchem.4c00028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Cationic polymers offer an alternative to viral vectors in nucleic acid delivery. However, the development of polymer vehicles capable of high transfection efficiency and minimal toxicity has remained elusive, and continued exploration of the vast design space is required. Traditional single polymer syntheses with large monomer bases are very time-intensive, limiting the speed at which new formulations are identified. In this work, we present an experimental method for the quick probing of the design space, utilizing a combinatorial set of 90 polymer blends, derived from 6 statistical copolymers, to deliver pDNA. This workflow facilitated rapid screening of polyplex compositions, successfully tailoring polyplex hydrophobicity, particle size, and payload binding affinity. This workflow identified blended polyplexes with high levels of transfection efficiency and cell viability relative to single copolymer controls and commercial JetPEI, indicating synergistic benefits from copolymer blending. Polyplex composition was coupled with biological outputs to guide the synthesis of single terpolymer vehicles, with high-performing polymers P10 and M20, providing superior transfection of HEK293T cells in serum-free and serum-containing media, respectively. Machine learning coupled with SHapley Additive exPlanations (SHAP) was used to identify polymer/polyplex attributes that most impact transfection efficiency, viability, and overall effective efficiency. Subsequent transfections on ARPE-19 and HDFn cells found that P10 and M20 were surpassed in performance by M10, contrasting with results in HEK293T cells. This cell type dependency reinforced the need to evaluate transfection conditions with multiple cell models to potentially identify moieties more beneficial to delivery in certain tissues. Overall, the workflow employed can be used to expedite the exploration of the polymer design space, bypassing extensive synthesis, and to develop improved polymer delivery vehicles more readily for nucleic acid therapies.
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Affiliation(s)
- Michael C Leyden
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Felipe Oviedo
- Nanite Inc., Boston, Massachusetts 02109, United States
| | - Sonashree Saxena
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ramya Kumar
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Ngoc Le
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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6
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Delgado Gonzalez B, Lopez-Blanco R, Parcero-Bouzas S, Barreiro-Piñeiro N, Garcia-Abuin L, Fernandez-Megia E. Dynamic Covalent Boronate Chemistry Accelerates the Screening of Polymeric Gene Delivery Vectors via In Situ Complexation of Nucleic Acids. J Am Chem Soc 2024; 146:17211-17219. [PMID: 38864331 PMCID: PMC11212051 DOI: 10.1021/jacs.4c03384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/13/2024]
Abstract
Gene therapy provides exciting new therapeutic opportunities beyond the reach of traditional treatments. Despite the tremendous progress of viral vectors, their high cost, complex manufacturing, and side effects have encouraged the development of nonviral alternatives, including cationic polymers. However, these are less efficient in overcoming cellular barriers, resulting in lower transfection efficiencies. Although the exquisite structural tunability of polymers might be envisaged as a versatile tool for improving transfection, the need to fine-tune several structural parameters represents a bottleneck in current screening technologies. By taking advantage of the fast-forming and strong boronate ester bond, an archetypal example of dynamic covalent chemistry, a highly adaptable gene delivery platform is presented, in which the polycation synthesis and pDNA complexation occur in situ. The robustness of the strategy entitles the simultaneous evaluation of several structural parameters at will, enabling the accelerated screening and adaptive optimization of lead polymeric vectors using dynamic covalent libraries.
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Affiliation(s)
- Bruno Delgado Gonzalez
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Roi Lopez-Blanco
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Samuel Parcero-Bouzas
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Natalia Barreiro-Piñeiro
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Departamento de Bioquímica
e Bioloxía Molecular, Universidade
de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Lucas Garcia-Abuin
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Eduardo Fernandez-Megia
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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7
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Dalal RJ, Oviedo F, Leyden MC, Reineke TM. Polymer design via SHAP and Bayesian machine learning optimizes pDNA and CRISPR ribonucleoprotein delivery. Chem Sci 2024; 15:7219-7228. [PMID: 38756796 PMCID: PMC11095369 DOI: 10.1039/d3sc06920f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
We present the facile synthesis of a clickable polymer library with systematic variations in length, binary composition, pKa, and hydrophobicity (clog P) to optimize intracellular pDNA and CRISPR-Cas9 ribonucleoprotein (RNP) performance. We couple physicochemical characterization and machine learning to interpret quantitative structure-property relationships within the combinatorial design space. For the first time, we reveal unexpected disparate design parameters for nucleic acid carriers; via explainable machine learning on 432 formulations, we discover that lower polymer pKa and higher percentages of benzimidazole ethanethiol enhance pDNA delivery, yet polymer length and captamine cation identity improve RNP delivery. Closed-loop Bayesian optimization of 552 formulation ratios further enhances in vitro performance. The top three polymers yield a higher signal and stable transgene expression over 20 days in vivo, and a 1.7-fold enhancement over controls. Our facile coupling of synthesis, characterization, and machine analysis provides powerful tools to quantitate performance parameters accelerating next-generation vehicles for nucleic acid medicines.
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Affiliation(s)
- Rishad J Dalal
- Department of Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
| | | | - Michael C Leyden
- Department of Chemical Engineering and Materials Science, University of Minnesota Minneapolis Minnesota 55455 USA
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
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8
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Berger AG, DeLorenzo C, Vo C, Kaskow JA, Nabar N, Hammond PT. Poly(β-aminoester) Physicochemical Properties Govern the Delivery of siRNA from Electrostatically Assembled Coatings. Biomacromolecules 2024; 25:2934-2952. [PMID: 38687965 PMCID: PMC11117021 DOI: 10.1021/acs.biomac.4c00062] [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] [Indexed: 05/02/2024]
Abstract
Localized short interfering RNA (siRNA) therapy has the potential to drive high-specificity molecular-level treatment of a variety of disease states. Unfortunately, effective siRNA therapy suffers from several barriers to its intracellular delivery. Thus, drug delivery systems that package and control the release of therapeutic siRNAs are necessary to overcome these obstacles to clinical translation. Layer-by-layer (LbL) electrostatic assembly of thin film coatings containing siRNA and protonatable, hydrolyzable poly(β-aminoester) (PBAE) polymers is one such drug delivery strategy. However, the impact of PBAE physicochemical properties on the transfection efficacy of siRNA released from LbL thin film coatings has not been systematically characterized. In this study, we investigate the siRNA transfection efficacy of four structurally similar PBAEs in vitro. We demonstrate that small changes in structure yield large changes in physicochemical properties, such as hydrophobicity, pKa, and amine chemical structure, driving differences in the interactions between PBAEs and siRNA in polyplexes and in LbL thin film coatings for wound dressings. In our polymer set, Poly3 forms the most stable interactions with siRNA (Keff,w/w = 0.298) to slow release kinetics and enhance transfection of reporter cells in both colloidal and thin film coating approaches. This is due to its unique physiochemical properties: high hydrophobicity (clog P = 7.86), effective pKa closest to endosomal pH (pKa = 6.21), and high cooperativity in buffering (nhill = 7.2). These properties bestow Poly3 with enhanced endosomal buffering and escape properties. Taken together, this work elucidates the connections between small changes in polymer structure, emergent properties, and polyelectrolyte theory to better understand PBAE transfection efficacy.
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Affiliation(s)
- Adam G. Berger
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Charles DeLorenzo
- Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chau Vo
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Justin A. Kaskow
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Namita Nabar
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Paula T. Hammond
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
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9
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Danaeifar M, Najafi A. Artificial Intelligence and Computational Biology in Gene Therapy: A Review. Biochem Genet 2024:10.1007/s10528-024-10799-1. [PMID: 38635012 DOI: 10.1007/s10528-024-10799-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
One of the trending fields in almost all areas of science and technology is artificial intelligence. Computational biology and artificial intelligence can help gene therapy in many steps including: gene identification, gene editing, vector design, development of new macromolecules and modeling of gene delivery. There are various tools used by computational biology and artificial intelligence in this field, such as genomics, transcriptomic and proteomics data analysis, machine learning algorithms and molecular interaction studies. These tools can introduce new gene targets, novel vectors, optimized experiment conditions, predict the outcomes and suggest the best solutions to avoid undesired immune responses following gene therapy treatment.
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Affiliation(s)
- Mohsen Danaeifar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Science, P.O. Box 19395-5487, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Science, P.O. Box 19395-5487, Tehran, Iran.
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10
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Sánchez-Morán H, Kaar JL, Schwartz DK. Combinatorial High-Throughput Screening of Complex Polymeric Enzyme Immobilization Supports. J Am Chem Soc 2024; 146:9112-9123. [PMID: 38500441 DOI: 10.1021/jacs.3c14273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Recent advances have demonstrated the promise of complex multicomponent polymeric supports to enable supra-biological enzyme performance. However, the discovery of such supports has been limited by time-consuming, low-throughput synthesis and screening. Here, we describe a novel combinatorial and high-throughput platform that enables rapid screening of complex and heterogeneous copolymer brushes as enzyme immobilization supports, named combinatorial high-throughput enzyme support screening (CHESS). Using a 384-well plate format, we synthesized arrays of three-component polymer brushes in the microwells using photoactivated surface-initiated polymerization and immobilized enzymes in situ. The utility of CHESS to identify optimal immobilization supports under thermally and chemically denaturing conditions was demonstrated usingBacillus subtilisLipase A (LipA). The identification of supports with optimal compositions was validated by immobilizing LipA on polymer-brush-modified biocatalyst particles. We further demonstrated that CHESS could be used to predict the optimal composition of polymer brushes a priori for the previously unexplored enzyme, alkaline phosphatase (AlkP). Our findings demonstrate that CHESS represents a predictable and reliable platform for dramatically accelerating the search of chemical compositions for immobilization supports and further facilitates the discovery of biocompatible and stabilizing materials.
