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Formen JSSK, Howard JR, Anslyn EV, Wolf C. Circular Dichroism Sensing: Strategies and Applications. Angew Chem Int Ed Engl 2024; 63:e202400767. [PMID: 38421186 DOI: 10.1002/anie.202400767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/02/2024]
Abstract
The analysis of the absolute configuration, enantiomeric composition, and concentration of chiral compounds are frequently encountered tasks across the chemical and health sciences. Chiroptical sensing methods can streamline this work and allow high-throughput screening with remarkable reduction of operational time and cost. During the last few years, significant methodological advances with innovative chirality sensing systems, the use of computer-generated calibration curves, machine learning assistance, and chemometric data processing, to name a few, have emerged and are now matched with commercially available multi-well plate CD readers. These developments have reframed the chirality sensing space and provide new opportunities that are of interest to a large group of chemists. This review will discuss chirality sensing strategies and applications with representative small-molecule CD sensors. Emphasis will be given to important milestones and recent advances that accelerate chiral compound analysis by outperforming traditional methods, conquer new directions, and pioneering efforts that lie at the forefront of chiroptical high-throughput screening developments. The goal is to provide the reader with a thorough understanding of the current state and a perspective of future directions of this rapidly emerging field.
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Affiliation(s)
| | - James R Howard
- Chemistry Department, University of Texas at Austin, Austin TX, USA
| | - Eric V Anslyn
- Chemistry Department, University of Texas at Austin, Austin TX, USA
| | - Christian Wolf
- Chemistry Department, Georgetown University, Washington DC, USA
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2
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Franks SNJ, Heon-Roberts R, Ryan BJ. CRISPRi: a way to integrate iPSC-derived neuronal models. Biochem Soc Trans 2024; 52:539-551. [PMID: 38526223 DOI: 10.1042/bst20230190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 02/28/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
The genetic landscape of neurodegenerative diseases encompasses genes affecting multiple cellular pathways which exert effects in an array of neuronal and glial cell-types. Deconvolution of the roles of genes implicated in disease and the effects of disease-associated variants remains a vital step in the understanding of neurodegeneration and the development of therapeutics. Disease modelling using patient induced pluripotent stem cells (iPSCs) has enabled the generation of key cell-types associated with disease whilst maintaining the genomic variants that predispose to neurodegeneration. The use of CRISPR interference (CRISPRi), alongside other CRISPR-perturbations, allows the modelling of the effects of these disease-associated variants or identifying genes which modify disease phenotypes. This review summarises the current applications of CRISPRi in iPSC-derived neuronal models, such as fluorescence-activated cell sorting (FACS)-based screens, and discusses the future opportunities for disease modelling, identification of disease risk modifiers and target/drug discovery in neurodegeneration.
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Affiliation(s)
- Sarah N J Franks
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Rachel Heon-Roberts
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Brent J Ryan
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
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3
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Park S, Kim M, Lee JW. Optimizing Nucleic Acid Delivery Systems through Barcode Technology. ACS Synth Biol 2024; 13:1006-1018. [PMID: 38526308 DOI: 10.1021/acssynbio.3c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Conventional biological experiments often focus on in vitro assays because of the inherent limitations when handling multiple variables in vivo, including labor-intensive and time-consuming procedures. Often only a subset of samples demonstrating significant efficacy in the in vitro assays can be evaluated in vivo. Nonetheless, because of the low correlation between the in vitro and in vivo tests, evaluation of the variables under examination in vivo and not solely in vitro is critical. An emerging approach to achieve high-throughput in vivo tests involves using a barcode system consisting of various nucleotide combinations. Unique barcodes for each variant enable the simultaneous testing of multiple entities, eliminating the need for separate individual tests. Subsequently, to identify crucial parameters, samples were collected and analyzed using barcode sequencing. This review explores the development of barcode design and its applications, including the evaluation of nucleic acid delivery systems and the optimization of gene expression in vivo.
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Affiliation(s)
- Soan Park
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 CheongamRo, Gyeongbuk, 37673 NamGu, Pohang, Republic of Korea
| | - Mibang Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 CheongamRo, Gyeongbuk, 37673 NamGu, Pohang, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 CheongamRo, Gyeongbuk, 37673 NamGu, Pohang, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 CheongamRo, Gyeongbuk, 37673 NamGu, Pohang, Republic of Korea
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Reed KB, d'Oelsnitz S, Brooks SM, Wells J, Zhao M, Trivedi A, Eshraghi S, Alper HS. Fluorescence-Based Screens for Engineering Enzymes Linked to Halogenated Tryptophan. ACS Synth Biol 2024; 13:1373-1381. [PMID: 38533851 DOI: 10.1021/acssynbio.3c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Directed evolution is often limited by the throughput of accurate screening methods. Here we demonstrate the feasibility of utilizing a singular transcription factor (TF)-system that can be refactored in two ways (both as an activator and repressor). Specifically, we showcase the use of previously evolved 5-halo- or 6-halo-tryptophan-specific TF biosensors suitable for the detection of a halogenated tryptophan molecule in vivo. We subsequently validate the biosensor's utility for two halogenase-specific halo-tryptophan accumulation screens. First, we isolated 5-tryptophan-halogenase, XsHal, from a mixed pool of halogenases with 100% efficiency. Thereafter, we generated a targeted library of the catalytic residue of 6-tryptophan halogenase, Th-Hal, and isolated functioning halogenases with 100% efficiency. Lastly, we refactor the TF circuit to respond to the depletion of halogenated tryptophan and prototype a high-throughput biosensor-directed evolution scheme to screen for downstream enzyme variants capable of promiscuously converting halogenated tryptophan. Altogether, this work takes a significant step toward the rapid and higher throughput screening of halogenases and halo-tryptophan converting enzymes to further reinforce efforts to enable high-level bioproduction of halogenated chemicals.
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Affiliation(s)
- Kevin B Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Simon d'Oelsnitz
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas 78712, United States
| | | | - Jordan Wells
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Minye Zhao
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Adit Trivedi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Selina Eshraghi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas 78712, United States
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5
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Lim FS, González-Cabrera J, Keilwagen J, Kleespies RG, Jehle JA, Wennmann JT. Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets. Sci Rep 2024; 14:8525. [PMID: 38609404 PMCID: PMC11014933 DOI: 10.1038/s41598-024-58768-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Rapid and reliable detection of pathogens is crucial to complement the growing industry of mass-reared insects, in order to safeguard the insect colonies from outbreak of diseases, which may cause significant economic loss. Current diagnostic methods are mainly based on conventional PCR and microscopic examination, requiring prior knowledge of disease symptoms and are limited to identifying known pathogens. Here, we present a rapid nanopore-based metagenomics approach for detecting entomopathogens from the European house cricket (Acheta domesticus). In this study, the Acheta domesticus densovirus (AdDV) was detected from diseased individuals using solely Nanopore sequencing. Virus reads and genome assemblies were obtained within twenty-four hours after sequencing. Subsequently, due to the length of the Nanopore reads, it was possible to reconstruct significantly large parts or even the entire AdDV genome to conduct studies for genotype identification. Variant analysis indicated the presence of three AdDV genotypes within the same house cricket population, with association to the vital status of the diseased crickets. This contrast provided compelling evidence for the existence of non-lethal AdDV genotypes. These findings demonstrated nanopore-based metagenomics sequencing as a powerful addition to the diagnostic tool kit for routine pathogen surveillance and diagnosis in the insect rearing industry.
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Affiliation(s)
- Fang Shiang Lim
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
- Department of Genetics and Institute BIOTECMED, Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain
| | - Joel González-Cabrera
- Department of Genetics and Institute BIOTECMED, Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain
| | - Jens Keilwagen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for the Safety of Biotechnological Processes in Plants, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Regina G Kleespies
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
| | - Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany.
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Sofyantoro F, Septriani NI, Yudha DS, Wicaksono EA, Priyono DS, Putri WA, Primahesa A, Raharjeng ARP, Purwestri YA, Nuringtyas TR. Zebrafish as Versatile Model for Assessing Animal Venoms and Toxins: Current Applications and Future Prospects. Zebrafish 2024. [PMID: 38608228 DOI: 10.1089/zeb.2023.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] Open
Abstract
Animal venoms and toxins hold promise as sources of novel drug candidates, therapeutic agents, and biomolecules. To fully harness their potential, it is crucial to develop reliable testing methods that provide a comprehensive understanding of their effects and mechanisms of action. However, traditional rodent assays encounter difficulties in mimicking venom-induced effects in human due to the impractical venom dosage levels. The search for reliable testing methods has led to the emergence of zebrafish (Danio rerio) as a versatile model organism for evaluating animal venoms and toxins. Zebrafish possess genetic similarities to humans, rapid development, transparency, and amenability to high-throughput assays, making it ideal for assessing the effects of animal venoms and toxins. This review highlights unique attributes of zebrafish and explores their applications in studying venom- and toxin-induced effects from various species, including snakes, jellyfish, cuttlefish, anemones, spiders, and cone snails. Through zebrafish-based research, intricate physiological responses, developmental alterations, and potential therapeutic interventions induced by venoms are revealed. Novel techniques such as CRISPR/Cas9 gene editing, optogenetics, and high-throughput screening hold great promise for advancing venom research. As zebrafish-based insights converge with findings from other models, the comprehensive understanding of venom-induced effects continues to expand, guiding the development of targeted interventions and promoting both scientific knowledge and practical applications.
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Affiliation(s)
- Fajar Sofyantoro
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | | | - Ega Adhi Wicaksono
- Faculties of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Sendi Priyono
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Alfian Primahesa
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Anita Restu Puji Raharjeng
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Science and Technology, Universitas Islam Negeri Raden Fatah Palembang, South Sumatera, Indonesia
| | - Yekti Asih Purwestri
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Rini Nuringtyas
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Deng H, Deng D, Jin S, Tian Z, Yang LM. Unraveling the Activity and Mechanism of TM@g-C 4N 3 Electrocatalysts in the Oxygen Reduction Reaction. ACS Appl Mater Interfaces 2024; 16:17617-17625. [PMID: 38530989 DOI: 10.1021/acsami.4c01342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
In this work, a high-throughput screening strategy and density functional theory (DFT) are jointly employed to identify high-performance TM@g-C4N3 (TM = 3d, 4d, 5d transition metals) single-atom catalysts (SACs) for the oxygen reduction reaction (ORR). Comprehensive studies demonstrated that Cu@, Zn@, and Ag@g-C4N3 show high ORR catalytic activities under both acidic and alkaline conditions with favorable overpotentials (ηORR) of 0.70, 0.89, and 0.89 V, respectively; among them, Cu@g-C4N3 is the best candidate. The ORR follows a four-electron mechanism with the final product H2O/OH-. Cu@, Zn@, and Ag@g-C4N3 catalysts also exhibit good thermal (500 K) and electrochemical (0.93-3.14 V) stabilities. Cu@, Zn@, and Ag@g-C4N3 demonstrate superior activities with low ηORR due to its moderate adsorption strength of *OH. The ηORR and the Gibbs free energy changes of *OH (ΔG4(acidic)/ΔG4(alkaline)) resemble a volcano-type relationship under acidic/alkaline conditions, respectively. Additionally, the O-O bond length in *OOH emerged as an effective structural descriptor for rapidly identifying the promising electrocatalysts. This research provides valuable insights into the origin of the ORR activity on TM@g-C4N3 and offers useful guidance for the efficient exploration of high-performance catalyst candidates.
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Affiliation(s)
- Hao Deng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Materials Chemistry and Service Failure, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dan Deng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Materials Chemistry and Service Failure, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shangbin Jin
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhihong Tian
- Engineering Research Center for Nanomaterials, Henan University, Kaifeng 475004, PR China
| | - Li-Ming Yang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Materials Chemistry and Service Failure, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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8
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Roux S, Cherradi S, Duong HT. Exploiting the predictive power of educated spheroids to detect immune-mediated idiosyncratic drug-induced liver injury: the case of troglitazone. Front Pharmacol 2024; 15:1378371. [PMID: 38659594 PMCID: PMC11039894 DOI: 10.3389/fphar.2024.1378371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
Idiosyncratic drug-induced liver injury (iDILI) is a major concern in drug development because its occurrence is unpredictable. Presently, iDILI prediction is a challenge, and cell toxicity is observed only at concentrations that are much higher than the therapeutic doses in preclinical models. Applying a proprietary cell educating technology, we developed a person-dependent spheroid system that contains autologous educated immune cells that can detect iDILI risk at therapeutic concentrations. Integrating this system into a high-throughput screening platform will help pharmaceutical companies accurately detect the iDILI risk of new molecules de-risking drug development.