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Affiliation(s)
- Héctor Sánchez-Morán
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, Colorado 80309, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, Colorado 80309, United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, Colorado 80309, United States
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11
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Yu H, Liu L, Yin R, Jayapurna I, Wang R, Xu T. Mapping Composition Evolution through Synthesis, Purification, and Depolymerization of Random Heteropolymers. J Am Chem Soc 2024; 146:6178-6188. [PMID: 38387070 PMCID: PMC10921401 DOI: 10.1021/jacs.3c13909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024]
Abstract
Random heteropolymers (RHPs) consisting of three or more comonomers have been routinely used to synthesize functional materials. While increasing the monomer variety diversifies the side-chain chemistry, this substantially expands the sequence space and leads to ensemble-level sequence heterogeneity. Most studies have relied on monomer composition and simulated sequences to design RHPs, but the questions remain unanswered regarding heterogeneities within each RHP ensemble and how closely these simulated sequences reflect the experimental outcomes. Here, we quantitatively mapped out the evolution of monomer compositions in four-monomer-based RHPs throughout a design-synthesis-purification-depolymerization process. By adopting a Jaacks method, we first determined 12 reactivity ratios directly from quaternary methacrylate RAFT copolymerization experiments to account for the influences of competitive monomer addition and the reversible activation/deactivation equilibria. The reliability of in silico analysis was affirmed by a quantitative agreement (<4% difference) between the simulated RHP compositions and the experimental results. Furthermore, we mapped out the conformation distribution within each ensemble in different solvents as a function of monomer chemistry, composition, and segmental characteristics via high-throughput computation based on self-consistent field theory (SCFT). These comprehensive studies confirmed monomer composition as a viable design parameter to engineer RHP-based functional materials as long as the reactivity ratios are accurately determined and the livingness of RHP synthesis is ensured.
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Affiliation(s)
- Hao Yu
- California
Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720, United States
| | - Luofu Liu
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ruilin Yin
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Ivan Jayapurna
- Department
of Materials Science and Engineering, University
of California, Berkeley, Berkeley, California 94720, United States
| | - Rui Wang
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Materials Science and Engineering, University
of California, Berkeley, Berkeley, California 94720, United States
| | - Ting Xu
- California
Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Department
of Materials Science and Engineering, University
of California, Berkeley, Berkeley, California 94720, United States
- Departent
of Materials Science and Engineering, University
of California, Berkeley, Berkeley, California 94720, United States
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12
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Patel RA, Webb MA. Data-Driven Design of Polymer-Based Biomaterials: High-throughput Simulation, Experimentation, and Machine Learning. ACS APPLIED BIO MATERIALS 2024; 7:510-527. [PMID: 36701125 DOI: 10.1021/acsabm.2c00962] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Polymers, with the capacity to tunably alter properties and response based on manipulation of their chemical characteristics, are attractive components in biomaterials. Nevertheless, their potential as functional materials is also inhibited by their complexity, which complicates rational or brute-force design and realization. In recent years, machine learning has emerged as a useful tool for facilitating materials design via efficient modeling of structure-property relationships in the chemical domain of interest. In this Spotlight, we discuss the emergence of data-driven design of polymers that can be deployed in biomaterials with particular emphasis on complex copolymer systems. We outline recent developments, as well as our own contributions and takeaways, related to high-throughput data generation for polymer systems, methods for surrogate modeling by machine learning, and paradigms for property optimization and design. Throughout this discussion, we highlight key aspects of successful strategies and other considerations that will be relevant to the future design of polymer-based biomaterials with target properties.
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Affiliation(s)
- Roshan A Patel
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08540, United States
| | - Michael A Webb
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08540, United States
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13
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Kreofsky NW, Roy P, Brown ME, Perez U, Leighton RE, Frontiera RR, Reineke TM. Cinchona Alkaloid Polymers Demonstrate Highly Efficient Gene Delivery Dependent on Stereochemistry, Methoxy Substitution, and Length. Biomacromolecules 2024; 25:486-501. [PMID: 38150323 DOI: 10.1021/acs.biomac.3c01099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Nucleic acid delivery with cationic polymers is a promising alternative to expensive viral-based methods; however, it often suffers from a lower performance. Herein, we present a highly efficient delivery system based on cinchona alkaloid natural products copolymerized with 2-hydroxyethyl acrylate. Cinchona alkaloids are an attractive monomer class for gene delivery applications, given their ability to bind to DNA via both electrostatics and intercalation. To uncover the structure-activity profile of the system, four structurally similar cinchona alkaloids were incorporated into polymers: quinine, quinidine, cinchonine, and cinchonidine. These polymers differed in the chain length, the presence or absence of a pendant methoxy group, and stereochemistry, all of which were found to alter gene delivery performance and the ways in which the polymers overcome biological barriers to transfection. Longer polymers that contained the methoxy-bearing cinchona alkaloids (i.e., quinine and quinidine) were found to have the best performance. These polymers exhibited the tightest DNA binding, largest and most abundant DNA-polymer complexes, and best endosomal escape thanks to their increased buffering capacity and closest nuclear proximity of the payload. Overall, this work highlights the remarkable efficiency of polymer systems that incorporate cinchona alkaloid natural products while demonstrating the profound impact that small structural changes can have on overcoming biological hurdles associated with gene delivery.
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Affiliation(s)
- Nicholas W Kreofsky
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Punarbasu Roy
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mary E Brown
- University Imaging Centers, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ulises Perez
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ryan E Leighton
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Renee R Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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14
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Hanson MG, Grimme CJ, Kreofsky NW, Panda S, Reineke TM. Blended Block Polycation Micelles Enhance Antisense Oligonucleotide Delivery. Bioconjug Chem 2023; 34:1418-1428. [PMID: 37437196 DOI: 10.1021/acs.bioconjchem.3c00186] [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: 07/14/2023]
Abstract
Nucleic acid-based medicines and vaccines are becoming an important part of our therapeutic toolbox. One key genetic medicine is antisense oligonucleotides (ASOs), which are short single-stranded nucleic acids that downregulate protein production by binding to mRNA. However, ASOs cannot enter the cell without a delivery vehicle. Diblock polymers containing cationic and hydrophobic blocks self-assemble into micelles that have shown improved delivery compared to linear nonmicelle variants. Yet synthetic and characterization bottlenecks have hindered rapid screening and optimization. In this study, we aim to develop a method to increase throughput and discovery of new micelle systems by mixing diblock polymers together to rapidly form new micelle formulations. We synthesized diblocks containing an n-butyl acrylate block chain extended with cationic moieties amino ethyl acrylamide (A), dimethyl amino ethyl acrylamide (D), or morpholino ethyl acrylamide (M). These diblocks were then self-assembled into homomicelles (A100, D100, and M100)), mixed micelles comprising 2 homomicelles (MixR%+R'%), and blended diblock micelles comprising 2 diblocks blended into one micelle (BldR%R'%) and tested for ASO delivery. Interestingly, we observed that mixing or blending M with A (BldA50M50 and MixA50+M50) did not improve transfection efficiency compared to A100; however, when M was mixed with D, there was a significant increase in transfection efficacy for the mixed micelle MixD50+M50 compared to D100. We further examined mixed and blended D systems at different ratios. We observed a large increase in transfection and minimal change in toxicity when M was mixed with D at a low percentage of D incorporation in mixed diblock micelles (i.e., BldD20M80) compared to D100 and MixD20+M80. To understand the cellular mechanisms that may result in these differences, we added proton pump inhibitor Bafilomycin-A1 (Baf-A1) to the transfection experiments. Formulations that contain D decreased in performance in the presence of Baf-A1, indicating that micelles with D rely on the proton sponge effect for endosomal escape more than micelles with A. This result supports our conclusion that M is able to modulate transfection of D, but not with A. This research shows that polymer blending in a manner similar to that of lipids can significantly boost transfection efficiency and is a facile way to increase throughput of testing, optimization, and successful formulation identification for polymeric nucleic acid delivery systems.
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Affiliation(s)
- Mckenna G Hanson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Christian J Grimme
- Department of Chemical Engineering & Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Nicholas W Kreofsky
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Sidharth Panda
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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15
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McDonald SM, Augustine EK, Lanners Q, Rudin C, Catherine Brinson L, Becker ML. Applied machine learning as a driver for polymeric biomaterials design. Nat Commun 2023; 14:4838. [PMID: 37563117 PMCID: PMC10415291 DOI: 10.1038/s41467-023-40459-8] [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: 02/08/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023] Open
Abstract
Polymers are ubiquitous to almost every aspect of modern society and their use in medical products is similarly pervasive. Despite this, the diversity in commercial polymers used in medicine is stunningly low. Considerable time and resources have been extended over the years towards the development of new polymeric biomaterials which address unmet needs left by the current generation of medical-grade polymers. Machine learning (ML) presents an unprecedented opportunity in this field to bypass the need for trial-and-error synthesis, thus reducing the time and resources invested into new discoveries critical for advancing medical treatments. Current efforts pioneering applied ML in polymer design have employed combinatorial and high throughput experimental design to address data availability concerns. However, the lack of available and standardized characterization of parameters relevant to medicine, including degradation time and biocompatibility, represents a nearly insurmountable obstacle to ML-aided design of biomaterials. Herein, we identify a gap at the intersection of applied ML and biomedical polymer design, highlight current works at this junction more broadly and provide an outlook on challenges and future directions.
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Affiliation(s)
| | - Emily K Augustine
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, USA
| | - Quinn Lanners
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Cynthia Rudin
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - L Catherine Brinson
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, USA
| | - Matthew L Becker
- Department of Chemistry, Duke University, Durham, NC, USA.
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, USA.