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Affiliation(s)
| | | | - Hong Tuan Duong
- PredictCan Biotechnologies SAS, Biopôle Euromédecine, Grabels, France
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Ohnishi Y, Masui A, Suezawa T, Mikawa R, Hirai T, Hagiwara M, Gotoh S. Screening of factors inducing alveolar type 1 epithelial cells using human pluripotent stem cells. Stem Cell Reports 2024; 19:529-544. [PMID: 38552636 DOI: 10.1016/j.stemcr.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 04/12/2024] Open
Abstract
Alveolar type 2 (AT2) epithelial cells are tissue stem cells capable of differentiating into alveolar type 1 (AT1) cells for injury repair and maintenance of lung homeostasis. However, the factors involved in human AT2-to-AT1 cell differentiation are not fully understood. Here, we established SFTPCGFP and AGERmCherry-HiBiT dual-reporter induced pluripotent stem cells (iPSCs), which detected AT2-to-AT1 cell differentiation with high sensitivity and identified factors inducing AT1 cell differentiation from AT2 and their progenitor cells. We also established an "on-gel" alveolar epithelial spheroid culture suitable for medium-throughput screening. Among the 274 chemical compounds, several single compounds, including LATS-IN-1, converted AT1 cells from AT2 and their progenitor cells. Moreover, YAP/TAZ signaling activation and AKT signaling suppression synergistically recapitulated the induction of transcriptomic, morphological, and functionally mature AT1 cells. Our findings provide novel insights into human lung development and lung regenerative medicine.
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Affiliation(s)
- Yuko Ohnishi
- Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Atsushi Masui
- Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Takahiro Suezawa
- Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Ryuta Mikawa
- Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Toyohiro Hirai
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Shimpei Gotoh
- Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.
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Zhao Q, Zheng Y, Qiu Y, Yu Y, Huang M, Wu Y, Chen X, Huang Y, Cui S, Zhuang S. Graph Convolutional Network-Enhanced Model for Screening Persistent, Mobile, and Toxic and Very Persistent and Very Mobile Substances. Environ Sci Technol 2024; 58:6149-6157. [PMID: 38556993 DOI: 10.1021/acs.est.4c01201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The global management for persistent, mobile, and toxic (PMT) and very persistent and very mobile (vPvM) substances has been further strengthened with the rapid increase of emerging contaminants. The development of a ready-to-use and publicly available tool for the high-throughput screening of PMT/vPvM substances is thus urgently needed. However, the current model building with the coupling of conventional algorithms, small-scale data set, and simplistic features hinders the development of a robust model for screening PMT/vPvM with wide application domains. Here, we construct a graph convolutional network (GCN)-enhanced model with feature fusion of a molecular graph and molecular descriptors to effectively utilize the significant correlation between critical descriptors and PMT/vPvM substances. The model is built with 213,084 substances following the latest PMT classification criteria. The application domains of the GCN-enhanced model assessed by kernel density estimation demonstrate the high suitability for high-throughput screening PMT/vPvM substances with both a high accuracy rate (86.6%) and a low false-negative rate (6.8%). An online server named PMT/vPvM profiler is further developed with a user-friendly web interface (http://www.pmt.zj.cn/). Our study facilitates a more efficient evaluation of PMT/vPvM substances with a globally accessible screening platform.
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Affiliation(s)
- Qiming Zhao
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yuting Zheng
- Solid Waste and Chemicals Management Center, Ministry of Ecology and Environment of the People's Republic of China, Beijing 100029, China
| | - Yu Qiu
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yang Yu
- Solid Waste and Chemicals Management Center, Ministry of Ecology and Environment of the People's Republic of China, Beijing 100029, China
| | - Meiling Huang
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yiqu Wu
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xiyu Chen
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yizhou Huang
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shixuan Cui
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shulin Zhuang
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
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11
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Prosz A, Sahgal P, Huffman BM, Sztupinszki Z, Morris CX, Chen D, Börcsök J, Diossy M, Tisza V, Spisak S, Likasitwatanakul P, Rusz O, Csabai I, Cecchini M, Baca Y, Elliot A, Enzinger P, Singh H, Ubellaker J, Lazaro JB, Cleary JM, Szallasi Z, Sethi NS. Mutational signature-based identification of DNA repair deficient gastroesophageal adenocarcinomas for therapeutic targeting. NPJ Precis Oncol 2024; 8:87. [PMID: 38589664 PMCID: PMC11001913 DOI: 10.1038/s41698-024-00561-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/22/2024] [Indexed: 04/10/2024] Open
Abstract
Homologous recombination (HR) and nucleotide excision repair (NER) are the two most frequently disabled DNA repair pathways in cancer. HR-deficient breast, ovarian, pancreatic and prostate cancers respond well to platinum chemotherapy and PARP inhibitors. However, the frequency of HR deficiency in gastric and esophageal adenocarcinoma (GEA) still lacks diagnostic and functional validation. Using whole exome and genome sequencing data, we found that a significant subset of GEA, but very few colorectal adenocarcinomas, show evidence of HR deficiency by mutational signature analysis (HRD score). High HRD gastric cancer cell lines demonstrated functional HR deficiency by RAD51 foci assay and increased sensitivity to platinum chemotherapy and PARP inhibitors. Of clinical relevance, analysis of three different GEA patient cohorts demonstrated that platinum treated HR deficient cancers had better outcomes. A gastric cancer cell line with strong sensitivity to cisplatin showed HR proficiency but exhibited NER deficiency by two photoproduct repair assays. Single-cell RNA-sequencing revealed that, in addition to inducing apoptosis, cisplatin treatment triggered ferroptosis in a NER-deficient gastric cancer, validated by intracellular GSH assay. Overall, our study provides preclinical evidence that a subset of GEAs harbor genomic features of HR and NER deficiency and may therefore benefit from platinum chemotherapy and PARP inhibitors.
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Affiliation(s)
- Aurel Prosz
- Danish Cancer Institute, Copenhagen, Denmark
| | - Pranshu Sahgal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Brandon M Huffman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zsofia Sztupinszki
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Clare X Morris
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Miklos Diossy
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Viktoria Tisza
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Sandor Spisak
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pornlada Likasitwatanakul
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Orsolya Rusz
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Michael Cecchini
- Department of Medical Oncology, Center for Gastrointestinal Cancers, Yale Medical Center, New Haven, CT, USA
| | | | | | - Peter Enzinger
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jessalyn Ubellaker
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for DNA Damage and Repair (CDDR), Dana-Farber Cancer Institute, Boston, MA, USA
| | - James M Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zoltan Szallasi
- Danish Cancer Institute, Copenhagen, Denmark.
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.
- Department of Bioinformatics and Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary.
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA.
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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Wu X, Qiao T, Huang J, Li J, Wei S, Yang J, Zhang Y, Li Y. Rebaudioside B Attenuates Lung Ischemia-reperfusion Injury-associated Apoptosis and Inflammation. Recent Adv Inflamm Allergy Drug Discov 2024:RAIAD-EPUB-139601. [PMID: 38584527 DOI: 10.2174/0127722708295154240327035857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 04/09/2024]
Abstract
OBJECTIVE At present, no proven effective treatment is available for Lung Ischemiareperfusion Injury (LIRI). Natural compounds offer promising prospects for developing new drugs to address various diseases. This study sought to explore the potential of Rebaudioside B (Reb B) as a treatment compound for LIRI, both in vivo and in vitro. METHODS This study involved utilizing the human pulmonary alveolar cell line A549, consisting of epithelial type II cells, subjected to Oxygen-glucose Deprivation/recovery (OGD/R) for highthroughput in vitro cell viability screening. The aim was to identify the most promising candidate compounds. Additionally, an in vivo rat model of lung ischemia-reperfusion was employed to evaluate the potential protective effects of Reb B. RESULTS Through high-throughput screening, Reb B emerged as the most promising natural compound among those tested. In the A549 OGD/R models, Reb B exhibited a capacity to enhance cell viability by mitigating apoptosis. In the in vivo LIRI model, pre-treatment with Reb B notably decreased apoptotic cells, perivascular edema, and neutrophil infiltration within lung tissues. Furthermore, Reb B demonstrated its ability to attenuate lung inflammation associated with LIRI primarily by elevating IL-10 levels while reducing levels of IL-6, IL-8, and TNF-α. CONCLUSION The comprehensive outcomes strongly suggest Reb B's potential as a protective agent against LIRI. This effect is attributed to its inhibition of the mitochondrial apoptotic pathway and its ability to mitigate the inflammatory response.
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Affiliation(s)
- Xiangyang Wu
- Department of Cardiac Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
| | - Tao Qiao
- Department of Cardiac Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
| | - Jian Huang
- Department of Thoracic Surgery, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
| | - Jian Li
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
| | - Shilin Wei
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
| | - Jianbao Yang
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
| | - Yanchun Zhang
- Department of Cardiac Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
| | - Yongnan Li
- Department of Cardiac Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
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13
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Li H, Li XD, Yan CH, Ni ZH, Lü MH, Zou LW, Yang L. Rational design of a near-infrared fluorescent probe for monitoring butyrylcholinesterase activity and its application in development of inhibitors. Front Bioeng Biotechnol 2024; 12:1387146. [PMID: 38638318 PMCID: PMC11024273 DOI: 10.3389/fbioe.2024.1387146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
Butyrylcholinesterase (BChE) is widely expressed in multiple tissues and has a vital role in several key human disorders, such as Alzheimer's disease and tumorigenesis. However, the role of BChE in human disorders has not been investigated. Thus, to quantitatively detect and visualize dynamical variations in BChE activity is essential for exploring the biological roles of BChE in the progression of a number of human disorders. Herein, based on the substrate characteristics of BChE, we customized and synthesized three near-infrared (NIR) fluorescent probe substrates with cyanine-skeleton, and finally selected a NIR fluorescence probe substrate named CYBA. The CYBA demonstrated a significant increase in fluorescence when interacting with BChE, but mainly avoided AChE. Upon the addition of BChE, CYBA could be specifically hydrolyzed to TBO, resulting in a significant NIR fluorescence signal enhancement at 710 nm. Systematic evaluation revealed that CYBA exhibited exceptional chemical stability in complex biosamples and possessed remarkable selectivity and sensitivity towards BChE. Moreover, CYBA was successfully applied for real-time imaging of endogenous BChE activity in two types of nerve-related living cells. Additionally, CYBA demonstrated exceptional stability in the detection of complex biological samples in plasma recovery studies (97.51%-104.01%). Furthermore, CYBA was used to construct a high-throughput screening (HTS) method for BChE inhibitors using human plasma as the enzyme source. We evaluated inhibitory effects of a series of natural products and four flavonoids were identified as potent inhibitors of BChE. Collectively, CYBA can serve as a practical tool to track the changes of BChE activity in complicated biological environments due to its excellent capabilities.
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Affiliation(s)
- Hao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiao-Dong Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chao-Hua Yan
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhen-Hua Ni
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mu-Han Lü
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Li-Wei Zou
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ling Yang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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14
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Wallach I, Bernard D, Nguyen K, Ho G, Morrison A, Stecula A, Rosnik A, O’Sullivan AM, Davtyan A, Samudio B, Thomas B, Worley B, Butler B, Laggner C, Thayer D, Moharreri E, Friedland G, Truong H, van den Bedem H, Ng HL, Stafford K, Sarangapani K, Giesler K, Ngo L, Mysinger M, Ahmed M, Anthis NJ, Henriksen N, Gniewek P, Eckert S, de Oliveira S, Suterwala S, PrasadPrasad SVK, Shek S, Contreras S, Hare S, Palazzo T, O’Brien TE, Van Grack T, Williams T, Chern TR, Kenyon V, Lee AH, Cann AB, Bergman B, Anderson BM, Cox BD, Warrington JM, Sorenson JM, Goldenberg JM, Young MA, DeHaan N, Pemberton RP, Schroedl S, Abramyan TM, Gupta T, Mysore V, Presser AG, Ferrando AA, Andricopulo AD, Ghosh A, Ayachi AG, Mushtaq A, Shaqra AM, Toh AKL, Smrcka AV, Ciccia A, de Oliveira AS, Sverzhinsky A, de Sousa AM, Agoulnik AI, Kushnir A, Freiberg AN, Statsyuk AV, Gingras AR, Degterev A, Tomilov A, Vrielink A, Garaeva AA, Bryant-Friedrich A, Caflisch A, Patel AK, Rangarajan AV, Matheeussen A, Battistoni A, Caporali A, Chini A, Ilari A, Mattevi A, Foote AT, Trabocchi A, Stahl A, Herr AB, Berti A, Freywald A, Reidenbach AG, Lam A, Cuddihy AR, White A, Taglialatela A, Ojha AK, Cathcart AM, Motyl AAL, Borowska A, D’Antuono A, Hirsch AKH, Porcelli AM, Minakova A, Montanaro A, Müller A, Fiorillo A, Virtanen A, O’Donoghue AJ, Del Rio Flores A, Garmendia AE, Pineda-Lucena A, Panganiban AT, Samantha A, Chatterjee AK, Haas AL, Paparella AS, John ALS, Prince A, ElSheikh A, Apfel AM, Colomba A, O’Dea A, Diallo BN, Ribeiro BMRM, Bailey-Elkin BA, Edelman BL, Liou B, Perry B, Chua BSK, Kováts B, Englinger B, Balakrishnan B, Gong B, Agianian B, Pressly B, Salas BPM, Duggan BM, Geisbrecht BV, Dymock BW, Morten BC, Hammock BD, Mota BEF, Dickinson BC, Fraser C, Lempicki C, Novina CD, Torner C, Ballatore C, Bon C, Chapman CJ, Partch CL, Chaton CT, Huang C, Yang CY, Kahler CM, Karan C, Keller C, Dieck CL, Huimei C, Liu C, Peltier C, Mantri CK, Kemet CM, Müller CE, Weber C, Zeina CM, Muli CS, Morisseau C, Alkan C, Reglero C, Loy CA, Wilson CM, Myhr C, Arrigoni C, Paulino C, Santiago C, Luo D, Tumes DJ, Keedy DA, Lawrence DA, Chen D, Manor D, Trader DJ, Hildeman DA, Drewry DH, Dowling DJ, Hosfield DJ, Smith DM, Moreira D, Siderovski DP, Shum D, Krist DT, Riches DWH, Ferraris DM, Anderson DH, Coombe DR, Welsbie DS, Hu D, Ortiz D, Alramadhani D, Zhang D, Chaudhuri D, Slotboom DJ, Ronning DR, Lee D, Dirksen D, Shoue DA, Zochodne DW, Krishnamurthy D, Duncan D, Glubb DM, Gelardi ELM, Hsiao EC, Lynn EG, Silva EB, Aguilera E, Lenci E, Abraham ET, Lama E, Mameli E, Leung E, Christensen EM, Mason ER, Petretto E, Trakhtenberg EF, Rubin EJ, Strauss E, Thompson EW, Cione E, Lisabeth EM, Fan E, Kroon EG, Jo E, García-Cuesta EM, Glukhov E, Gavathiotis E, Yu F, Xiang F, Leng F, Wang F, Ingoglia F, van den Akker F, Borriello F, Vizeacoumar FJ, Luh F, Buckner FS, Vizeacoumar FS, Bdira FB, Svensson F, Rodriguez GM, Bognár G, Lembo G, Zhang G, Dempsey G, Eitzen G, Mayer G, Greene GL, Garcia GA, Lukacs GL, Prikler G, Parico GCG, Colotti G, De Keulenaer G, Cortopassi G, Roti G, Girolimetti G, Fiermonte G, Gasparre G, Leuzzi G, Dahal G, Michlewski G, Conn GL, Stuchbury GD, Bowman GR, Popowicz GM, Veit G, de Souza GE, Akk G, Caljon G, Alvarez G, Rucinski G, Lee G, Cildir G, Li H, Breton HE, Jafar-Nejad H, Zhou H, Moore HP, Tilford H, Yuan H, Shim H, Wulff H, Hoppe H, Chaytow H, Tam HK, Van Remmen H, Xu H, Debonsi HM, Lieberman HB, Jung H, Fan HY, Feng H, Zhou H, Kim HJ, Greig IR, Caliandro I, Corvo I, Arozarena I, Mungrue IN, Verhamme IM, Qureshi IA, Lotsaris I, Cakir I, Perry JJP, Kwiatkowski J, Boorman J, Ferreira J, Fries J, Kratz JM, Miner J, Siqueira-Neto JL, Granneman JG, Ng J, Shorter J, Voss JH, Gebauer JM, Chuah J, Mousa JJ, Maynes JT, Evans JD, Dickhout J, MacKeigan JP, Jossart JN, Zhou J, Lin J, Xu J, Wang J, Zhu J, Liao J, Xu J, Zhao J, Lin J, Lee J, Reis J, Stetefeld J, Bruning JB, Bruning JB, Coles JG, Tanner JJ, Pascal JM, So J, Pederick JL, Costoya JA, Rayman JB, Maciag JJ, Nasburg JA, Gruber JJ, Finkelstein JM, Watkins J, Rodríguez-Frade JM, Arias JAS, Lasarte JJ, Oyarzabal J, Milosavljevic J, Cools J, Lescar J, Bogomolovas J, Wang J, Kee JM, Kee JM, Liao J, Sistla JC, Abrahão JS, Sishtla K, Francisco KR, Hansen KB, Molyneaux KA, Cunningham KA, Martin KR, Gadar K, Ojo KK, Wong KS, Wentworth KL, Lai K, Lobb KA, Hopkins KM, Parang K, Machaca K, Pham K, Ghilarducci K, Sugamori KS, McManus KJ, Musta K, Faller KME, Nagamori K, Mostert KJ, Korotkov KV, Liu K, Smith KS, Sarosiek K, Rohde KH, Kim KK, Lee KH, Pusztai L, Lehtiö L, Haupt LM, Cowen LE, Byrne LJ, Su L, Wert-Lamas L, Puchades-Carrasco L, Chen L, Malkas LH, Zhuo L, Hedstrom L, Hedstrom L, Walensky LD, Antonelli L, Iommarini L, Whitesell L, Randall LM, Fathallah MD, Nagai MH, Kilkenny ML, Ben-Johny M, Lussier MP, Windisch MP, Lolicato M, Lolli ML, Vleminckx M, Caroleo MC, Macias MJ, Valli M, Barghash MM, Mellado M, Tye MA, Wilson MA, Hannink M, Ashton MR, Cerna MVC, Giorgis M, Safo MK, Maurice MS, McDowell MA, Pasquali M, Mehedi M, Serafim MSM, Soellner MB, Alteen MG, Champion MM, Skorodinsky M, O’Mara ML, Bedi M, Rizzi M, Levin M, Mowat M, Jackson MR, Paige M, Al-Yozbaki M, Giardini MA, Maksimainen MM, De Luise M, Hussain MS, Christodoulides M, Stec N, Zelinskaya N, Van Pelt N, Merrill NM, Singh N, Kootstra NA, Singh N, Gandhi NS, Chan NL, Trinh NM, Schneider NO, Matovic N, Horstmann N, Longo N, Bharambe N, Rouzbeh N, Mahmoodi N, Gumede NJ, Anastasio NC, Khalaf NB, Rabal O, Kandror O, Escaffre O, Silvennoinen O, Bishop OT, Iglesias P, Sobrado P, Chuong P, O’Connell P, Martin-Malpartida P, Mellor P, Fish PV, Moreira POL, Zhou P, Liu P, Liu P, Wu P, Agogo-Mawuli P, Jones PL, Ngoi P, Toogood P, Ip P, von Hundelshausen P, Lee PH, Rowswell-Turner RB, Balaña-Fouce R, Rocha REO, Guido RVC, Ferreira RS, Agrawal RK, Harijan RK, Ramachandran R, Verma R, Singh RK, Tiwari RK, Mazitschek R, Koppisetti RK, Dame RT, Douville RN, Austin RC, Taylor RE, Moore RG, Ebright RH, Angell RM, Yan R, Kejriwal R, Batey RA, Blelloch R, Vandenberg RJ, Hickey RJ, Kelm RJ, Lake RJ, Bradley RK, Blumenthal RM, Solano R, Gierse RM, Viola RE, McCarthy RR, Reguera RM, Uribe RV, do Monte-Neto RL, Gorgoglione R, Cullinane RT, Katyal S, Hossain S, Phadke S, Shelburne SA, Geden SE, Johannsen S, Wazir S, Legare S, Landfear SM, Radhakrishnan SK, Ammendola S, Dzhumaev S, Seo SY, Li S, Zhou S, Chu S, Chauhan S, Maruta S, Ashkar SR, Shyng SL, Conticello SG, Buroni S, Garavaglia S, White SJ, Zhu S, Tsimbalyuk S, Chadni SH, Byun SY, Park S, Xu SQ, Banerjee S, Zahler S, Espinoza S, Gustincich S, Sainas S, Celano SL, Capuzzi SJ, Waggoner SN, Poirier S, Olson SH, Marx SO, Van Doren SR, Sarilla S, Brady-Kalnay SM, Dallman S, Azeem SM, Teramoto T, Mehlman T, Swart T, Abaffy T, Akopian T, Haikarainen T, Moreda TL, Ikegami T, Teixeira TR, Jayasinghe TD, Gillingwater TH, Kampourakis T, Richardson TI, Herdendorf TJ, Kotzé TJ, O’Meara TR, Corson TW, Hermle T, Ogunwa TH, Lan T, Su T, Banjo T, O’Mara TA, Chou T, Chou TF, Baumann U, Desai UR, Pai VP, Thai VC, Tandon V, Banerji V, Robinson VL, Gunasekharan V, Namasivayam V, Segers VFM, Maranda V, Dolce V, Maltarollo VG, Scoffone VC, Woods VA, Ronchi VP, Van Hung Le V, Clayton WB, Lowther WT, Houry WA, Li W, Tang W, Zhang W, Van Voorhis WC, Donaldson WA, Hahn WC, Kerr WG, Gerwick WH, Bradshaw WJ, Foong WE, Blanchet X, Wu X, Lu X, Qi X, Xu X, Yu X, Qin X, Wang X, Yuan X, Zhang X, Zhang YJ, Hu Y, Aldhamen YA, Chen Y, Li Y, Sun Y, Zhu Y, Gupta YK, Pérez-Pertejo Y, Li Y, Tang Y, He Y, Tse-Dinh YC, Sidorova YA, Yen Y, Li Y, Frangos ZJ, Chung Z, Su Z, Wang Z, Zhang Z, Liu Z, Inde Z, Artía Z, Heifets A. AI is a viable alternative to high throughput screening: a 318-target study. Sci Rep 2024; 14:7526. [PMID: 38565852 PMCID: PMC10987645 DOI: 10.1038/s41598-024-54655-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.
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15
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Tan S, Gu Y, Zhu Y, Luo C, Li Z, Lin H, Zhang W. Insights from bioinformatics analysis reveal that lipopolysaccharide induces activation of chemokine-related signaling pathways in human nasal epithelial cells. Sci Rep 2024; 14:7672. [PMID: 38561377 PMCID: PMC10984988 DOI: 10.1038/s41598-024-58317-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Lipopolysaccharide (LPS) is known to elicit a robust immune response. This study aimed to investigate the impact of LPS on the transcriptome of human nasal epithelial cells (HNEpC). HNEpC were cultured and stimulated with LPS (1 μg/mL) or an equivalent amount of normal culture medium. Subsequently, total RNA was extracted, purified, and sequenced using next-generation RNA sequencing technology. Differentially expressed genes (DEGs) were identified and subjected to functional enrichment analysis. A protein-protein interaction (PPI) network of DEGs was constructed, followed by Ingenuity Pathway Analysis (IPA) to identify molecular pathways influenced by LPS exposure on HNEpC. Validation of key genes was performed using quantitative real-time PCR (qRT-PCR). A total of 97 DEGs, comprising 48 up-regulated genes and 49 down-regulated genes, were identified. Results from functional enrichment analysis, PPI, and IPA indicated that DEGs were predominantly enriched in chemokine-related signaling pathways. Subsequent qRT-PCR validation demonstrated significant upregulation of key genes in these pathways in LPS-treated HNEpC compared to control cells. In conclusion, LPS intervention profoundly altered the transcriptome of HNEpC, potentially exacerbating inflammatory responses through the activation of chemokine-related signaling pathways.
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Affiliation(s)
- Shaolin Tan
- Postgraduate Training Base of Shanghai Sixth People's Hospital, Jinzhou Medical University, Shanghai, China
- Department of Otolaryngology-Head and Neck Surgery & Allergy Center, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Otolaryngological Institute, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
| | - Yuelong Gu
- Department of Otolaryngology-Head and Neck Surgery & Allergy Center, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Otolaryngological Institute, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
| | - Ying Zhu
- Department of Otolaryngology-Head and Neck Surgery & Allergy Center, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Otolaryngological Institute, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
| | - Chunyu Luo
- Department of Otolaryngology-Head and Neck Surgery & Allergy Center, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Otolaryngological Institute, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
| | - Zhipeng Li
- Department of Otolaryngology-Head and Neck Surgery & Allergy Center, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Otolaryngological Institute, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
| | - Hai Lin
- Department of Otolaryngology-Head and Neck Surgery & Allergy Center, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Otolaryngological Institute, Shanghai Jiao Tong University, Shanghai, China.
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China.
| | - Weitian Zhang
- Department of Otolaryngology-Head and Neck Surgery & Allergy Center, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Otolaryngological Institute, Shanghai Jiao Tong University, Shanghai, China.
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China.
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Arndell T, Chen J, Sperschneider J, Upadhyaya NM, Blundell C, Niesner N, Outram MA, Wang A, Swain S, Luo M, Ayliffe MA, Figueroa M, Vanhercke T, Dodds PN. Pooled effector library screening in protoplasts rapidly identifies novel Avr genes. Nat Plants 2024; 10:572-580. [PMID: 38409291 PMCID: PMC11035141 DOI: 10.1038/s41477-024-01641-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024]
Abstract
Crop breeding for durable disease resistance is challenging due to the rapid evolution of pathogen virulence. While progress in resistance (R) gene cloning and stacking has accelerated in recent years1-3, the identification of corresponding avirulence (Avr) genes in many pathogens is hampered by the lack of high-throughput screening options. To address this technology gap, we developed a platform for pooled library screening in plant protoplasts to allow rapid identification of interacting R-Avr pairs. We validated this platform by isolating known and novel Avr genes from wheat stem rust (Puccinia graminis f. sp. tritici) after screening a designed library of putative effectors against individual R genes. Rapid Avr gene identification provides molecular tools to understand and track pathogen virulence evolution via genotype surveillance, which in turn will lead to optimized R gene stacking and deployment strategies. This platform should be broadly applicable to many crop pathogens and could potentially be adapted for screening genes involved in other protoplast-selectable traits.
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Affiliation(s)
- Taj Arndell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jian Chen
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | | | - Cheryl Blundell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Nathalie Niesner
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Megan A Outram
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Aihua Wang
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Steve Swain
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Ming Luo
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Michael A Ayliffe
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Thomas Vanhercke
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia.
| | - Peter N Dodds
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia.