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16
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Li Y, Wang X, He Z, Johnson M, A S, Lara-Sáez I, Lyu J, Wang W. 3D Macrocyclic Structure Boosted Gene Delivery: Multi-Cyclic Poly(β-Amino Ester)s from Step Growth Polymerization. J Am Chem Soc 2023; 145:17187-17200. [PMID: 37490481 PMCID: PMC10416306 DOI: 10.1021/jacs.3c04191] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Indexed: 07/27/2023]
Abstract
The topological structures of polymers play a critical role in determining their gene delivery efficiency. Exploring novel polymeric structures as gene delivery vectors is thus of great interest. In this work, a new generation of multi-cyclic poly(β-amino ester)s (CPAEs) with unique topology structure was synthesized for the first time via step growth polymerization. Through controlling the occurrence stage of cyclization, three types of CPAEs with rings of different sizes and topologies were obtained. In vitro experiments demonstrated that the CPAEs with macro rings (MCPAEs) significantly boosted the transgene expression comparing to their branched counterparts. Moreover, the MCPAE vector with optimized terminal group efficiently delivered the CRISPR plasmid coding both Staphylococcus aureus Cas9 nuclease and dual guide sgRNAs for gene editing therapy.
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Affiliation(s)
- Yinghao Li
- Research
and Clinical Translation Center of Gene Medicine and Tissue Engineering,
School of Public Health, Anhui University
of Science and Technology, Huainan 232001, China
- Charles
Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Dublin D04V1W8, Ireland
| | - Xianqing Wang
- Charles
Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Dublin D04V1W8, Ireland
| | - Zhonglei He
- Research
and Clinical Translation Center of Gene Medicine and Tissue Engineering,
School of Public Health, Anhui University
of Science and Technology, Huainan 232001, China
- Charles
Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Dublin D04V1W8, Ireland
| | - Melissa Johnson
- Charles
Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Dublin D04V1W8, Ireland
| | - Sigen A
- Charles
Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Dublin D04V1W8, Ireland
- School
of Medicine, Anhui University of Science
and Technology, Huainan 232001, China
| | - Irene Lara-Sáez
- Charles
Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Dublin D04V1W8, Ireland
| | - Jing Lyu
- Charles
Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Dublin D04V1W8, Ireland
| | - Wenxin Wang
- Research
and Clinical Translation Center of Gene Medicine and Tissue Engineering,
School of Public Health, Anhui University
of Science and Technology, Huainan 232001, China
- Charles
Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Dublin D04V1W8, Ireland
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17
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Roy P, Kreofsky NW, Brown ME, Van Bruggen C, Reineke TM. Enhancing pDNA Delivery with Hydroquinine Polymers by Modulating Structure and Composition. JACS AU 2023; 3:1876-1889. [PMID: 37502160 PMCID: PMC10369409 DOI: 10.1021/jacsau.3c00126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/26/2023] [Accepted: 06/12/2023] [Indexed: 07/29/2023]
Abstract
Quinine is a promising natural product building block for polymer-based nucleic acid delivery vehicles as its structure enables DNA binding through both intercalation and electrostatic interactions. However, studies exploring the potential of quinine-based polymers for nucleic acid delivery applications (transfection) are limited. In this work, we used a hydroquinine-functionalized monomer, HQ, with 2-hydroxyethyl acrylate to create a family of seven polymers (HQ-X, X = mole percentage of HQ), with mole percentages of HQ ranging from 12 to 100%. We developed a flow cytometer-based assay for studying the polymer-pDNA complexes (polyplex particles) directly and demonstrate that polymer composition and monomer structure influence polyplex characteristics such as the pDNA loading and the extent of adsorption of serum proteins on polyplex particles. Biological delivery experiments revealed that maximum transgene expression, outperforming commercial controls, was achieved with HQ-25 and HQ-35 as these two variants sustained gene expression over 96 h. HQ-44, HQ-60, and HQ-100 were not successful in inducing transgene expression, despite being able to deliver pDNA into the cells, highlighting that the release of pDNA is likely the bottleneck in transfection for polymers with higher HQ content. Using confocal imaging, we quantified the extent of colocalization between pDNA and lysosomes, proving the remarkable endosomal escape capabilities of the HQ-X polymers. Overall, this study demonstrates the advantages of HQ-X polymers as well as provides guiding principles for improving the monomer structure and polymer composition, supporting the development of the next generation of polymer-based nucleic acid delivery vehicles harnessing the power of natural products.
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Affiliation(s)
- Punarbasu Roy
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Nicholas W. Kreofsky
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mary E. Brown
- University
Imaging Centers, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Craig Van Bruggen
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Theresa M. Reineke
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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18
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Cheng F, Su T, Zhou S, Liu X, Yang S, Lin S, Guo W, Zhu G. Single-dose injectable nanovaccine-in-hydrogel for robust immunotherapy of large tumors with abscopal effect. SCIENCE ADVANCES 2023; 9:eade6257. [PMID: 37450588 PMCID: PMC10348685 DOI: 10.1126/sciadv.ade6257] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 06/09/2023] [Indexed: 07/18/2023]
Abstract
Current cancer immunotherapy [e.g., immune checkpoint blockade (ICB)] only benefits small subsets of patients, largely due to immunosuppressive tumor microenvironment (TME). In situ tumor vaccination can reduce TME immunosuppression and thereby improve cancer immunotherapy. Here, we present single-dose injectable (nanovaccines + ICBs)-in-hydrogel (NvIH) for robust immunotherapy of large tumors with abscopal effect. NvIH is thermo-responsive hydrogel co-encapsulated with ICB antibodies and novel polymeric nanoparticles loaded with three immunostimulatory agonists for Toll-like receptors 7/8/9 (TLR7/8/9) and stimulator of interferon genes (STING). Upon in situ tumor vaccination, NvIH undergoes rapid sol-to-gel transformation, prolongs tumor retention, sustains the release of immunotherapeutics, and reduces acute systemic inflammation. In multiple poorly immunogenic tumor models, single-dose NvIH reduces multitier TME immunosuppression, elicits potent TME and systemic innate and adaptive antitumor immunity with memory, and regresses both local (vaccinated) and distant large tumors with abscopal effect, including distant orthotopic glioblastoma. Overall, NvIH holds great potential for tumor immunotherapy.
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Affiliation(s)
- Furong Cheng
- Translational Medicine Center, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, Institute for Structural Biology and Drug Discovery, School of Pharmacy, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Ting Su
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, Institute for Structural Biology and Drug Discovery, School of Pharmacy, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Shurong Zhou
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, Institute for Structural Biology and Drug Discovery, School of Pharmacy, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiang Liu
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, Institute for Structural Biology and Drug Discovery, School of Pharmacy, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Suling Yang
- Department of Pharmaceutical Sciences, College of Pharmacy, Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Weisheng Guo
- Translational Medicine Center, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Guizhi Zhu
- Department of Pharmaceutical Sciences, College of Pharmacy, Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
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19
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Grimme CJ, Hanson MG, Reineke TM. Enhanced ASO-Mediated Gene Silencing with Lipophilic pH-Responsive Micelles. Bioconjug Chem 2023. [PMID: 37384839 DOI: 10.1021/acs.bioconjchem.3c00133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Herein, we examine the ASO-mediated gene silencing efficiency of pH-responsive micelles, by incorporating 2-(diisopropylamino)ethyl methacrylate (DIP) into the micelle core and comparing physical and biological properties with non-pH-responsive micelles. Additionally, the lipophilic effect of the micelle cores was examined in both types of micelles. Varying lipophilicity was achieved by varying alkyl monomer chain lengths─butyl (4), lauryl (12), and stearyl (18) methacrylate. Each of the micelles formed within our family offered the added benefit of well-defined and uniform templates for loading antisense oligonucleotide (ASO) payloads. Overall, the micelles followed previously established trends of outperforming their linear polymer (nonmicelle) analogs and ASO only control. More specifically, the highest performing micelles were the pH-responsive micelles with longer alkyl chains or higher lipophilicity─D-DIP+LMA and D-DIP+SMA (∼90% silencing). These two micelles demonstrated silencing efficiencies similar to Jet-PEI and Lipofectamine 2000 and caused lower toxicity than Lipofectamine 2000. The shortest alkyl chain pH-responsive micelle, D-DIP+BMA (64%), displayed strong gene silencing similar to that about that of its non-pH-responsive micelle, D-BMA (68%), and the pH-responsive micelle without an alkyl chain incorporated, D-DIP (59%). This work illuminates a minimum alkyl chain length dependence to allow gene silencing within our micelle family. However, including only longer alkyl chains into the micelle core without the pH-responsive unit DIP had a hindering effect, thus demonstrating the requirement of the DIP unit when including longer alkyl chain lengths. This work demonstrates the exemplary gene silencing efficiencies of polymeric micelles and uncovers the relationship between pH responsiveness and performance with lipophilic polymer micelles for enhancing ASO-mediated gene silencing.
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Affiliation(s)
- Christian J Grimme
- Department of Chemical Engineering & Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Mckenna G Hanson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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20
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Greenberg ZF, Graim KS, He M. Towards artificial intelligence-enabled extracellular vesicle precision drug delivery. Adv Drug Deliv Rev 2023:114974. [PMID: 37356623 DOI: 10.1016/j.addr.2023.114974] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Extracellular Vesicles (EVs), particularly exosomes, recently exploded into nanomedicine as an emerging drug delivery approach due to their superior biocompatibility, circulating stability, and bioavailability in vivo. However, EV heterogeneity makes molecular targeting precision a critical challenge. Deciphering key molecular drivers for controlling EV tissue targeting specificity is in great need. Artificial intelligence (AI) brings powerful prediction ability for guiding the rational design of engineered EVs in precision control for drug delivery. This review focuses on cutting-edge nano-delivery via integrating large-scale EV data with AI to develop AI-directed EV therapies and illuminate the clinical translation potential. We briefly review the current status of EVs in drug delivery, including the current frontier, limitations, and considerations to advance the field. Subsequently, we detail the future of AI in drug delivery and its impact on precision EV delivery. Our review discusses the current universal challenge of standardization and critical considerations when using AI combined with EVs for precision drug delivery. Finally, we will conclude this review with a perspective on future clinical translation led by a combined effort of AI and EV research.
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Affiliation(s)
- Zachary F Greenberg
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, 32610, USA
| | - Kiley S Graim
- Department of Computer & Information Science & Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, Florida, 32610, USA
| | - Mei He
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, 32610, USA.
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21
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Meyer T, Ramirez C, Tamasi MJ, Gormley AJ. A User's Guide to Machine Learning for Polymeric Biomaterials. ACS POLYMERS AU 2023; 3:141-157. [PMID: 37065715 PMCID: PMC10103193 DOI: 10.1021/acspolymersau.2c00037] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 11/18/2022]
Abstract
The development of novel biomaterials is a challenging process, complicated by a design space with high dimensionality. Requirements for performance in the complex biological environment lead to difficult a priori rational design choices and time-consuming empirical trial-and-error experimentation. Modern data science practices, especially artificial intelligence (AI)/machine learning (ML), offer the promise to help accelerate the identification and testing of next-generation biomaterials. However, it can be a daunting task for biomaterial scientists unfamiliar with modern ML techniques to begin incorporating these useful tools into their development pipeline. This Perspective lays the foundation for a basic understanding of ML while providing a step-by-step guide to new users on how to begin implementing these techniques. A tutorial Python script has been developed walking users through the application of an ML pipeline using data from a real biomaterial design challenge based on group's research. This tutorial provides an opportunity for readers to see and experiment with ML and its syntax in Python. The Google Colab notebook can be easily accessed and copied from the following URL: www.gormleylab.com/MLcolab.
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Affiliation(s)
- Travis
A. Meyer
- Department of Biomedical
Engineering, Rutgers, The State University
of New Jersey, Piscataway, New Jersey 08854, United States
| | - Cesar Ramirez
- Department of Biomedical
Engineering, Rutgers, The State University
of New Jersey, Piscataway, New Jersey 08854, United States
| | - Matthew J. Tamasi
- Department of Biomedical
Engineering, Rutgers, The State University
of New Jersey, Piscataway, New Jersey 08854, United States
| | - Adam J. Gormley
- Department of Biomedical
Engineering, Rutgers, The State University
of New Jersey, Piscataway, New Jersey 08854, United States
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22
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Yao Y, Ko Y, Grasman G, Raymond JE, Lahann J. The steep road to nonviral nanomedicines: Frequent challenges and culprits in designing nanoparticles for gene therapy. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2023; 14:351-361. [PMID: 36959977 PMCID: PMC10028570 DOI: 10.3762/bjnano.14.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The potential of therapeutically loaded nanoparticles (NPs) has been successfully demonstrated during the last decade, with NP-mediated nonviral gene delivery gathering significant attention as highlighted by the broad clinical acceptance of mRNA-based COVID-19 vaccines. A significant barrier to progress in this emerging area is the wild variability of approaches reported in published literature regarding nanoparticle characterizations. Here, we provide a brief overview of the current status and outline important concerns regarding the need for standardized protocols to evaluate NP uptake, NP transfection efficacy, drug dose determination, and variability of nonviral gene delivery systems. Based on these concerns, we propose wide adherence to multimodal, multiparameter, and multistudy analysis of NP systems. Adoption of these proposed approaches will ensure improved transparency, provide a better basis for interlaboratory comparisons, and will simplify judging the significance of new findings in a broader context, all critical requirements for advancing the field of nonviral gene delivery.
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Affiliation(s)
- Yao Yao
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yeongun Ko
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- School of Polymer Science and Engineering, Chonnam National University, Buk-gu, Gwangju 61186, South Korea
| | - Grant Grasman
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffery E Raymond
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joerg Lahann
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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23
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Heredero M, Beloqui A. Enzyme-Polymer Conjugates for Tuning, Enhancing, and Expanding Biocatalytic Activity. Chembiochem 2023; 24:e202200611. [PMID: 36507915 DOI: 10.1002/cbic.202200611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Combining polymers with functional proteins is an approach that has brought several successful stories in the field of biomedicine with PEGylated therapeutic proteins. The latest advances in polymer chemistry have facilitated the expansion of protein-polymer hybrids to other research areas such as biocatalysis. Polymers can impart stability and novel functionalities to the enzyme of interest, thereby improving the catalytic performance of a given reaction. In this review, we have revisited the main methodologies currently used for the synthesis of enzyme-polymer hybrids, unveiling the interplay between the configuration and the composition of the assembled structure and the eventual traits of the hybrid. Finally, the latest advances, such as the assembly of polymer-based chemoenzymatic nanoreactors and the use of deep learning methodologies to achieve the most suitable polymer compositions for catalysis, are discussed.
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Affiliation(s)
- Marcos Heredero
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel Lardizabal 3, 20018, Donostia-San Sebastián, Spain
| | - Ana Beloqui
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel Lardizabal 3, 20018, Donostia-San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, 48009, Bilbao, Spain
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24
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Jayapurna I, Ruan Z, Eres M, Jalagam P, Jenkins S, Xu T. Sequence Design of Random Heteropolymers as Protein Mimics. Biomacromolecules 2023; 24:652-660. [PMID: 36638823 PMCID: PMC9930114 DOI: 10.1021/acs.biomac.2c01036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Random heteropolymers (RHPs) have been computationally designed and experimentally shown to recapitulate protein-like phase behavior and function. However, unlike proteins, RHP sequences are only statistically defined and cannot be sequenced. Recent developments in reversible-deactivation radical polymerization allowed simulated polymer sequences based on the well-established Mayo-Lewis equation to more accurately reflect ground-truth sequences that are experimentally synthesized. This led to opportunities to perform bioinformatics-inspired analysis on simulated sequences to guide the design, synthesis, and interpretation of RHPs. We compared batches on the order of 10000 simulated RHP sequences that vary by synthetically controllable and measurable RHP characteristics such as chemical heterogeneity and average degree of polymerization. Our analysis spans across 3 levels: segments along a single chain, sequences within a batch, and batch-averaged statistics. We discuss simulator fidelity and highlight the importance of robust segment definition. Examples are presented that demonstrate the use of simulated sequence analysis for in-silico iterative design to mimic protein hydrophobic/hydrophilic segment distributions in RHPs and compare RHP and protein sequence segments to explain experimental results of RHPs that mimic protein function. To facilitate the community use of this workflow, the simulator and analysis modules have been made available through an open source toolkit, the RHPapp.
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Affiliation(s)
- Ivan Jayapurna
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Zhiyuan Ruan
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Marco Eres
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Prajna Jalagam
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Spencer Jenkins
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ting Xu
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, California 94720, United States.,Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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25
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Su DD, Ali LMA, Coste M, Laroui N, Bessin Y, Barboiu M, Bettache N, Ulrich S. Structure-Activity Relationships in Nucleic-Acid-Templated Vectors Based on Peptidic Dynamic Covalent Polymers. Chemistry 2023; 29:e202202921. [PMID: 36342312 PMCID: PMC10108046 DOI: 10.1002/chem.202202921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]
Abstract
The use of nucleic acids as templates, which can trigger the self-assembly of their own vectors represent an emerging, simple and versatile, approach toward the self-fabrication of tailored nucleic acids delivery vectors. However, the structure-activity relationships governing this complex templated self-assembly process that accompanies the complexation of nucleic acids remains poorly understood. Herein, the class of arginine-rich dynamic covalent polymers (DCPs) composed of different monomers varying the number and position of arginines were studied. The combinations that lead to nucleic acid complexation, in saline buffer, using different templates, from short siRNA to long DNA, are described. Finally, a successful peptidic DCP featuring six-arginine repeating unit that promote the safe and effective delivery of siRNA in live cancer cells was identified.
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Affiliation(s)
- Dan-Dan Su
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France.,Institut Européen des Membranes, Adaptive Supramolecular Nanosystems Group, Université de Montpellier, ENSCM, CNRS, Place Eugène Bataillon, CC 047, 34095, Montpellier, France
| | - Lamiaa M A Ali
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France.,Department of Biochemistry Medical Research Institute, University of Alexandria, 21561, Alexandria, Egypt
| | - Maëva Coste
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France
| | - Nabila Laroui
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France
| | - Yannick Bessin
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France
| | - Mihail Barboiu
- Institut Européen des Membranes, Adaptive Supramolecular Nanosystems Group, Université de Montpellier, ENSCM, CNRS, Place Eugène Bataillon, CC 047, 34095, Montpellier, France
| | - Nadir Bettache
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France
| | - Sébastien Ulrich
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France
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26
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Hausig-Punke F, Dekevic G, Sobotta FH, Solomun JI, Richter F, Salzig D, Traeger A, Brendel JC. Efficient Transfection via an Unexpected Mechanism by Near Neutral Polypiperazines with Tailored Response to Endosomal pH. Macromol Biosci 2023; 23:e2200517. [PMID: 36655803 DOI: 10.1002/mabi.202200517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Indexed: 01/20/2023]
Abstract
Cationic pH-responsive polymers promise to overcome critical challenges in cellular delivery. Ideally, the polymers become selectively charged along the endosomal pathway disturbing only the local membrane and avoiding unintended interactions or cytotoxic side effects at physiological conditions. Polypiperazines represent a novel, hydrophilic class of pH-responsive polymers whose response can be tuned within the relevant pH range (5-7.4). The authors discovered that the polypiperazines are effectively binding plasmid DNA (pDNA) and demonstrate high efficiency in transfection. By design of experiments (DoE), a wide parameter space (pDNA and polymer concentration) is screened to identify the range of effective concentrations for transfection. An isopropyl modified polypiperazine is highly efficient over a wide range of concentrations outperforming linear polyethylenimine (l-PEI, 25 kDa) in regions of low N*/P ratios. A quantitative polymerase chain reaction (qPCR) surprisingly revealed that the pDNA within the piperazine-based polyplexes can be amplified in contrast to polyplexes based on l-PEI. The pDNA must therefore be more accessible and bound differently than for other known transfection polymers. Considering the various opportunities to further optimize their structure, polypiperazines represent a promising platform for designing effective soluble polymeric vectors, which are charge-neutral at physiological conditions.