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17
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Sych T, Schlegel J, Barriga HMG, Ojansivu M, Hanke L, Weber F, Beklem Bostancioglu R, Ezzat K, Stangl H, Plochberger B, Laurencikiene J, El Andaloussi S, Fürth D, Stevens MM, Sezgin E. High-throughput measurement of the content and properties of nano-sized bioparticles with single-particle profiler. Nat Biotechnol 2024; 42:587-590. [PMID: 37308687 PMCID: PMC11021190 DOI: 10.1038/s41587-023-01825-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 05/10/2023] [Indexed: 06/14/2023]
Abstract
We introduce a method, single-particle profiler, that provides single-particle information on the content and biophysical properties of thousands of particles in the size range 5-200 nm. We use our single-particle profiler to measure the messenger RNA encapsulation efficiency of lipid nanoparticles, the viral binding efficiencies of different nanobodies, and the biophysical heterogeneity of liposomes, lipoproteins, exosomes and viruses.
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Affiliation(s)
- Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Jan Schlegel
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Hanna M G Barriga
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Miina Ojansivu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Florian Weber
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
- Department Medical Engineering, University of Applied Sciences Upper Austria, Linz, Austria
| | | | - Kariem Ezzat
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Herbert Stangl
- Medical University of Vienna, Center for Pathobiochemistry and Genetics, Institute of Medical Chemistry, Vienna, Austria
| | - Birgit Plochberger
- Department Medical Engineering, University of Applied Sciences Upper Austria, Linz, Austria
- LBG Ludwig Boltzmann Institute for Traumatology, Nanoscopy, Vienna, Austria
| | - Jurga Laurencikiene
- Lipid Laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | | | - Daniel Fürth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Molly M Stevens
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden.
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18
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McCarty SM, Clasby MC, Sexton JZ. High-Throughput Methods for the Discovery of Small Molecule Modulators of Pancreatic Beta-Cell Function and Regeneration. Assay Drug Dev Technol 2024; 22:148-159. [PMID: 38526231 DOI: 10.1089/adt.2023.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
The progression of type II diabetes (T2D) is characterized by a complex and highly variable loss of beta-cell mass, resulting in impaired insulin secretion. Many T2D drug discovery efforts aimed at discovering molecules that can protect or restore beta-cell mass and function have been developed using limited beta-cell lines and primary rodent/human pancreatic islets. Various high-throughput screening methods have been used in the context of drug discovery, including luciferase-based reporter assays, glucose-stimulated insulin secretion, and high-content screening. In this context, a cornerstone of small molecule discovery has been the use of immortalized rodent beta-cell lines. Although insightful, this usage has led to a more comprehensive understanding of rodent beta-cell proliferation pathways rather than their human counterparts. Advantages gained in enhanced physiological relevance are offered by three-dimensional (3D) primary islets and pseudoislets in contrast to monolayer cultures, but these approaches have been limited to use in low-throughput experiments. Emerging methods, such as high-throughput 3D islet imaging coupled with machine learning, aim to increase the feasibility of integrating 3D microtissue structures into high-throughput screening. This review explores the current methods used in high-throughput screening for small molecule modulators of beta-cell mass and function, a potentially pivotal strategy for diabetes drug discovery.
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Affiliation(s)
- Sean M McCarty
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, Michigan, USA
| | - Martin C Clasby
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonathan Z Sexton
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, Michigan, USA
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19
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Acanda De La Rocha AM, Berlow NE, Fader M, Coats ER, Saghira C, Espinal PS, Galano J, Khatib Z, Abdella H, Maher OM, Vorontsova Y, Andrade-Feraud CM, Daccache A, Jacome A, Reis V, Holcomb B, Ghurani Y, Rimblas L, Guilarte TR, Hu N, Salyakina D, Azzam DJ. Feasibility of functional precision medicine for guiding treatment of relapsed or refractory pediatric cancers. Nat Med 2024; 30:990-1000. [PMID: 38605166 PMCID: PMC11031400 DOI: 10.1038/s41591-024-02848-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/31/2024] [Indexed: 04/13/2024]
Abstract
Children with rare, relapsed or refractory cancers often face limited treatment options, and few predictive biomarkers are available that can enable personalized treatment recommendations. The implementation of functional precision medicine (FPM), which combines genomic profiling with drug sensitivity testing (DST) of patient-derived tumor cells, has potential to identify treatment options when standard-of-care is exhausted. The goal of this prospective observational study was to generate FPM data for pediatric patients with relapsed or refractory cancer. The primary objective was to determine the feasibility of returning FPM-based treatment recommendations in real time to the FPM tumor board (FPMTB) within a clinically actionable timeframe (<4 weeks). The secondary objective was to assess clinical outcomes from patients enrolled in the study. Twenty-five patients with relapsed or refractory solid and hematological cancers were enrolled; 21 patients underwent DST and 20 also completed genomic profiling. Median turnaround times for DST and genomics were within 10 days and 27 days, respectively. Treatment recommendations were made for 19 patients (76%), of whom 14 received therapeutic interventions. Six patients received subsequent FPM-guided treatments. Among these patients, five (83%) experienced a greater than 1.3-fold improvement in progression-free survival associated with their FPM-guided therapy relative to their previous therapy, and demonstrated a significant increase in progression-free survival and objective response rate compared to those of eight non-guided patients. The findings from our proof-of-principle study illustrate the potential for FPM to positively impact clinical care for pediatric and adolescent patients with relapsed or refractory cancers and warrant further validation in large prospective studies. ClinicalTrials.gov registration: NCT03860376 .
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Affiliation(s)
- Arlet M Acanda De La Rocha
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | | | - Maggie Fader
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Ebony R Coats
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Cima Saghira
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Paula S Espinal
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Jeanette Galano
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Ziad Khatib
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Haneen Abdella
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Ossama M Maher
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Yana Vorontsova
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Cristina M Andrade-Feraud
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Aimee Daccache
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Alexa Jacome
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Victoria Reis
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Baylee Holcomb
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Yasmin Ghurani
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Lilliam Rimblas
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Tomás R Guilarte
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Nan Hu
- Department of Biostatistics, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Daria Salyakina
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Diana J Azzam
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA.
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20
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Lin F, Li W, Wang D, Hu G, Qin Z, Xia X, Hu L, Liu X, Luo R. Advances in succinic acid production: the enhancement of CO 2 fixation for the carbon sequestration benefits. Front Bioeng Biotechnol 2024; 12:1392414. [PMID: 38605985 PMCID: PMC11007169 DOI: 10.3389/fbioe.2024.1392414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Succinic acid (SA), one of the 12 top platform chemicals produced from biomass, is a precursor of various high value-added derivatives. Specially, 1 mol CO2 is assimilated in 1 mol SA biosynthetic route under anaerobic conditions, which helps to achieve carbon reduction goals. In this review, methods for enhanced CO2 fixation in SA production and utilization of waste biomass for SA production are reviewed. Bioelectrochemical and bioreactor coupling systems constructed with off-gas reutilization to capture CO2 more efficiently were highlighted. In addition, the techno-economic analysis and carbon sequestration benefits for the synthesis of bio-based SA from CO2 and waste biomass are analyzed. Finally, a droplet microfluidics-based high-throughput screening technique applied to the future bioproduction of SA is proposed as a promising approach.
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Affiliation(s)
| | | | - Dan Wang
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, China
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21
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Perez-Bermejo JA, Efagene O, Matern WM, Holden JK, Kabir S, Chew GM, Andreoletti G, Catton E, Ennis CL, Garcia A, Gerstenberg TL, Hill KA, Jain A, Krassovsky K, Lalisan CD, Lord D, Quejarro BJ, Sales-Lee J, Shah M, Silva BJ, Skowronski J, Strukov YG, Thomas J, Veraz M, Vijay T, Wallace KA, Yuan Y, Grogan JL, Wienert B, Lahiri P, Treusch S, Dever DP, Soros VB, Partridge JR, Seim KL. Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair. Nat Commun 2024; 15:2625. [PMID: 38521763 PMCID: PMC10960832 DOI: 10.1038/s41467-024-46816-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/06/2024] [Indexed: 03/25/2024] Open
Abstract
Homology Directed Repair (HDR) enables precise genome editing, but the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alternative DNA repair routes, such as Non-Homologous End Joining (NHEJ). In this study, we develop a functional, pooled screening platform to identify protein-based reagents that improve HDR in human hematopoietic stem and progenitor cells (HSPCs). We leverage this screening platform to explore sequence diversity at the binding interface of the NHEJ inhibitor i53 and its target, 53BP1, identifying optimized variants that enable new intermolecular bonds and robustly increase HDR. We show that these variants specifically reduce insertion-deletion outcomes without increasing off-target editing, synergize with a DNAPK inhibitor molecule, and can be applied at manufacturing scale to increase the fraction of cells bearing repaired alleles. This screening platform can enable the discovery of future gene editing reagents that improve HDR outcomes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Meet Shah
- Graphite Bio, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Yue Yuan
- Graphite Bio, South San Francisco, CA, USA
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22
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Ai C, Chang JH, Tygesen AS, Vegge T, Hansen HA. High-throughput Compositional Screening of Pd xTi 1-xH y and Pd xNb 1-xH y Hydrides for CO 2 Reduction. ChemSusChem 2024; 17:e202301277. [PMID: 37965780 DOI: 10.1002/cssc.202301277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/16/2023]
Abstract
Electrochemical experiments and theoretical calculations have shown that Pd-based metal hydrides can perform well for the CO2 reduction reaction (CO2RR). Our previous work on doped-PdH showed that doping Ti and Nb into PdH can improve the CO2RR activity, suggesting that the Pd alloy hydrides with better performance are likely to be found in the PdxTi1-xHy and PdxNb1-xHy phase space. However, the vast compositional and structural space with different alloy hydride compositions and surface adsorbates, makes it intractable to screen out the stable and active PdxM1-xHy catalysts using density functional theory calculations. Herein, an active learning cluster expansion (ALCE) surrogate model equipped with Monte Carlo simulated annealing (MCSA), a CO* binding energy filter and a kinetic model are used to identify promising PdxTi1-xHy and PdxNb1-xHy catalysts with high stability and superior activity. Using our approach, we identify 24 stable and active candidates of PdxTi1-xHy and 5 active candidates of PdxNb1-xHy. Among these candidates, the Pd0.23Ti0.77H, Pd0.19Ti0.81H0.94, and Pd0.17Nb0.83H0.25 are predicted to display current densities of approximately 5.1, 5.1 and 4.6 μA cm-2 at -0.5 V overpotential, respectively, which are significantly higher than that of PdH at 3.7 μA cm-2.
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Affiliation(s)
- Changzhi Ai
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej 1, Bygning 101A, 2800, Kongens Lyngby, Dänemark
| | - Jin Hyun Chang
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej 1, Bygning 101A, 2800, Kongens Lyngby, Dänemark
| | - Alexander Sougaard Tygesen
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej 1, Bygning 101A, 2800, Kongens Lyngby, Dänemark
| | - Tejs Vegge
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej 1, Bygning 101A, 2800, Kongens Lyngby, Dänemark
| | - Heine Anton Hansen
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej 1, Bygning 101A, 2800, Kongens Lyngby, Dänemark
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23
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Mok DH, Back S, Siahrostami S. Validating ΔΔG Selectivity Descriptor for Electrosynthesis of H 2O 2 from Oxygen Reduction Reaction. Angew Chem Int Ed Engl 2024:e202404677. [PMID: 38513003 DOI: 10.1002/anie.202404677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024]
Abstract
Understanding selectivity trends is a crucial hurdle in the developing innovative catalysts for generating hydrogen peroxide through the two-electron oxygen reduction reaction (2e-ORR). The identification of selectivity patterns has been made more accessible through the introduction of a newly developed selectivity descriptor derived from thermodynamics, denoted as ΔΔG introduced in Chem Catal. 2023, 3(3), 100568. To validate the suitability of this parameter as a descriptor for 2e-ORR selectivity, we utilize an extensive library of 155 binary alloys. We validate that ΔΔG reliably depicts the selectivity trends in binary alloys reported for their high activity in the 2e-ORR. This analysis also enables the identification of nine selective 2e-ORR catalysts underscoring the efficacy of ΔΔG as 2e-ORR selectivity descriptor. This work highlights the significance of concurrently considering both selectivity and activity trends. This holistic approach is crucial for obtaining a comprehensive understanding in the identification of high-performance catalyst materials for optimal efficiency in various applications.
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Affiliation(s)
- Dong Hyeon Mok
- Department of Chemical and Biomolecular Engineering, Institute of Emergent Materials, Sogang University, Seoul, 04107, Republic of Korea
| | - Seoin Back
- Department of Chemical and Biomolecular Engineering, Institute of Emergent Materials, Sogang University, Seoul, 04107, Republic of Korea
| | - Samira Siahrostami
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C. V5 A 1S6, Canada
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24
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Wang Z, Yang X, Chen D, Liu Y, Li Z, Duan S, Zhang Z, Jiang X, Stockwell BR, Gu W. GAS41 modulates ferroptosis by anchoring NRF2 on chromatin. Nat Commun 2024; 15:2531. [PMID: 38514704 PMCID: PMC10957913 DOI: 10.1038/s41467-024-46857-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
YEATS domain-containing protein GAS41 is a histone reader and oncogene. Here, through genome-wide CRISPR-Cas9 screenings, we identify GAS41 as a repressor of ferroptosis. GAS41 interacts with NRF2 and is critical for NRF2 to activate its targets such as SLC7A11 for modulating ferroptosis. By recognizing the H3K27-acetylation (H3K27-ac) marker, GAS41 is recruited to the SLC7A11 promoter, independent of NRF2 binding. By bridging the interaction between NRF2 and the H3K27-ac marker, GAS41 acts as an anchor for NRF2 on chromatin in a promoter-specific manner for transcriptional activation. Moreover, the GAS41-mediated effect on ferroptosis contributes to its oncogenic role in vivo. These data demonstrate that GAS41 is a target for modulating tumor growth through ferroptosis. Our study reveals a mechanism for GAS41-mediated regulation in transcription by anchoring NRF2 on chromatin, and provides a model in which the DNA binding activity on chromatin by transcriptional factors (NRF2) can be directly regulated by histone markers (H3K27-ac).