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Affiliation(s)
- Franziska Hausig-Punke
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743, Jena, Germany
| | - Gregor Dekevic
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390, Giessen, Germany
| | - Fabian H Sobotta
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743, Jena, Germany
| | - Jana I Solomun
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743, Jena, Germany
| | - Friederike Richter
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743, Jena, Germany
| | - Denise Salzig
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390, Giessen, Germany
| | - Anja Traeger
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743, Jena, Germany.,Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743, Jena, Germany
| | - Johannes C Brendel
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743, Jena, Germany.,Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743, Jena, Germany
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27
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Kapelner RA, Fisher RS, Elbaum-Garfinkle S, Obermeyer AC. Protein charge parameters that influence stability and cellular internalization of polyelectrolyte complex micelles. Chem Sci 2022; 13:14346-14356. [PMID: 36545145 PMCID: PMC9749388 DOI: 10.1039/d2sc00192f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Proteins are an important class of biologics, but there are several recurring challenges to address when designing protein-based therapeutics. These challenges include: the propensity of proteins to aggregate during formulation, relatively low loading in traditional hydrophobic delivery vehicles, and inefficient cellular uptake. This last criterion is particularly challenging for anionic proteins as they cannot cross the anionic plasma membrane. Here we investigated the complex coacervation of anionic proteins with a block copolymer of opposite charge to form polyelectrolyte complex (PEC) micelles for use as a protein delivery vehicle. Using genetically modified variants of the model protein green fluorescent protein (GFP), we evaluated the role of protein charge and charge localization in the formation and stability of PEC micelles. A neutral-cationic block copolymer, poly(oligoethylene glycol methacrylate-block-quaternized 4-vinylpyridine), POEGMA79-b-qP4VP175, was prepared via RAFT polymerization for complexation and microphase separation with the panel of engineered anionic GFPs. We found that isotropically supercharged proteins formed micelles at higher ionic strength relative to protein variants with charge localized to a polypeptide tag. We then studied GFP delivery by PEC micelles and found that they effectively delivered the protein cargo to mammalian cells. However, cellular delivery varied as a function of protein charge and charge distribution and we found an inverse relationship between the PEC micelle critical salt concentration and delivery efficiency. This model system has highlighted the potential of polyelectrolyte complexes to deliver anionic proteins intracellularly. Using this model system, we have identified requirements for the formation of PEC micelles that are stable at physiological ionic strength and that smaller protein-polyelectrolyte complexes effectively deliver proteins to Jurkat cells.
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Affiliation(s)
- Rachel A Kapelner
- Department of Chemical Engineering, Columbia University New York NY 10027 USA +1-212-853-1215
| | - Rachel S Fisher
- Department of Chemical Engineering, Columbia University New York NY 10027 USA +1-212-853-1215
- Structural Biology Initiative, CUNY Advanced Science Research Center New York NY USA
| | - Shana Elbaum-Garfinkle
- Structural Biology Initiative, CUNY Advanced Science Research Center New York NY USA
- PhD Programs in Biochemistry and Biology at the Graduate Center, City University of New York NY USA
| | - Allie C Obermeyer
- Department of Chemical Engineering, Columbia University New York NY 10027 USA +1-212-853-1215
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28
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Dalal RJ, Ohnsorg ML, Panda S, Reineke TM. Hydrophilic Surface Modification of Cationic Unimolecular Bottlebrush Vectors Moderate pDNA and RNP Bottleplex Stability and Delivery Efficacy. Biomacromolecules 2022; 23:5179-5192. [PMID: 36445696 DOI: 10.1021/acs.biomac.2c00999] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A cationic unimolecular bottlebrush polymer with chemically modified end-groups was synthesized to understand the impact of hydrophilicity on colloidal stability, nucleic acid delivery performance, and toxicity. The bottlebrush polymer template was synthesized using grafting-through techniques and was therefore composed of a polynorbornene backbone with poly(2-(dimethylamino)ethyl methacrylate) side chains with dodecyl trithiocarbonate end-groups. Postpolymerization modification was performed to fully remove the end-groups or install hydroxy and methoxy poly(ethylene glycol) functional groups on the bottlebrush exterior. The bottlebrush family was preformulated with biological payloads of pDNA and CRISPR-Cas9 RNP in both water and PBS to understand binding, aggregation kinetics, cytotoxicity, and delivery efficacy. Increasing end-group hydrophilicity and preformulation of bottleplexes in PBS increased colloidal stability and cellular viability; however, this did not always result in increased transfection efficiency. The bottlebrush family exemplifies how formulation conditions, polymer loading, and end-group functionality of bottlebrushes can be tuned to balance expression with cytotoxicity ratios and result in enhanced overall performance.
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Affiliation(s)
- Rishad J Dalal
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Monica L Ohnsorg
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sidharth Panda
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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29
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Hasanzadeh A, Hamblin MR, Kiani J, Noori H, Hardie JM, Karimi M, Shafiee H. Could artificial intelligence revolutionize the development of nanovectors for gene therapy and mRNA vaccines? NANO TODAY 2022; 47:101665. [PMID: 37034382 PMCID: PMC10081506 DOI: 10.1016/j.nantod.2022.101665] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Gene therapy enables the introduction of nucleic acids like DNA and RNA into host cells, and is expected to revolutionize the treatment of a wide range of diseases. This growth has been further accelerated by the discovery of CRISPR/Cas technology, which allows accurate genomic editing in a broad range of cells and organisms in vitro and in vivo. Despite many advances in gene delivery and the development of various viral and non-viral gene delivery vectors, the lack of highly efficient non-viral systems with low cellular toxicity remains a challenge. The application of cutting-edge technologies such as artificial intelligence (AI) has great potential to find new paradigms to solve this issue. Herein, we review AI and its major subfields including machine learning (ML), neural networks (NNs), expert systems, deep learning (DL), computer vision and robotics. We discuss the potential of AI-based models and algorithms in the design of targeted gene delivery vehicles capable of crossing extracellular and intracellular barriers by viral mimicry strategies. We finally discuss the role of AI in improving the function of CRISPR/Cas systems, developing novel nanobots, and mRNA vaccine carriers.
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Affiliation(s)
- Akbar Hasanzadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
- Radiation Biology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Jafar Kiani
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Noori
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Joseph M. Hardie
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02139 USA
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran 141556559, Iran
- Applied Biotechnology Research Centre, Tehran Medical Science, Islamic Azad University, Tehran 1584743311, Iran
| | - Hadi Shafiee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02139 USA
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30
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Terzioğlu İ, Ventura-Hunter C, Ulbrich J, Saldívar-Guerra E, Schubert US, Guerrero-Sánchez C. Automated Parallel Dialysis for Purification of Polymers. Polymers (Basel) 2022; 14:polym14224835. [PMID: 36432962 PMCID: PMC9697721 DOI: 10.3390/polym14224835] [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: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022] Open
Abstract
The implementation of a dialysis method for the simultaneous purification of different polymer materials in a commercially available automated parallel synthesizer (APS) is discussed. The efficiency of this "unattended" automated parallel dialysis (APD) method was investigated by means of proton nuclear magnetic resonance (1H-NMR) measurements, which confirmed that the method enables the removal of up to 99% of the unreacted monomer derived from the synthesis of the corresponding polymers in the APS. Size-exclusion chromatography (SEC) revealed that the molar mass and molar mass distribution of the investigated polymers did not undergo significant changes after the application of the APD method. The method discussed herein can be regarded as a good alternative to the "unattended" and reliable purification of polymer libraries prepared in APS. This method may be useful for overcoming current limitations of high-throughput/-output (HT/O) synthesis of polymer libraries, where purification of the generated materials currently represents a significant constraint for establishing fully automated experimental workflows necessary to advance towards a full digitalization of research and development of new polymers for diverse applications.
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Affiliation(s)
- İpek Terzioğlu
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743 Jena, Germany
| | - Carolina Ventura-Hunter
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743 Jena, Germany
- Polymerization Processes Department, Centro de Investigación en Química Aplicada (CIQA), Blvd. Enrique Reyna No. 140, Saltillo 25294, Coahuila, Mexico
| | - Jens Ulbrich
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743 Jena, Germany
| | - Enrique Saldívar-Guerra
- Polymerization Processes Department, Centro de Investigación en Química Aplicada (CIQA), Blvd. Enrique Reyna No. 140, Saltillo 25294, Coahuila, Mexico
| | - Ulrich S. Schubert
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743 Jena, Germany
| | - Carlos Guerrero-Sánchez
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743 Jena, Germany
- Correspondence:
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31
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Li Y, He Z, Lyu J, Wang X, Qiu B, Lara-Sáez I, Zhang J, Zeng M, Xu Q, A S, Curtin JF, Wang W. Hyperbranched Poly(β-amino ester)s (HPAEs) Structure Optimisation for Enhanced Gene Delivery: Non-Ideal Termination Elimination. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12213892. [PMID: 36364669 PMCID: PMC9656648 DOI: 10.3390/nano12213892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/29/2022] [Accepted: 11/02/2022] [Indexed: 05/31/2023]
Abstract
Many polymeric gene delivery nano-vectors with hyperbranched structures have been demonstrated to be superior to their linear counterparts. The higher delivery efficacy is commonly attributed to the abundant terminal groups of branched polymers, which play critical roles in cargo entrapment, material-cell interaction, and endosome escape. Hyperbranched poly(β-amino ester)s (HPAEs) have developed as a class of safe and efficient gene delivery vectors. Although numerous research has been conducted to optimise the HPAE structure for gene delivery, the effect of the secondary amine residue on its backbone monomer, which is considered the non-ideal termination, has never been optimised. In this work, the effect of the non-ideal termination was carefully evaluated. Moreover, a series of HPAEs with only ideal terminations were synthesised by adjusting the backbone synthesis strategy to further explore the merits of hyperbranched structures. The HPAE obtained from modified synthesis methods exhibited more than twice the amounts of the ideal terminal groups compared to the conventional ones, determined by NMR. Their transfection performance enhanced significantly, where the optimal HPAE candidates developed in this study outperformed leading commercial benchmarks for DNA delivery, including Lipofectamine 3000, jetPEI, and jetOPTIMUS.
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Affiliation(s)
- Yinghao Li
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Zhonglei He
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- BioPlasma Research Group, School of Food Science and Environmental Health, Technological University Dublin, D07 H6K8 Dublin, Ireland
| | - Jing Lyu
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Xianqing Wang
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Bei Qiu
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Irene Lara-Sáez
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Jing Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, China
| | - Ming Zeng
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou Overseas Chinese Hospital, Guangzhou 510630, China
| | - Qian Xu
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Sigen A
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - James F. Curtin
- BioPlasma Research Group, School of Food Science and Environmental Health, Technological University Dublin, D07 H6K8 Dublin, Ireland
- Faculty of Engineering and Built Environment, Technological University Dublin, D07 H6K8 Dublin, Ireland
| | - Wenxin Wang
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
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32
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Goswami PP, Deshpande T, Rotake DR, Singh SG. Near perfect classification of cardiac biomarker Troponin-I in human serum assisted by SnS2-CNT composite, explainable ML, and operating-voltage-selection-algorithm. Biosens Bioelectron 2022; 220:114915. [DOI: 10.1016/j.bios.2022.114915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/03/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
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33
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Zhou L, Emenuga M, Kumar S, Lamantia Z, Figueiredo M, Emrick T. Designing Synthetic Polymers for Nucleic Acid Complexation and Delivery: From Polyplexes to Micelleplexes to Triggered Degradation. Biomacromolecules 2022; 23:4029-4040. [PMID: 36125365 DOI: 10.1021/acs.biomac.2c00767] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gene delivery as a therapeutic tool continues to advance toward impacting human health, with several gene therapy products receiving FDA approval over the past 5 years. Despite this important progress, the safety and efficacy of gene therapy methodology requires further improvement to ensure that nucleic acid therapeutics reach the desired targets while minimizing adverse effects. Synthetic polymers offer several enticing features as nucleic acid delivery vectors due to their versatile functionalities and architectures and the ability of synthetic chemists to rapidly build large libraries of polymeric candidates equipped for DNA/RNA complexation and transport. Current synthetic designs are pursuing challenging objectives that seek to improve transfection efficiency and, at the same time, mitigate cytotoxicity. This Perspective will describe recent work in polymer-based gene complexation and delivery vectors in which cationic polyelectrolytes are modified synthetically by introduction of additional components─including hydrophobic, hydrophilic, and fluorinated units─as well as embedding of degradable linkages within the macromolecular structure. As will be seen, recent advances employing these emerging design strategies are promising with respect to their excellent biocompatibility and transfection capability, suggesting continued promise of synthetic polymer gene delivery vectors going forward.
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Affiliation(s)
- Le Zhou
- Polymer Science & Engineering Department, Conte Center for Polymer Research, University of Massachusetts, 120 Governors Drive, Amherst, Massachusetts 01003, United States
| | - Miracle Emenuga
- Polymer Science & Engineering Department, Conte Center for Polymer Research, University of Massachusetts, 120 Governors Drive, Amherst, Massachusetts 01003, United States
| | - Shreya Kumar
- Department of Basic Medical Sciences, Purdue University, 625 Harrison Street, West Lafayette, Indiana 47907, United States
| | - Zachary Lamantia
- Department of Basic Medical Sciences, Purdue University, 625 Harrison Street, West Lafayette, Indiana 47907, United States
| | - Marxa Figueiredo
- Department of Basic Medical Sciences, Purdue University, 625 Harrison Street, West Lafayette, Indiana 47907, United States
| | - Todd Emrick
- Polymer Science & Engineering Department, Conte Center for Polymer Research, University of Massachusetts, 120 Governors Drive, Amherst, Massachusetts 01003, United States
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34
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Horn JM, Zhu Y, Ahn SY, Obermeyer AC. Self-assembly of globular proteins with intrinsically disordered protein polyelectrolytes and block copolymers. SOFT MATTER 2022; 18:5759-5769. [PMID: 35912826 PMCID: PMC9446422 DOI: 10.1039/d2sm00415a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Intrinsically disordered polypeptides are a versatile class of materials, combining the biocompatibility of peptides with the disordered structure and diverse phase behaviors of synthetic polymers. Synthetic polyelectrolytes are capable of complex phase behavior when mixed with oppositely charged polyelectrolytes, facilitating nanoparticle formation and bulk phase separation. However, there has been limited exploration of intrinsically disordered protein polyelectrolytes as potential bio-based replacements for synthetic polyelectrolytes. Here, we produce negatively charged, intrinsically disordered polypeptides, capable of high-yield expression in E. coli and use this intrinsically disordered peptide to produce entirely protein-based polyelectrolyte complexes. The complexes display rich phase behavior, showing sensitivity to charge density, salt concentration, temperature, and charge fraction. We characterize this behavior through a combination of turbidity assays, dynamic light scattering, and transmission electron microscopy. The robust expression profile and stimuli-responsive phase behavior of the intrinsically disordered peptides demonstrates their potential as easily producible, biocompatible substitutes for synthetic polyelectrolytes.
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Affiliation(s)
- Justin M Horn
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
| | - Yuncan Zhu
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
| | - So Yeon Ahn
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
| | - Allie C Obermeyer
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
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35
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Cunitz V, Stacy E, Jankoski P, Clemons T. Machine learning makes magnificent macromolecules for medicine. MATTER 2022; 5:2558-2561. [PMID: 38827387 PMCID: PMC11142474 DOI: 10.1016/j.matt.2022.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
At the University of Minnesota, scientists explore the application of machine learning to screen a multiparametric library of polymers to investigate the relationship between polymer attributes, payload type, and biological outcomes to optimize polymeric vector development for delivery of nucleic acid payloads.
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Affiliation(s)
- Veronica Cunitz
- School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
- Department of Chemical Engineering, The University of Mississippi, Oxford, MS 38677, USA
- These authors contributed equally
| | - Evan Stacy
- School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
- These authors contributed equally
| | - Penelope Jankoski
- School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
- These authors contributed equally
| | - Tristan Clemons
- School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
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36
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Grimme CJ, Hanson MG, Corcoran LG, Reineke TM. Polycation Architecture Affects Complexation and Delivery of Short Antisense Oligonucleotides: Micelleplexes Outperform Polyplexes. Biomacromolecules 2022; 23:3257-3271. [PMID: 35862267 DOI: 10.1021/acs.biomac.2c00338] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein, we examine the complexation and biological delivery of a short single-stranded antisense oligonucleotide (ASO) payload with four polymer derivatives that form two architectural variants (polyplexes and micelleplexes): a homopolymer poly(2-dimethylaminoethyl methacrylate) (D), a diblock polymer poly(ethylene glycol)methylether methacrylate-block-poly(2-dimethylaminoethyl methacrylate) (ObD), and two micelle-forming variants, poly(2-dimethylaminoethyl methacrylate)-block-poly(n-butyl methacrylate) (DB) and poly(ethylene glycol)methylether methacrylate-block-poly(2-dimethylaminoethyl methacrylate)-block-poly(n-butyl methacrylate) (ObDB). Both polyplexes and micelleplexes complexed ASOs, and the incorporation of an Ob brush enhances colloidal stability. Micellplexes are templated by the size and shape of the unloaded micelle and that micelle-ASO complexation is not sensitive to formulation/mixing order, allowing ease, versatility, and reproducibility in packaging short oligonucleotides. The DB micelleplexes promoted the largest gene silencing, internalization, and tolerable toxicity while the ObDB micelleplexes displayed enhanced colloidal stability and highly efficient payload trafficking despite having lower cellular uptake. Overall, this work demonstrates that cationic micelles are superior delivery vehicles for ASOs denoting the importance of vehicle architecture in biological performance.
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Affiliation(s)
- Christian J Grimme
- Department of Chemical Engineering & Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Mckenna G Hanson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Louis G Corcoran
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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37
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A Microfluidic System of Gene Transfer by Ultrasound. MICROMACHINES 2022; 13:mi13071126. [PMID: 35888943 PMCID: PMC9318161 DOI: 10.3390/mi13071126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/05/2022] [Accepted: 07/12/2022] [Indexed: 01/29/2023]
Abstract
Ultrasonic gene transfer has advantages beyond other cell transfer techniques because ultrasound does not directly act on cells, but rather pushes the gene fragments around the cells into cells through an acoustic hole effect. Most examples reported were carried out in macro volumes with conventional ultrasonic equipment. In the present study, a MEMS focused ultrasonic transducer based on piezoelectric thin film with flexible substrate was integrated with microchannels to form a microfluidic system of gene transfer. The core part of the system is a bowl-shaped curved piezoelectric film structure that functions to focus ultrasonic waves automatically. Therefore, the low input voltage and power can obtain the sound pressure exceeding the cavitation threshold in the local area of the microchannel in order to reduce the damage to cells. The feasibility of the system is demonstrated by finite element simulation and an integrated system of MEMS ultrasonic devices and microchannels are developed to successfully carry out the ultrasonic gene transfection experiments for HeLa cells. The results show that having more ultrasonic transducers leads a higher transfection rate. The system is of great significance to the development of single-cell biochip platforms for early cancer diagnosis and assessment of cancer treatment.