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Affiliation(s)
- Zhe Wang
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Xin Yang
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Delin Chen
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Yanqing Liu
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Zhiming Li
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Shoufu Duan
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Department of Pediatrics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Department of Genetics and Development, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Xuejun Jiang
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Brent R Stockwell
- Department of Chemistry, Columbia University, New York, NY, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Wei Gu
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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25
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Vaknin I, Willinger O, Mandl J, Heuberger H, Ben-Ami D, Zeng Y, Goldberg S, Orenstein Y, Amit R. A universal system for boosting gene expression in eukaryotic cell-lines. Nat Commun 2024; 15:2394. [PMID: 38493141 PMCID: PMC10944472 DOI: 10.1038/s41467-024-46573-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
We demonstrate a transcriptional regulatory design algorithm that can boost expression in yeast and mammalian cell lines. The system consists of a simplified transcriptional architecture composed of a minimal core promoter and a synthetic upstream regulatory region (sURS) composed of up to three motifs selected from a list of 41 motifs conserved in the eukaryotic lineage. The sURS system was first characterized using an oligo-library containing 189,990 variants. We validate the resultant expression model using a set of 43 unseen sURS designs. The validation sURS experiments indicate that a generic set of grammar rules for boosting and attenuation may exist in yeast cells. Finally, we demonstrate that this generic set of grammar rules functions similarly in mammalian CHO-K1 and HeLa cells. Consequently, our work provides a design algorithm for boosting the expression of promoters used for expressing industrially relevant proteins in yeast and mammalian cell lines.
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Affiliation(s)
- Inbal Vaknin
- Department of Biotechnology and Food Engineering, Technion, Haifa, Israel
| | - Or Willinger
- Department of Biotechnology and Food Engineering, Technion, Haifa, Israel
| | - Jonathan Mandl
- Department of Computer Science, Bar-Ilan University, Ramat Gan, Israel
| | - Hadar Heuberger
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Dan Ben-Ami
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yi Zeng
- Department of Biotechnology and Food Engineering, Technion, Haifa, Israel
| | - Sarah Goldberg
- Department of Biotechnology and Food Engineering, Technion, Haifa, Israel
| | - Yaron Orenstein
- Department of Computer Science, Bar-Ilan University, Ramat Gan, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Roee Amit
- Department of Biotechnology and Food Engineering, Technion, Haifa, Israel.
- The Russell Berrie Nanotechnology Institute, Technion, Haifa, Israel.
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26
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Mizuno S, Wagata M, Nagaie S, Ishikuro M, Obara T, Tamiya G, Kuriyama S, Tanaka H, Yaegashi N, Yamamoto M, Sugawara J, Ogishima S. Development of phenotyping algorithms for hypertensive disorders of pregnancy (HDP) and their application in more than 22,000 pregnant women. Sci Rep 2024; 14:6292. [PMID: 38491024 PMCID: PMC10943000 DOI: 10.1038/s41598-024-55914-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
Recently, many phenotyping algorithms for high-throughput cohort identification have been developed. Prospective genome cohort studies are critical resources for precision medicine, but there are many hurdles in the precise cohort identification. Consequently, it is important to develop phenotyping algorithms for cohort data collection. Hypertensive disorders of pregnancy (HDP) is a leading cause of maternal morbidity and mortality. In this study, we developed, applied, and validated rule-based phenotyping algorithms of HDP. Two phenotyping algorithms, algorithms 1 and 2, were developed according to American and Japanese guidelines, and applied into 22,452 pregnant women in the Birth and Three-Generation Cohort Study of the Tohoku Medical Megabank project. To precise cohort identification, we analyzed both structured data (e.g., laboratory and physiological tests) and unstructured clinical notes. The identified subtypes of HDP were validated against reference standards. Algorithms 1 and 2 identified 7.93% and 8.08% of the subjects as having HDP, respectively, along with their HDP subtypes. Our algorithms were high performing with high positive predictive values (0.96 and 0.90 for algorithms 1 and 2, respectively). Overcoming the hurdle of precise cohort identification from large-scale cohort data collection, we achieved both developed and implemented phenotyping algorithms, and precisely identified HDP patients and their subtypes from large-scale cohort data collection.
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Affiliation(s)
- Satoshi Mizuno
- Department of Informatics for Genomic Medicine, Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Maiko Wagata
- Department of Feto-Maternal Medical Science, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Satoshi Nagaie
- Department of Informatics for Genomic Medicine, Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Mami Ishikuro
- Department of Molecular Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Taku Obara
- Department of Molecular Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Gen Tamiya
- Department of Statistical Genetics and Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Shinichi Kuriyama
- Department of Molecular Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | | | - Nobuo Yaegashi
- Department of Gynecology and Obstetrics, Tohoku University Graduate School of Medicine, Tohoku University, Miyagi, Japan
| | - Masayuki Yamamoto
- Department of Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Junichi Sugawara
- Department of Gynecology and Obstetrics, Tohoku University Graduate School of Medicine, Tohoku University, Miyagi, Japan
- Suzuki Memorial Hospital, 3-5-5, Satonomori, Iwanumashi, Miyagi, Japan
| | - Soichi Ogishima
- Department of Informatics for Genomic Medicine, Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan.
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Miyagi, Japan.
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Lefferts JW, Kroes S, Smith MB, Niemöller PJ, Nieuwenhuijze NDA, Sonneveld van Kooten HN, van der Ent CK, Beekman JM, van Beuningen SFB. OrgaSegment: deep-learning based organoid segmentation to quantify CFTR dependent fluid secretion. Commun Biol 2024; 7:319. [PMID: 38480810 PMCID: PMC10937908 DOI: 10.1038/s42003-024-05966-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Epithelial ion and fluid transport studies in patient-derived organoids (PDOs) are increasingly being used for preclinical studies, drug development and precision medicine applications. Epithelial fluid transport properties in PDOs can be measured through visual changes in organoid (lumen) size. Such organoid phenotypes have been highly instrumental for the studying of diseases, including cystic fibrosis (CF), which is characterized by genetic mutations of the CF transmembrane conductance regulator (CFTR) ion channel. Here we present OrgaSegment, a MASK-RCNN based deep-learning segmentation model allowing for the segmentation of individual intestinal PDO structures from bright-field images. OrgaSegment recognizes spherical structures in addition to the oddly-shaped organoids that are a hallmark of CF organoids and can be used in organoid swelling assays, including the new drug-induced swelling assay that we show here. OrgaSegment enabled easy quantification of organoid swelling and could discriminate between organoids with different CFTR mutations, as well as measure responses to CFTR modulating drugs. The easy-to-apply label-free segmentation tool can help to study CFTR-based fluid secretion and possibly other epithelial ion transport mechanisms in organoids.
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Affiliation(s)
- Juliet W Lefferts
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Suzanne Kroes
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Matthew B Smith
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands
| | - Paul J Niemöller
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Natascha D A Nieuwenhuijze
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands
| | - Heleen N Sonneveld van Kooten
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands.
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands.
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands.
| | - Sam F B van Beuningen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands.
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands.
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands.
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28
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Neri F, Takajjart SN, Lerner CA, Desprez PY, Schilling B, Campisi J, Gerencser AA. A Fully-Automated Senescence Test (FAST) for the high-throughput quantification of senescence-associated markers. bioRxiv 2024:2023.12.22.573123. [PMID: 38187756 PMCID: PMC10769423 DOI: 10.1101/2023.12.22.573123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Cellular senescence is a major driver of aging and age-related diseases. Quantification of senescent cells remains challenging due to the lack of senescence-specific markers and generalist, unbiased methodology. Here, we describe the Fully-Automated Senescence Test (FAST), an image-based method for the high-throughput, single-cell assessment of senescence in cultured cells. FAST quantifies three of the most widely adopted senescence-associated markers for each cell imaged: senescence-associated β-galactosidase activity (SA-β-Gal) using X-Gal, proliferation arrest via lack of 5-ethynyl-2'-deoxyuridine (EdU) incorporation, and enlarged morphology via increased nuclear area. The presented workflow entails microplate image acquisition, image processing, data analysis, and graphing. Standardization was achieved by i) quantifying colorimetric SA-β-Gal via optical density; ii) implementing staining background controls; iii) automating image acquisition, image processing, and data analysis. In addition to the automated threshold-based scoring, a multivariate machine learning approach is provided. We show that FAST accurately quantifies senescence burden and is agnostic to cell type and microscope setup. Moreover, it effectively mitigates false-positive senescence marker staining, a common issue arising from culturing conditions. Using FAST, we compared X-Gal with fluorescent C12FDG live-cell SA-β-Gal staining on the single-cell level. We observed only a modest correlation between the two, indicating that those stains are not trivially interchangeable. Finally, we provide proof of concept that our method is suitable for screening compounds that modify senescence burden. This method will be broadly useful to the aging field by enabling rapid, unbiased, and user-friendly quantification of senescence burden in culture, as well as facilitating large-scale experiments that were previously impractical.
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Affiliation(s)
- Francesco Neri
- Buck Institute for Research on Aging, Novato, CA, USA
- USC Leonard Davis School of Gerontology, Los Angeles, CA, USA
| | | | | | - Pierre-Yves Desprez
- Buck Institute for Research on Aging, Novato, CA, USA
- California Pacific Medical Center, San Francisco, CA, USA
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, CA, USA
- USC Leonard Davis School of Gerontology, Los Angeles, CA, USA
| | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA, USA
- USC Leonard Davis School of Gerontology, Los Angeles, CA, USA
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Dong X, Huang H, Huang L, Zhou Y, Zhang B, Zeng H, Lin Z, Zou G. Unearthing Superior Inorganic UV Second-Order Nonlinear Optical Materials: A Mineral-Inspired Method Integrating First-Principles High-Throughput Screening and Crystal Engineering. Angew Chem Int Ed Engl 2024; 63:e202318976. [PMID: 38258950 DOI: 10.1002/anie.202318976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 01/24/2024]
Abstract
Natural minerals, with their adaptable framework structures exemplified by perovskite and lyonsite, have sparked substantial interest as potential templates for the design of advanced functional solid-state materials. Nonetheless, the quest for new materials with desired properties remains a substantial challenge, primarily due to the scarcity of effective and practical synthetic approaches. In this study, we have harnessed a synergistic approach that seamlessly integrates first-principles high-throughput screening and crystal engineering to reinvigorate the often-overlooked fresnoite mineral, Ba2 TiOSi2 O7 . This innovative strategy has culminated in the successful synthesis of two superior inorganic UV nonlinear optical materials, namely Rb2 TeOP2 O7 and Rb2 SbFP2 O7 . Notably, Rb2 SbFP2 O7 demonstrates a comprehensive enhancement in nonlinear optical performance, featuring a shortened UV absorption edge (260 nm) and a more robust second-harmonic generation response (5.1×KDP). Particularly striking is its significantly increased birefringence (0.15@546 nm), which is approximately 30 times higher than the prototype Ba2 TiOSi2 O7 (0.005@546 nm). Our research has not only revitalized the potential of the fresnoite mineral for the development of new high-performance UV nonlinear optical materials but has also provided a clearly defined roadmap for the efficient exploration of novel structure-driven functional materials with targeted properties.