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38
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Tamasi MJ, Patel RA, Borca CH, Kosuri S, Mugnier H, Upadhya R, Murthy NS, Webb MA, Gormley AJ. Machine Learning on a Robotic Platform for the Design of Polymer-Protein Hybrids. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2201809. [PMID: 35593444 PMCID: PMC9339531 DOI: 10.1002/adma.202201809] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/26/2022] [Indexed: 06/04/2023]
Abstract
Polymer-protein hybrids are intriguing materials that can bolster protein stability in non-native environments, thereby enhancing their utility in diverse medicinal, commercial, and industrial applications. One stabilization strategy involves designing synthetic random copolymers with compositions attuned to the protein surface, but rational design is complicated by the vast chemical and composition space. Here, a strategy is reported to design protein-stabilizing copolymers based on active machine learning, facilitated by automated material synthesis and characterization platforms. The versatility and robustness of the approach is demonstrated by the successful identification of copolymers that preserve, or even enhance, the activity of three chemically distinct enzymes following exposure to thermal denaturing conditions. Although systematic screening results in mixed success, active learning appropriately identifies unique and effective copolymer chemistries for the stabilization of each enzyme. Overall, this work broadens the capabilities to design fit-for-purpose synthetic copolymers that promote or otherwise manipulate protein activity, with extensions toward the design of robust polymer-protein hybrid materials.
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Affiliation(s)
- Matthew J Tamasi
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Roshan A Patel
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Carlos H Borca
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Shashank Kosuri
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Heloise Mugnier
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Rahul Upadhya
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - N Sanjeeva Murthy
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Michael A Webb
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Adam J Gormley
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
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39
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Kumar R. Materiomically Designed Polymeric Vehicles for Nucleic Acids: Quo Vadis? ACS APPLIED BIO MATERIALS 2022; 5:2507-2535. [PMID: 35642794 DOI: 10.1021/acsabm.2c00346] [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: 11/28/2022]
Abstract
Despite rapid advances in molecular biology, particularly in site-specific genome editing technologies, such as CRISPR/Cas9 and base editing, financial and logistical challenges hinder a broad population from accessing and benefiting from gene therapy. To improve the affordability and scalability of gene therapy, we need to deploy chemically defined, economical, and scalable materials, such as synthetic polymers. For polymers to deliver nucleic acids efficaciously to targeted cells, they must optimally combine design attributes, such as architecture, length, composition, spatial distribution of monomers, basicity, hydrophilic-hydrophobic phase balance, or protonation degree. Designing polymeric vectors for specific nucleic acid payloads is a multivariate optimization problem wherein even minuscule deviations from the optimum are poorly tolerated. To explore the multivariate polymer design space rapidly, efficiently, and fruitfully, we must integrate parallelized polymer synthesis, high-throughput biological screening, and statistical modeling. Although materiomics approaches promise to streamline polymeric vector development, several methodological ambiguities must be resolved. For instance, establishing a flexible polymer ontology that accommodates recent synthetic advances, enforcing uniform polymer characterization and data reporting standards, and implementing multiplexed in vitro and in vivo screening studies require considerable planning, coordination, and effort. This contribution will acquaint readers with the challenges associated with materiomics approaches to polymeric gene delivery and offers guidelines for overcoming these challenges. Here, we summarize recent developments in combinatorial polymer synthesis, high-throughput screening of polymeric vectors, omics-based approaches to polymer design, barcoding schemes for pooled in vitro and in vivo screening, and identify materiomics-inspired research directions that will realize the long-unfulfilled clinical potential of polymeric carriers in gene therapy.
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Affiliation(s)
- Ramya Kumar
- Department of Chemical & Biological Engineering, Colorado School of Mines, 1613 Illinois St, Golden, Colorado 80401, United States
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40
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Rickert CA, Lieleg O. Machine learning approaches for biomolecular, biophysical, and biomaterials research. BIOPHYSICS REVIEWS 2022; 3:021306. [PMID: 38505413 PMCID: PMC10914139 DOI: 10.1063/5.0082179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/12/2022] [Indexed: 03/21/2024]
Abstract
A fluent conversation with a virtual assistant, person-tailored news feeds, and deep-fake images created within seconds-all those things that have been unthinkable for a long time are now a part of our everyday lives. What these examples have in common is that they are realized by different means of machine learning (ML), a technology that has fundamentally changed many aspects of the modern world. The possibility to process enormous amount of data in multi-hierarchical, digital constructs has paved the way not only for creating intelligent systems but also for obtaining surprising new insight into many scientific problems. However, in the different areas of biosciences, which typically rely heavily on the collection of time-consuming experimental data, applying ML methods is a bit more challenging: Here, difficulties can arise from small datasets and the inherent, broad variability, and complexity associated with studying biological objects and phenomena. In this Review, we give an overview of commonly used ML algorithms (which are often referred to as "machines") and learning strategies as well as their applications in different bio-disciplines such as molecular biology, drug development, biophysics, and biomaterials science. We highlight how selected research questions from those fields were successfully translated into machine readable formats, discuss typical problems that can arise in this context, and provide an overview of how to resolve those encountered difficulties.
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41
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Merging data curation and machine learning to improve nanomedicines. Adv Drug Deliv Rev 2022; 183:114172. [PMID: 35189266 PMCID: PMC9233944 DOI: 10.1016/j.addr.2022.114172] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/28/2022] [Accepted: 02/16/2022] [Indexed: 12/12/2022]
Abstract
Nanomedicine design is often a trial-and-error process, and the optimization of formulations and in vivo properties requires tremendous benchwork. To expedite the nanomedicine research progress, data science is steadily gaining importance in the field of nanomedicine. Recently, efforts have explored the potential to predict nanomaterials synthesis and biological behaviors via advanced data analytics. Machine learning algorithms process large datasets to understand and predict various material properties in nanomedicine synthesis, pharmacologic parameters, and efficacy. "Big data" approaches may enable even larger advances, especially if researchers capitalize on data curation methods. However, the concomitant use of data curation processes needed to facilitate the acquisition and standardization of large, heterogeneous data sets, to support advanced data analytics methods such as machine learning has yet to be leveraged. Currently, data curation and data analytics areas of nanotechnology-focused data science, or 'nanoinformatics', have been proceeding largely independently. This review highlights the current efforts in both areas and the potential opportunities for coordination to advance the capabilities of data analytics in nanomedicine.
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42
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Kumar R, Le N, Oviedo F, Brown ME, Reineke TM. Combinatorial Polycation Synthesis and Causal Machine Learning Reveal Divergent Polymer Design Rules for Effective pDNA and Ribonucleoprotein Delivery. JACS AU 2022; 2:428-442. [PMID: 35252992 PMCID: PMC8889556 DOI: 10.1021/jacsau.1c00467] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 06/14/2023]
Abstract
The development of polymers that can replace engineered viral vectors in clinical gene therapy has proven elusive despite the vast portfolios of multifunctional polymers generated by advances in polymer synthesis. Functional delivery of payloads such as plasmids (pDNA) and ribonucleoproteins (RNP) to various cellular populations and tissue types requires design precision. Herein, we systematically screen a combinatorially designed library of 43 well-defined polymers, ultimately identifying a lead polycationic vehicle (P38) for efficient pDNA delivery. Further, we demonstrate the versatility of P38 in codelivering spCas9 RNP and pDNA payloads to mediate homology-directed repair as well as in facilitating efficient pDNA delivery in ARPE-19 cells. P38 achieves nuclear import of pDNA and eludes lysosomal processing far more effectively than a structural analogue that does not deliver pDNA as efficiently. To reveal the physicochemical drivers of P38's gene delivery performance, SHapley Additive exPlanations (SHAP) are computed for nine polyplex features, and a causal model is applied to evaluate the average treatment effect of the most important features selected by SHAP. Our machine learning interpretability and causal inference approach derives structure-function relationships underlying delivery efficiency, polyplex uptake, and cellular viability and probes the overlap in polymer design criteria between RNP and pDNA payloads. Together, combinatorial polymer synthesis, parallelized biological screening, and machine learning establish that pDNA delivery demands careful tuning of polycation protonation equilibria while RNP payloads are delivered most efficaciously by polymers that deprotonate cooperatively via hydrophobic interactions. These payload-specific design guidelines will inform further design of bespoke polymers for specific therapeutic contexts.
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Affiliation(s)
- Ramya Kumar
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Ngoc Le
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Felipe Oviedo
- Nanite
Inc., 6 Liberty Square
#6128, Boston, Massachusetts 02109, United States
| | - Mary E. Brown
- University
Imaging Centers, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Theresa M. Reineke
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
- Nanite
Inc., 6 Liberty Square
#6128, Boston, Massachusetts 02109, United States
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43
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Hooshmand SE, Sabet MJ, Hasanzadeh A, Mousavi SMK, Moghadam NH, Hooshmand SA, Rabiee N, Liu Y, Hamblin MR, Karimi M. Histidine‐enhanced gene delivery systems: The state of the art. J Gene Med 2022; 24:e3415. [DOI: 10.1002/jgm.3415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Seyyed Emad Hooshmand
- Cellular and Molecular Research Center Iran University of Medical Sciences Tehran Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine Iran University of Medical Sciences Tehran Iran
| | - Makkieh Jahanpeimay Sabet
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine Iran University of Medical Sciences Tehran Iran
| | - Akbar Hasanzadeh
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine Iran University of Medical Sciences Tehran Iran
| | - Seyede Mahtab Kamrani Mousavi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine Iran University of Medical Sciences Tehran Iran
| | - Niloofar Haeri Moghadam
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine Iran University of Medical Sciences Tehran Iran
| | - Seyed Aghil Hooshmand
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics University of Tehran Tehran Iran
| | - Navid Rabiee
- Department of Physics Sharif University of Technology Tehran Iran
- School of Engineering Macquarie University Sydney New South Wales Australia
| | - Yong Liu
- Institute of Functional Nano & Soft Materials (FUNSOM) Soochow University Suzhou Jiangsu China
| | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science University of Johannesburg South Africa
| | - Mahdi Karimi
- Cellular and Molecular Research Center Iran University of Medical Sciences Tehran Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine Iran University of Medical Sciences Tehran Iran
- Oncopathology Research Center Iran University of Medical Sciences Tehran Iran
- Research Center for Science and Technology in Medicine Tehran University of Medical Sciences Tehran Iran
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44
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Boehnke N, Hammond PT. Power in Numbers: Harnessing Combinatorial and Integrated Screens to Advance Nanomedicine. JACS AU 2022; 2:12-21. [PMID: 35098219 PMCID: PMC8791056 DOI: 10.1021/jacsau.1c00313] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 05/02/2023]
Abstract
Nanocarriers have significant potential to advance personalized medicine through targeted drug delivery. However, to date, efforts to improve nanoparticle accumulation at target disease sites have largely failed to translate clinically, stemming from an incomplete understanding of nano-bio interactions. While progress has been made to evaluate the effects of specific physical and chemical nanoparticle properties on trafficking and uptake, there is much to be gained from controlling these properties singularly and in combination to determine their interactions with different cell types. We and others have recently begun leveraging library-based nanoparticle screens to study structure-function relationships of lipid- and polymer-based drug delivery systems to guide nanoparticle design. These combinatorial screening efforts are showing promise in leading to the successful identification of critical characteristics that yield improved and specific accumulation at target sites. However, there is a crucial need to equally consider the influence of biological complexity on nanoparticle delivery, particularly in the context of clinical translation. For example, tissue and cellular heterogeneity presents an additional dimension to nanoparticle trafficking, uptake, and accumulation; applying imaging and screening tools as well as bioinformatics may further expand our understanding of how nanoparticles engage with cells and tissues. Given recent advances in the fields of omics and machine learning, there is substantial promise to revolutionize nanocarrier development through the use of integrated screens, harnessing the combinatorial parameter space afforded both by nanoparticle libraries and clinically annotated biological data sets in combination with high throughput in vivo studies.
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Affiliation(s)
- Natalie Boehnke
- Koch
Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
| | - Paula T. Hammond
- Koch
Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, 25 Ames
Street, Cambridge, Massachusetts 02142, United States
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45
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Lin Y, Wagner E, Lächelt U. Non-viral delivery of the CRISPR/Cas system: DNA versus RNA versus RNP. Biomater Sci 2022; 10:1166-1192. [DOI: 10.1039/d1bm01658j] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Since its discovery, the CRISPR/Cas technology has rapidly become an essential tool in modern biomedical research. The opportunities to specifically modify and correct genomic DNA has also raised big hope...
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46
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Aldeghi M, Coley CW. A graph representation of molecular ensembles for polymer property prediction. Chem Sci 2022; 13:10486-10498. [PMID: 36277616 PMCID: PMC9473492 DOI: 10.1039/d2sc02839e] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/15/2022] [Indexed: 12/02/2022] Open
Abstract
Synthetic polymers are versatile and widely used materials. Similar to small organic molecules, a large chemical space of such materials is hypothetically accessible. Computational property prediction and virtual screening can accelerate polymer design by prioritizing candidates expected to have favorable properties. However, in contrast to organic molecules, polymers are often not well-defined single structures but an ensemble of similar molecules, which poses unique challenges to traditional chemical representations and machine learning approaches. Here, we introduce a graph representation of molecular ensembles and an associated graph neural network architecture that is tailored to polymer property prediction. We demonstrate that this approach captures critical features of polymeric materials, like chain architecture, monomer stoichiometry, and degree of polymerization, and achieves superior accuracy to off-the-shelf cheminformatics methodologies. While doing so, we built a dataset of simulated electron affinity and ionization potential values for >40k polymers with varying monomer composition, stoichiometry, and chain architecture, which may be used in the development of other tailored machine learning approaches. The dataset and machine learning models presented in this work pave the path toward new classes of algorithms for polymer informatics and, more broadly, introduce a framework for the modeling of molecular ensembles. A graph representation that captures critical features of polymeric materials and an associated graph neural network achieve superior accuracy to off-the-shelf cheminformatics methodologies.![]()
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Affiliation(s)
- Matteo Aldeghi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Connor W. Coley
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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47
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Hirata M, Wittayarat M, Namula Z, Le QA, Lin Q, Takebayashi K, Thongkittidilok C, Mito T, Tomonari S, Tanihara F, Otoi T. Generation of mutant pigs by lipofection-mediated genome editing in embryos. Sci Rep 2021; 11:23806. [PMID: 34903813 PMCID: PMC8668999 DOI: 10.1038/s41598-021-03325-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 11/30/2021] [Indexed: 01/03/2023] Open
Abstract
The specificity and efficiency of CRISPR/Cas9 gene-editing systems are determined by several factors, including the mode of delivery, when applied to mammalian embryos. Given the limited time window for delivery, faster and more reliable methods to introduce Cas9-gRNA ribonucleoprotein complexes (RNPs) into target embryos are needed. In pigs, somatic cell nuclear transfer using gene-modified somatic cells and the direct introduction of gene editors into the cytoplasm of zygotes/embryos by microinjection or electroporation have been used to generate gene-edited embryos; however, these strategies require expensive equipment and sophisticated techniques. In this study, we developed a novel lipofection-mediated RNP transfection technique that does not require specialized equipment for the generation of gene-edited pigs and produced no detectable off-target events. In particular, we determined the concentration of lipofection reagent for efficient RNP delivery into embryos and successfully generated MSTN gene-edited pigs (with mutations in 7 of 9 piglets) after blastocyst transfer to a recipient gilt. This newly established lipofection-based technique is still in its early stages and requires improvements, particularly in terms of editing efficiency. Nonetheless, this practical method for rapid and large-scale lipofection-mediated gene editing in pigs has important agricultural and biomedical applications.
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Affiliation(s)
- Maki Hirata
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan.,Bio-Innovation Research Center, Tokushima University, Tokushima, Japan
| | - Manita Wittayarat
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla, Thailand
| | - Zhao Namula
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan.,College of Coastal Agricultural Sciences, Guangdong Ocean University, Guangdong, China
| | - Quynh Anh Le
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Qingyi Lin
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Koki Takebayashi
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | | | - Taro Mito
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan.,Bio-Innovation Research Center, Tokushima University, Tokushima, Japan
| | - Sayuri Tomonari
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Fuminori Tanihara
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan. .,Center for Development of Advanced Medical Technology, Jichi Medical University, Tochigi, Japan.
| | - Takeshige Otoi
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan.,Bio-Innovation Research Center, Tokushima University, Tokushima, Japan
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48
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Chen C, Richter F, Zhang J, Guerrero-Sanchez C, Traeger A, Schubert US, Feng A, Thang SH. Synthesis of functional miktoarm star polymers in an automated parallel synthesizer. Eur Polym J 2021. [DOI: 10.1016/j.eurpolymj.2021.110777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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49
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Kim HJ, Kim A, Miyata K. Synthetic molecule libraries for nucleic acid delivery: Design parameters in cationic/ionizable lipids and polymers. Drug Metab Pharmacokinet 2021; 42:100428. [PMID: 34837771 DOI: 10.1016/j.dmpk.2021.100428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
Recent progress in the design of cationic lipids and polymers has successfully translated nucleic acid drugs into clinical applications, such as the treatment of liver diseases and the prevention of virus infection. Small or large libraries of delivery molecules have been used to find the key chemical structures to protect nucleic acids from nucleases in the extracellular milieu and to facilitate the endosomal escape after endocytosis. This review introduces three essential design parameters (i.e., acid dissociation constant, hydrophobicity, and biodegradability) to develop synthetic molecules for nucleic acid delivery. The significance and mechanism of each parameter are described based on the results obtained from in vitro and in vivo evaluations. Other design parameters were then discussed to create the next generation of delivery molecules for future nucleic acid therapeutics.
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Affiliation(s)
- Hyun Jin Kim
- Department of Biological Engineering, College of Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, South Korea; Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, South Korea.
| | - Ahram Kim
- Research Center for Functional Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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50
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Reis M, Gusev F, Taylor NG, Chung SH, Verber MD, Lee YZ, Isayev O, Leibfarth FA. Machine-Learning-Guided Discovery of 19F MRI Agents Enabled by Automated Copolymer Synthesis. J Am Chem Soc 2021; 143:17677-17689. [PMID: 34637304 PMCID: PMC10833148 DOI: 10.1021/jacs.1c08181] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Modern polymer science suffers from the curse of multidimensionality. The large chemical space imposed by including combinations of monomers into a statistical copolymer overwhelms polymer synthesis and characterization technology and limits the ability to systematically study structure-property relationships. To tackle this challenge in the context of 19F magnetic resonance imaging (MRI) agents, we pursued a computer-guided materials discovery approach that combines synergistic innovations in automated flow synthesis and machine learning (ML) method development. A software-controlled, continuous polymer synthesis platform was developed to enable iterative experimental-computational cycles that resulted in the synthesis of 397 unique copolymer compositions within a six-variable compositional space. The nonintuitive design criteria identified by ML, which were accomplished by exploring <0.9% of the overall compositional space, lead to the identification of >10 copolymer compositions that outperformed state-of-the-art materials.
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Affiliation(s)
- Marcus Reis
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Filipp Gusev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Nicholas G Taylor
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sang Hun Chung
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew D Verber
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yueh Z Lee
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Olexandr Isayev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Frank A Leibfarth
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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