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Affiliation(s)
- Xuehua Dong
- College of Chemistry, Sichuan University, Chengdu, 610065, P. R. China
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, 610066, P. R. China
| | - Hongbo Huang
- College of Chemistry and Materials Science, Institute of Life Science and Green Development, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, State Key Laboratory of New Pharmaceutical Preparations and Excipients, Hebei University, Baoding, 071002, P. R. China
| | - Ling Huang
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, 610066, P. R. China
| | - Yuqiao Zhou
- College of Chemistry, Sichuan University, Chengdu, 610065, P. R. China
| | - Bingbing Zhang
- College of Chemistry and Materials Science, Institute of Life Science and Green Development, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, State Key Laboratory of New Pharmaceutical Preparations and Excipients, Hebei University, Baoding, 071002, P. R. China
| | - Hongmei Zeng
- College of Chemistry, Sichuan University, Chengdu, 610065, P. R. China
| | - Zhien Lin
- College of Chemistry, Sichuan University, Chengdu, 610065, P. R. China
| | - Guohong Zou
- College of Chemistry, Sichuan University, Chengdu, 610065, P. R. China
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30
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Smiejkowska N, Oorts L, Van Calster K, De Vooght L, Geens R, Mattelaer HP, Augustyns K, Strelkov SV, Lamprecht D, Temmerman K, Sterckx YGJ, Cappoen D, Cos P. A high-throughput target-based screening approach for the identification and assessment of Mycobacterium tuberculosis mycothione reductase inhibitors. Microbiol Spectr 2024; 12:e0372323. [PMID: 38315026 PMCID: PMC10913476 DOI: 10.1128/spectrum.03723-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/21/2023] [Indexed: 02/07/2024] Open
Abstract
The World Health Organization's goal to combat tuberculosis (TB) is hindered by the emergence of anti-microbial resistance, therefore necessitating the exploration of new drug targets. Multidrug regimens are indispensable in TB therapy as they provide synergetic bactericidal effects, shorten treatment duration, and reduce the risk of resistance development. The research within our European RespiriTB consortium explores Mycobacterium tuberculosis energy metabolism to identify new drug candidates that synergize with bedaquiline, with the aim of discovering more efficient combination drug regimens. In this study, we describe the development and validation of a luminescence-coupled, target-based assay for the identification of novel compounds inhibiting Mycobacterium tuberculosis mycothione reductase (MtrMtb), an enzyme with a role in the protection against oxidative stress. Recombinant MtrMtb was employed for the development of a highly sensitive, robust high-throughput screening (HTS) assay by coupling enzyme activity to a bioluminescent readout. Its application in a semi-automated setting resulted in the screening of a diverse library of ~130,000 compounds, from which 19 hits were retained after an assessment of their potency, selectivity, and specificity. The selected hits formed two clusters and four fragment molecules, which were further evaluated in whole-cell and intracellular infection assays. The established HTS discovery pipeline offers an opportunity to deliver novel MtrMtb inhibitors and lays the foundation for future efforts in developing robust biochemical assays for the identification and triaging of inhibitors from high-throughput library screens. IMPORTANCE The growing anti-microbial resistance poses a global public health threat, impeding progress toward eradicating tuberculosis. Despite decades of active research, there is still a dire need for the discovery of drugs with novel modes of action and exploration of combination drug regimens. Within the European RespiriTB consortium, we explore Mycobacterium tuberculosis energy metabolism to identify new drug candidates that synergize with bedaquiline, with the aim of discovering more efficient combination drug regimens. In this study, we present the development of a high-throughput screening pipeline that led to the identification of M. tuberculosis mycothione reductase inhibitors.
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Affiliation(s)
- Natalia Smiejkowska
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
- Laboratory of Medical Biochemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Lauren Oorts
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Kevin Van Calster
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Linda De Vooght
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Rob Geens
- Laboratory of Medical Biochemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Henri-Philippe Mattelaer
- Laboratory of Medicinal Chemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Sergei V. Strelkov
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | | | | | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Davie Cappoen
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
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31
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Edholm F, Nandy A, Reinhardt CR, Kastner DW, Kulik HJ. Protein3D: Enabling analysis and extraction of metal-containing sites from the Protein Data Bank with molSimplify. J Comput Chem 2024; 45:352-361. [PMID: 37873926 DOI: 10.1002/jcc.27242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
Metalloenzymes catalyze a wide range of chemical transformations, with the active site residues playing a key role in modulating chemical reactivity and selectivity. Unlike smaller synthetic catalysts, a metalloenzyme active site is embedded in a larger protein, which makes interrogation of electronic properties and geometric features with quantum mechanical calculations challenging. Here we implement the ability to fetch crystallographic structures from the Protein Data Bank and analyze the metal binding sites in the program molSimplify. We show the usefulness of the newly created protein3D class to extract the local environment around non-heme iron enzymes containing a two histidine motif and prepare 372 structures for quantum mechanical calculations. Our implementation of protein3D serves to expand the range of systems molSimplify can be used to analyze and will enable high-throughput study of metal-containing active sites in proteins.
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Affiliation(s)
- Freya Edholm
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Clorice R Reinhardt
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David W Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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32
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Heuberger L, Messmer D, dos Santos EC, Scherrer D, Lörtscher E, Schoenenberger C, Palivan CG. Microfluidic Giant Polymer Vesicles Equipped with Biopores for High-Throughput Screening of Bacteria. Adv Sci (Weinh) 2024; 11:e2307103. [PMID: 38158637 PMCID: PMC10953582 DOI: 10.1002/advs.202307103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Indexed: 01/03/2024]
Abstract
Understanding the mechanisms of antibiotic resistance is critical for the development of new therapeutics. Traditional methods for testing bacteria are often limited in their efficiency and reusability. Single bacterial cells can be studied at high throughput using double emulsions, although the lack of control over the oil shell permeability and limited access to the droplet interior present serious drawbacks. Here, a straightforward strategy for studying bacteria-encapsulating double emulsion-templated giant unilamellar vesicles (GUVs) is introduced. This microfluidic approach serves to simultaneously load bacteria inside synthetic GUVs and to permeabilize their membrane with the pore-forming peptide melittin. This enables antibiotic delivery or the influx of fresh medium into the GUV lumen for highly parallel cultivation and antimicrobial efficacy testing. Polymer-based GUVs proved to be efficient culture and analysis microvessels, as microfluidics allow easy selection and encapsulation of bacteria and rapid modification of culture conditions for antibiotic development. Further, a method for in situ profiling of biofilms within GUVs for high-throughput screening is demonstrated. Conceivably, synthetic GUVs equipped with biopores can serve as a foundation for the high-throughput screening of bacterial colony interactions during biofilm formation and for investigating the effect of antibiotics on biofilms.
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Affiliation(s)
- Lukas Heuberger
- Department of ChemistryUniversity of BaselMattenstrasse 22Basel4002Switzerland
| | - Daniel Messmer
- Department of ChemistryUniversity of BaselMattenstrasse 22Basel4002Switzerland
| | - Elena C. dos Santos
- Department of ChemistryUniversity of BaselMattenstrasse 22Basel4002Switzerland
| | - Dominik Scherrer
- IBM Research Europe–ZürichSäumerstrasse 4Rüschlikon8803Switzerland
| | - Emanuel Lörtscher
- IBM Research Europe–ZürichSäumerstrasse 4Rüschlikon8803Switzerland
- NCCR‐Molecular Systems EngineeringMattenstrasse 24a, BPR 1095Basel4058Switzerland
| | | | - Cornelia G. Palivan
- Department of ChemistryUniversity of BaselMattenstrasse 22Basel4002Switzerland
- NCCR‐Molecular Systems EngineeringMattenstrasse 24a, BPR 1095Basel4058Switzerland
- Swiss Nanoscience Institute (SNI)University of BaselKlingelbergstrasse 82Basel4056Switzerland
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33
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Li J, Canham SM, Wu H, Henault M, Chen L, Liu G, Chen Y, Yu G, Miller HR, Hornak V, Brittain SM, Michaud GA, Tutter A, Broom W, Digan ME, McWhirter SM, Sivick KE, Pham HT, Chen CH, Tria GS, McKenna JM, Schirle M, Mao X, Nicholson TB, Wang Y, Jenkins JL, Jain RK, Tallarico JA, Patel SJ, Zheng L, Ross NT, Cho CY, Zhang X, Bai XC, Feng Y. Activation of human STING by a molecular glue-like compound. Nat Chem Biol 2024; 20:365-372. [PMID: 37828400 PMCID: PMC10907298 DOI: 10.1038/s41589-023-01434-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/02/2023] [Indexed: 10/14/2023]
Abstract
Stimulator of interferon genes (STING) is a dimeric transmembrane adapter protein that plays a key role in the human innate immune response to infection and has been therapeutically exploited for its antitumor activity. The activation of STING requires its high-order oligomerization, which could be induced by binding of the endogenous ligand, cGAMP, to the cytosolic ligand-binding domain. Here we report the discovery through functional screens of a class of compounds, named NVS-STGs, that activate human STING. Our cryo-EM structures show that NVS-STG2 induces the high-order oligomerization of human STING by binding to a pocket between the transmembrane domains of the neighboring STING dimers, effectively acting as a molecular glue. Our functional assays showed that NVS-STG2 could elicit potent STING-mediated immune responses in cells and antitumor activities in animal models.
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Affiliation(s)
- Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephen M Canham
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
| | - Hua Wu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Martin Henault
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Lihao Chen
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Guoxun Liu
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Yu Chen
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Gary Yu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Howard R Miller
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Viktor Hornak
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | - Antonin Tutter
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Wendy Broom
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | | | - Helen T Pham
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - George S Tria
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Xiaohong Mao
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Yuan Wang
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Rishi K Jain
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Sejal J Patel
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Lianxing Zheng
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Nathan T Ross
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Charles Y Cho
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Xuewu Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Yan Feng
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
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Nagel A, Huegel J, Petrilli A, Rosario R, Victoria B, Hardin HM, Fernandez-Valle C. Simultaneous inhibition of PI3K and PAK in preclinical models of neurofibromatosis type 2-related schwannomatosis. Oncogene 2024; 43:921-930. [PMID: 38336988 PMCID: PMC10959746 DOI: 10.1038/s41388-024-02958-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]
Abstract
Neurofibromatosis Type 2 (NF2)-related schwannomatosis is a genetic disorder that causes development of multiple types of nervous system tumors. The primary and diagnostic tumor type is bilateral vestibular schwannoma. There is no cure or drug therapy for NF2. Recommended treatments include surgical resection and radiation, both of which can leave patients with severe neurological deficits or increase the risk of future malignant tumors. Results of our previous pilot high-throughput drug screen identified phosphoinositide 3-kinase (PI3K) inhibitors as strong candidates based on loss of viability of mouse merlin-deficient Schwann cells (MD-SCs). Here we used novel human schwannoma model cells to conduct combination drug screens. We identified a class I PI3K inhibitor, pictilisib and p21 activated kinase (PAK) inhibitor, PF-3758309 as the top combination due to high synergy in cell viability assays. Both single and combination therapies significantly reduced growth of mouse MD-SCs in an orthotopic allograft mouse model. The inhibitor combination promoted cell cycle arrest and apoptosis in mouse merlin-deficient Schwann (MD-SCs) cells and cell cycle arrest in human MD-SCs. This study identifies the PI3K and PAK pathways as potential targets for combination drug treatment of NF2-related schwannomatosis.
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Affiliation(s)
- Anna Nagel
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Julianne Huegel
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Alejandra Petrilli
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Rosa Rosario
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Berta Victoria
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Haley M Hardin
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Cristina Fernandez-Valle
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA.
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35
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Yang J, Ran Y, Liu S, Ren C, Lou Y, Ju P, Li G, Li X, Zhang D. Synergistic D-Amino Acids Based Antimicrobial Cocktails Formulated via High-Throughput Screening and Machine Learning. Adv Sci (Weinh) 2024; 11:e2307173. [PMID: 38126652 PMCID: PMC10916672 DOI: 10.1002/advs.202307173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/29/2023] [Indexed: 12/23/2023]
Abstract
Antimicrobial resistance (AMR) from pathogenic bacterial biofilms has become a global health issue while developing novel antimicrobials is inefficient and costly. Combining existing multiple drugs with enhanced efficacy and/or reduced toxicity may be a promising approach to treat AMR. D-amino acids mixtures coupled with antibiotics can provide new therapies for drug-resistance infection with reduced toxicity by lower drug dosage requirements. However, iterative trial-and-error experiments are not tenable to prioritize credible drug formulations, owing to the extremely large number of possible combinations. Herein, a new avenue is provide to accelerate the exploration of desirable antimicrobial formulations via high-throughput screening and machine learning optimization. Such an intelligent method can navigate the large search space and rapidly identify the D-amino acid mixtures with the highest anti-biofilm efficiency and also the synergisms between D-amino acid mixtures and antibiotics. The optimized drug cocktails exhibit high antimicrobial efficacy while remaining non-toxic, which is demonstrated not only from in vitro assessments but also the first in vivo study using a lung infection mouse model.
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Affiliation(s)
- Jingzhi Yang
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
| | - Yami Ran
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
- BRI Southeast Asia Network for Corrosion and ProtectionShunde Graduate School of University of Science and Technology BeijingFoshan528000China
| | - Shaopeng Liu
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
| | - Chenhao Ren
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
| | - Yuntian Lou
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
- BRI Southeast Asia Network for Corrosion and ProtectionShunde Graduate School of University of Science and Technology BeijingFoshan528000China
| | - Pengfei Ju
- Shanghai Aerospace Equipment ManufacturerShanghai200245China
| | - Guoliang Li
- College of Materials Science and EngineeringBeijing University of Chemical TechnologyBeijing100029China
| | - Xiaogang Li
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
- BRI Southeast Asia Network for Corrosion and ProtectionShunde Graduate School of University of Science and Technology BeijingFoshan528000China
| | - Dawei Zhang
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
- BRI Southeast Asia Network for Corrosion and ProtectionShunde Graduate School of University of Science and Technology BeijingFoshan528000China
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Mirzaie M, Gholizadeh E, Miettinen JJ, Ianevski F, Ruokoranta T, Saarela J, Manninen M, Miettinen S, Heckman CA, Jafari M. Designing patient-oriented combination therapies for acute myeloid leukemia based on efficacy/toxicity integration and bipartite network modeling. Oncogenesis 2024; 13:11. [PMID: 38429288 PMCID: PMC10907624 DOI: 10.1038/s41389-024-00510-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024] Open
Abstract
Acute myeloid leukemia (AML), a heterogeneous and aggressive blood cancer, does not respond well to single-drug therapy. A combination of drugs is required to effectively treat this disease. Computational models are critical for combination therapy discovery due to the tens of thousands of two-drug combinations, even with approved drugs. While predicting synergistic drugs is the focus of current methods, few consider drug efficacy and potential toxicity, which are crucial for treatment success. To find effective new drug candidates, we constructed a bipartite network using patient-derived tumor samples and drugs. The network is based on drug-response screening and summarizes all treatment response heterogeneity as drug response weights. This bipartite network is then projected onto the drug part, resulting in the drug similarity network. Distinct drug clusters were identified using community detection methods, each targeting different biological processes and pathways as revealed by enrichment and pathway analysis of the drugs' protein targets. Four drugs with the highest efficacy and lowest toxicity from each cluster were selected and tested for drug sensitivity using cell viability assays on various samples. Results show that ruxolitinib-ulixertinib and sapanisertib-LY3009120 are the most effective combinations with the least toxicity and the best synergistic effect on blast cells. These findings lay the foundation for personalized and successful AML therapies, ultimately leading to the development of drug combinations that can be used alongside standard first-line AML treatment.
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Affiliation(s)
- Mehdi Mirzaie
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Elham Gholizadeh
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Juho J Miettinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Filipp Ianevski
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Tanja Ruokoranta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - Susanna Miettinen
- Adult Stem Cell Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
| | - Mohieddin Jafari
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
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Vlasveld M, Callegaro G, Fisher C, Eakins J, Walker P, Lok S, van Oost S, de Jong B, Pellegrino-Coppola D, Burger G, Wink S, van de Water B. The integrated stress response-related expression of CHOP due to mitochondrial toxicity is a warning sign for DILI liability. Liver Int 2024; 44:760-775. [PMID: 38217387 DOI: 10.1111/liv.15822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 01/15/2024]
Abstract
BACKGROUND AND AIMS Drug-induced liver injury (DILI) is one of the most frequent reasons for failure of drugs in clinical trials or market withdrawal. Early assessment of DILI risk remains a major challenge during drug development. Here, we present a mechanism-based weight-of-evidence approach able to identify certain candidate compounds with DILI liabilities due to mitochondrial toxicity. METHODS A total of 1587 FDA-approved drugs and 378 kinase inhibitors were screened for cellular stress response activation associated with DILI using an imaging-based HepG2 BAC-GFP reporter platform including the integrated stress response (CHOP), DNA damage response (P21) and oxidative stress response (SRXN1). RESULTS In total 389, 219 and 104 drugs were able to induce CHOP-GFP, P21-GFP and SRXN1-GFP expression at 50 μM respectively. Concentration response analysis identified 154 FDA-approved drugs as critical CHOP-GFP inducers. Based on predicted and observed (pre-)clinical DILI liabilities of these drugs, nine antimycotic drugs (e.g. butoconazole, miconazole, tioconazole) and 13 central nervous system (CNS) agents (e.g. duloxetine, fluoxetine) were selected for transcriptomic evaluation using whole-genome RNA-sequencing of primary human hepatocytes. Gene network analysis uncovered mitochondrial processes, NRF2 signalling and xenobiotic metabolism as most affected by the antimycotic drugs and CNS agents. Both the selected antimycotics and CNS agents caused impairment of mitochondrial oxygen consumption in both HepG2 and primary human hepatocytes. CONCLUSIONS Together, the results suggest that early pre-clinical screening for CHOP expression could indicate liability of mitochondrial toxicity in the context of DILI, and, therefore, could serve as an important warning signal to consider during decision-making in drug development.
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Affiliation(s)
- Matthijs Vlasveld
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Giulia Callegaro
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | | | | | | | - Samantha Lok
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Siddh van Oost
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Brechtje de Jong
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Damiano Pellegrino-Coppola
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Gerhard Burger
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Steven Wink
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
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38
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Mattson NM, Chan AKN, Miyashita K, Mukhaleva E, Chang WH, Yang L, Ma N, Wang Y, Pokharel SP, Li M, Liu Q, Xu X, Chen R, Singh P, Zhang L, Elsayed Z, Chen B, Keen D, Pirrotte P, Rosen ST, Chen J, LaBarge MA, Shively JE, Vaidehi N, Rockne RC, Feng M, Chen CW. A novel class of inhibitors that disrupts the stability of integrin heterodimers identified by CRISPR-tiling-instructed genetic screens. Nat Struct Mol Biol 2024; 31:465-475. [PMID: 38316881 PMCID: PMC10948361 DOI: 10.1038/s41594-024-01211-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024]
Abstract
The plasma membrane is enriched for receptors and signaling proteins that are accessible from the extracellular space for pharmacological intervention. Here we conducted a series of CRISPR screens using human cell surface proteome and integrin family libraries in multiple cancer models. Our results identified ITGAV (integrin αV) and its heterodimer partner ITGB5 (integrin β5) as the essential integrin α/β pair for cancer cell expansion. High-density CRISPR gene tiling further pinpointed the integral pocket within the β-propeller domain of ITGAV for integrin αVβ5 dimerization. Combined with in silico compound docking, we developed a CRISPR-Tiling-Instructed Computer-Aided (CRISPR-TICA) pipeline for drug discovery and identified Cpd_AV2 as a lead inhibitor targeting the β-propeller central pocket of ITGAV. Cpd_AV2 treatment led to rapid uncoupling of integrin αVβ5 and cellular apoptosis, providing a unique class of therapeutic action that eliminates the integrin signaling via heterodimer dissociation. We also foresee the CRISPR-TICA approach to be an accessible method for future drug discovery studies.
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Affiliation(s)
- Nicole M Mattson
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Anthony K N Chan
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Kazuya Miyashita
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Elizaveta Mukhaleva
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Wen-Han Chang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Yingyu Wang
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sheela Pangeni Pokharel
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Mingli Li
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Qiao Liu
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Xiaobao Xu
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Renee Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Priyanka Singh
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Leisi Zhang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Zeinab Elsayed
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Bryan Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Denise Keen
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Patrick Pirrotte
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Steven T Rosen
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Mark A LaBarge
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - John E Shively
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Immunology and Theranostics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Russell C Rockne
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Mingye Feng
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA.
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA.
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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Adams DJ, Barlas B, McIntyre RE, Salguero I, van der Weyden L, Barros A, Vicente JR, Karimpour N, Haider A, Ranzani M, Turner G, Thompson NA, Harle V, Olvera-León R, Robles-Espinoza CD, Speak AO, Geisler N, Weninger WJ, Geyer SH, Hewinson J, Karp NA, Fu B, Yang F, Kozik Z, Choudhary J, Yu L, van Ruiten MS, Rowland BD, Lelliott CJ, Del Castillo Velasco-Herrera M, Verstraten R, Bruckner L, Henssen AG, Rooimans MA, de Lange J, Mohun TJ, Arends MJ, Kentistou KA, Coelho PA, Zhao Y, Zecchini H, Perry JRB, Jackson SP, Balmus G. Genetic determinants of micronucleus formation in vivo. Nature 2024; 627:130-136. [PMID: 38355793 PMCID: PMC10917660 DOI: 10.1038/s41586-023-07009-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/21/2023] [Indexed: 02/16/2024]
Abstract
Genomic instability arising from defective responses to DNA damage1 or mitotic chromosomal imbalances2 can lead to the sequestration of DNA in aberrant extranuclear structures called micronuclei (MN). Although MN are a hallmark of ageing and diseases associated with genomic instability, the catalogue of genetic players that regulate the generation of MN remains to be determined. Here we analyse 997 mouse mutant lines, revealing 145 genes whose loss significantly increases (n = 71) or decreases (n = 74) MN formation, including many genes whose orthologues are linked to human disease. We found that mice null for Dscc1, which showed the most significant increase in MN, also displayed a range of phenotypes characteristic of patients with cohesinopathy disorders. After validating the DSCC1-associated MN instability phenotype in human cells, we used genome-wide CRISPR-Cas9 screening to define synthetic lethal and synthetic rescue interactors. We found that the loss of SIRT1 can rescue phenotypes associated with DSCC1 loss in a manner paralleling restoration of protein acetylation of SMC3. Our study reveals factors involved in maintaining genomic stability and shows how this information can be used to identify mechanisms that are relevant to human disease biology1.
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Affiliation(s)
- D J Adams
- Wellcome Sanger Institute, Cambridge, UK.
| | - B Barlas
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - I Salguero
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - A Barros
- Wellcome Sanger Institute, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - J R Vicente
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - N Karimpour
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - A Haider
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - M Ranzani
- Wellcome Sanger Institute, Cambridge, UK
| | - G Turner
- Wellcome Sanger Institute, Cambridge, UK
| | | | - V Harle
- Wellcome Sanger Institute, Cambridge, UK
| | | | - C D Robles-Espinoza
- Wellcome Sanger Institute, Cambridge, UK
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, México
| | - A O Speak
- Wellcome Sanger Institute, Cambridge, UK
| | - N Geisler
- Wellcome Sanger Institute, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W J Weninger
- Division of Anatomy, MIC, Medical University of Vienna, Wien, Austria
| | - S H Geyer
- Division of Anatomy, MIC, Medical University of Vienna, Wien, Austria
| | - J Hewinson
- Wellcome Sanger Institute, Cambridge, UK
| | - N A Karp
- Wellcome Sanger Institute, Cambridge, UK
| | - B Fu
- Wellcome Sanger Institute, Cambridge, UK
| | - F Yang
- Wellcome Sanger Institute, Cambridge, UK
| | - Z Kozik
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - J Choudhary
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - L Yu
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - M S van Ruiten
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - B D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - L Bruckner
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - A G Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M A Rooimans
- Department of Human Genetics, Section of Oncogenetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - J de Lange
- Department of Human Genetics, Section of Oncogenetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - T J Mohun
- Division of Developmental Biology, MRC, National Institute for Medical Research, London, UK
| | - M J Arends
- Division of Pathology, Cancer Research UK Scotland Centre, Institute of Genetics & Cancer The University of Edinburgh, Edinburgh, UK
| | - K A Kentistou
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - P A Coelho
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Y Zhao
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - H Zecchini
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - J R B Perry
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - S P Jackson
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - G Balmus
- Wellcome Sanger Institute, Cambridge, UK.
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK.
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Department of Molecular Neuroscience, Transylvanian Institute of Neuroscience, Cluj-Napoca, Romania.
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40
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Zhang R, Yan H, Zhou J, Yan G, Liu X, Shang C, Chen Y. Improved fluorescence-based assay for rapid screening and evaluation of SARS-CoV-2 main protease inhibitors. J Med Virol 2024; 96:e29498. [PMID: 38436148 DOI: 10.1002/jmv.29498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global threat to human health. In parallel with vaccines, efficacious antivirals are urgently needed. SARS-CoV-2 main protease (Mpro) is an attractive drug target for antiviral development owing to its key roles in virus replication and host immune evasion. Due to the limitations of currently available methods, the development of novel high-throughput screening assays is of the highest importance for the discovery of Mpro inhibitors. In this study, we first developed an improved fluorescence-based assay for rapid screening of Mpro inhibitors from an anti-infection compound library using a versatile dimerization-dependent red fluorescent protein (ddRFP) biosensor. Utilizing this assay, we identified MG-101 as a competitive Mpro inhibitor in vitro. Moreover, our results revealed that ensitrelvir is a potent Mpro inhibitor, but baicalein, chloroquine, ebselen, echinatin, and silibinin are not. Therefore, this robust ddRFP assay provides a faithful avenue for rapid screening and evaluation of Mpro inhibitors to fight against COVID-19.
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Affiliation(s)
- Rui Zhang
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Haohao Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Jiahao Zhou
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Gangan Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Xiaoping Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Chao Shang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yunyu Chen
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
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41
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Qin P, Lu XY, Xu JH, Yu HL. Directed evolution of Baeyer-Villiger monooxygenase for highly secretory expressed in Pichia pastoris and efficient preparation of chiral pyrazole sulfoxide. Biotechnol Bioeng 2024; 121:971-979. [PMID: 38088450 DOI: 10.1002/bit.28617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/23/2023] [Accepted: 11/26/2023] [Indexed: 02/20/2024]
Abstract
The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is a highly distinguished expression platform for the excellent synthesis of various heterologous proteins in recent years. With the advantages of high-density fermentation, P. pastoris can produce gram amounts of recombinant proteins. While not every protein of interest can be expressed to such high titers, such as Baeyer-Villiger monooxygenase (BVMO) (AcPSMO) which is responsible for pyrazole sulfide asymmetric oxidation. In this work, an excellent yeast expression system was established to facilitate efficient AcPSMO expression, which exhibited 9.5-fold enhanced secretion. Subsequently, an ultrahigh throughput screening method based on fluorescence-activated cell sorting by fusing super folder green fluorescent protein (sfGFP) in the C-terminal of AcPSMO was developed, and directed evolution was performed. The protein expression level of the superior mutant AcPSMOP1 (S58T/T252P/E336N/H456D) reached 84.6 mg/L at 100 mL shaking flask, which was 4.7 times higher than the levels obtained with the wild-type. Finally, the optimized chassis cells were used for high-density fermentation on a 5-L scale, and AcPSMOP1 protein yield of 3.4 g/L was achieved, representing approximately 85% of the total protein secreted. By directly employing the pH-adjusted supernatant as a biocatalyst, 20 g/L pyrmetazole sulfide was completely transformed into the corresponding (S)-sulfoxide, with a 78.8% isolated yield. This work confers dramatic benefits for efficient secretion of other BVMOs in P. pastoris.
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Affiliation(s)
- Peng Qin
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, China
| | - Xin-Yi Lu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, China
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42
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Pitrez PR, Monteiro LM, Borgogno O, Nissan X, Mertens J, Ferreira L. Cellular reprogramming as a tool to model human aging in a dish. Nat Commun 2024; 15:1816. [PMID: 38418829 PMCID: PMC10902382 DOI: 10.1038/s41467-024-46004-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
The design of human model systems is highly relevant to unveil the underlying mechanisms of aging and to provide insights on potential interventions to extend human health and life span. In this perspective, we explore the potential of 2D or 3D culture models comprising human induced pluripotent stem cells and transdifferentiated cells obtained from aged or age-related disorder-affected donors to enhance our understanding of human aging and to catalyze the discovery of anti-aging interventions.
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Affiliation(s)
- Patricia R Pitrez
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, 3000-548, Coimbra, Portugal
| | - Luis M Monteiro
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, 3000-548, Coimbra, Portugal
- IIIUC-institute of Interdisciplinary Research, University of Coimbra, Casa Costa Alemão, Coimbra, 3030-789, Portugal
| | - Oliver Borgogno
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Xavier Nissan
- CECS, I-STEM, AFM, Institute for Stem Cell Therapy and Exploration of Monogenic diseases, Evry cedex, France
| | - Jerome Mertens
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Lino Ferreira
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.
- Faculty of Medicine, University of Coimbra, 3000-548, Coimbra, Portugal.
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43
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Callahan AJ, Gandhesiri S, Travaline TL, Reja RM, Lozano Salazar L, Hanna S, Lee YC, Li K, Tokareva OS, Swiecicki JM, Loas A, Verdine GL, McGee JH, Pentelute BL. Mirror-image ligand discovery enabled by single-shot fast-flow synthesis of D-proteins. Nat Commun 2024; 15:1813. [PMID: 38418820 PMCID: PMC10901774 DOI: 10.1038/s41467-024-45634-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Widespread adoption of mirror-image biological systems presents difficulties in accessing the requisite D-protein substrates. In particular, mirror-image phage display has the potential for high-throughput generation of biologically stable macrocyclic D-peptide binders with potentially unique recognition modes but is hindered by the individualized optimization required for D-protein chemical synthesis. We demonstrate a general mirror-image phage display pipeline that utilizes automated flow peptide synthesis to prepare D-proteins in a single run. With this approach, we prepare and characterize 12 D-proteins - almost one third of all reported D-proteins to date. With access to mirror-image protein targets, we describe the successful discovery of six macrocyclic D-peptide binders: three to the oncoprotein MDM2, and three to the E3 ubiquitin ligase CHIP. Reliable production of mirror-image proteins can unlock the full potential of D-peptide drug discovery and streamline the study of mirror-image biology more broadly.
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Affiliation(s)
- Alex J Callahan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Satish Gandhesiri
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Tara L Travaline
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
| | - Rahi M Reja
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Lia Lozano Salazar
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Stephanie Hanna
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Yen-Chun Lee
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Chemistry, National Cheng Kung University, No.1, University Road, Tainan City, 701, Taiwan
| | - Kunhua Li
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
| | - Olena S Tokareva
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
| | - Jean-Marie Swiecicki
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
- Relay Therapeutics, Inc., 399 Binney Street, 2nd Floor, Cambridge, MA, 02139, USA
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Gregory L Verdine
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA, 02138, USA
| | - John H McGee
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA.
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02142, USA.
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
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44
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Zheng K, Hu J, Hu C, Liu X, Wang Y, Han H, Xing W, Yang L, Zhang J, Hong Q, Hao F, Li W. Establishing an ANO1-Based Cell Model for High-Throughput Screening Targeting TRPV4 Regulators. Molecules 2024; 29:1036. [PMID: 38474548 DOI: 10.3390/molecules29051036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Transient receptor potential vanilloid 4 (TRPV4) is a widely expressed cation channel that plays an important role in many physiological and pathological processes. However, most TRPV4 drugs carry a risk of side effects. Moreover, existing screening methods are not suitable for the high-throughput screening (HTS) of drugs. In this study, a cell model and HTS method for targeting TRPV4 channel drugs were established based on a calcium-activated chloride channel protein 1 Anoctamin 1 (ANO1) and a double mutant (YFP-H148Q/I152L) of the yellow fluorescent protein (YFP). Patch-clamp experiments and fluorescence quenching kinetic experiments were used to verify that the model could sensitively detect changes in intracellular Ca2+ concentration. The functionality of the TRPV4 cell model was examined through temperature variations and different concentrations of TRPV4 modulators, and the performance of the model in HTS was also evaluated. The model was able to sensitively detect changes in the intracellular Ca2+ concentration and also excelled at screening TRPV4 drugs, and the model was more suitable for HTS. We successfully constructed a drug cell screening model targeting the TRPV4 channel, which provides a tool to study the pathophysiological functions of TRPV4 in vitro.
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Affiliation(s)
- Kai Zheng
- College of Laboratory Medicine, Jilin Medical University, Jilin 132000, China
| | - Jiang Hu
- College of Laboratory Medicine, Jilin Medical University, Jilin 132000, China
| | - Cheng Hu
- College of Laboratory Medicine, Jilin Medical University, Jilin 132000, China
| | - Xueying Liu
- School of Medical Technology, Beihua University, Jilin 132000, China
| | - Yanyan Wang
- School of Medical Technology, Beihua University, Jilin 132000, China
| | - Haojian Han
- College of Laboratory Medicine, Jilin Medical University, Jilin 132000, China
| | - Wenzhu Xing
- School of Medical Technology, Beihua University, Jilin 132000, China
| | - Liu Yang
- School of Medical Technology, Beihua University, Jilin 132000, China
| | - Junran Zhang
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiyuan Hong
- College of Laboratory Medicine, Jilin Medical University, Jilin 132000, China
| | - Feng Hao
- College of Laboratory Medicine, Jilin Medical University, Jilin 132000, China
| | - Wenliang Li
- Jilin Collaborative Innovation Center for Antibody Engineering, Jilin Medical University, Jilin 132000, China
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45
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Li L, Liu X, Bai Y, Yao B, Luo H, Tu T. High-Throughput Screening Techniques for the Selection of Thermostable Enzymes. J Agric Food Chem 2024; 72:3833-3845. [PMID: 38285533 DOI: 10.1021/acs.jafc.3c07554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
The acquisition of a thermostable enzyme is an indispensable prerequisite for its successful implementation in industrial applications and the development of novel functionalities. Various protein engineering approaches, including rational design, semirational design, and directed evolution, have been employed to enhance thermostability. However, all of these approaches require sensitive and reliable high-throughput screening (HTS) technologies to efficiently and rapidly identify variants with improved properties. While numerous reviews focus on modification strategies for enhancing enzyme thermostability, there is a dearth of literature reviewing HTS methods specifically aimed at this objective. Herein, we present a comprehensive overview of various HTS methods utilized for modifying enzyme thermostability across different screening platforms. Additionally, we highlight significant recent examples that demonstrate the successful application of these methods. Furthermore, we address the technical challenges associated with HTS technologies used for screening thermostable enzyme variants and discuss valuable perspectives to promote further advancements in this field. This review serves as an authoritative reference source offering theoretical support for selecting appropriate screening strategies tailored to specific enzymes with the aim of improving their thermostability.
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Affiliation(s)
- Lanxue Li
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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46
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Lethe MCL, Bui D, Hu M, Wang X, Singh R, Chan CTY. Discovering New Substrates of a UDP-Glycosyltransferase with a High-Throughput Method. Int J Mol Sci 2024; 25:2725. [PMID: 38473971 PMCID: PMC10931590 DOI: 10.3390/ijms25052725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
UDP-glycosyltransferases (UGTs) form a large enzyme family that is found in a wide range of organisms. These enzymes are known for accepting a wide variety of substrates, and they derivatize xenobiotics and metabolites for detoxification. However, most UGT homologs have not been well characterized, and their potential for biomedical and environmental applications is underexplored. In this work, we have used a fluorescent assay for screening substrates of a plant UGT homolog by monitoring the formation of UDP. We optimized the assay such that it could be used for high-throughput screening of substrates of the Medicago truncatula UGT enzyme, UGT71G1, and our results show that 34 of the 159 screened compound samples are potential substrates. With an LC-MS/MS method, we confirmed that three of these candidates indeed were glycosylated by UGT71G1, which includes bisphenol A (BPA) and 7-Ethyl-10-hydroxycamptothecin (SN-38); derivatization of these toxic compounds can lead to new environmental and medical applications. This work suggests that UGT homologs may recognize a substrate profile that is much broader than previously anticipated. Additionally, it demonstrates that this screening method provides a new means to study UDP-glycosyltransferases, facilitating the use of these enzymes to tackle a wide range of problems.
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Affiliation(s)
- Mary C. L. Lethe
- Department of Biomedical Engineering, College of Engineering, University of North Texas, 3940 N Elm Street, Denton, TX 76207, USA;
| | - Dinh Bui
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 4349 Martin Luther King Boulevard, Houston, TX 77204, USA; (D.B.); (M.H.); (R.S.)
| | - Ming Hu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 4349 Martin Luther King Boulevard, Houston, TX 77204, USA; (D.B.); (M.H.); (R.S.)
| | - Xiaoqiang Wang
- Department of Biological Sciences, College of Science, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA;
| | - Rashim Singh
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 4349 Martin Luther King Boulevard, Houston, TX 77204, USA; (D.B.); (M.H.); (R.S.)
- Sanarentero LLC, 514 N. Elder Grove Drive, Pearland, TX 77584, USA
| | - Clement T. Y. Chan
- Department of Biomedical Engineering, College of Engineering, University of North Texas, 3940 N Elm Street, Denton, TX 76207, USA;
- BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
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47
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Traynor R, Moran J, Stevens M, Antico O, Knebel A, Behrouz B, Merchant K, Hastie CJ, Davies P, Muqit MMK, De Cesare V. Design and high-throughput implementation of MALDI-TOF/MS-based assays for Parkin E3 ligase activity. Cell Rep Methods 2024; 4:100712. [PMID: 38382522 PMCID: PMC10921019 DOI: 10.1016/j.crmeth.2024.100712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 10/11/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Parkinson's disease (PD) is a progressive neurological disorder that manifests clinically as alterations in movement as well as multiple non-motor symptoms including but not limited to cognitive and autonomic abnormalities. Loss-of-function mutations in the gene encoding the ubiquitin E3 ligase Parkin are causal for familial and juvenile PD. Among several therapeutic approaches being explored to treat or improve the prognosis of patients with PD, the use of small molecules able to reinstate or boost Parkin activity represents a potential pharmacological treatment strategy. A major barrier is the lack of high-throughput platforms for the robust and accurate quantification of Parkin activity in vitro. Here, we present two different and complementary Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF/MS)-based approaches for the quantification of Parkin E3 ligase activity in vitro. Both approaches are scalable for high-throughput primary screening to facilitate the identification of Parkin modulators.
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Affiliation(s)
- Ryan Traynor
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Jennifer Moran
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Michael Stevens
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Bahareh Behrouz
- Vincere Biosciences, Inc., 245 Main St. Fl 2, Cambridge, MA 02142, USA
| | - Kalpana Merchant
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - C James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, School of Life Sciences, University of Dundee, Dow St., Dundee DD1 5EH, Scotland, UK
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK.
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48
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Tung YT, Chen YC, Derr K, Wilson K, Song MJ, Ferrer M. A 3D Bioprinted Human Neurovascular Unit Model of Glioblastoma Tumor Growth. Adv Healthc Mater 2024:e2302831. [PMID: 38394389 DOI: 10.1002/adhm.202302831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/29/2024] [Indexed: 02/25/2024]
Abstract
A 3D bioprinted neurovascular unit (NVU) model is developed to study glioblastoma (GBM) tumor growth in a brain-like microenvironment. The NVU model includes human primary astrocytes, pericytes and brain microvascular endothelial cells, and patient-derived glioblastoma cells (JHH-520) are used for this study. Fluorescence reporters are used with confocal high content imaging to quantitate real-time microvascular network formation and tumor growth. Extensive validation of the NVU-GBM model includes immunostaining for brain relevant cellular markers and extracellular matrix components; single cell RNA sequencing (scRNAseq) to establish physiologically relevant transcriptomics changes; and secretion of NVU and GBM-relevant cytokines. The scRNAseq reveals changes in gene expression and cytokines secretion associated with wound healing/angiogenesis, including the appearance of an endothelial mesenchymal transition cell population. The NVU-GBM model is used to test 18 chemotherapeutics and anti-cancer drugs to assess the pharmacological relevance of the model and robustness for high throughput screening.
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Affiliation(s)
- Yen-Ting Tung
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Yu-Chi Chen
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Kristy Derr
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Kelli Wilson
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Min Jae Song
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Marc Ferrer
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
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49
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Sharma V, Yakimovich A. A deep learning dataset for sample preparation artefacts detection in multispectral high-content microscopy. Sci Data 2024; 11:232. [PMID: 38395957 PMCID: PMC10891121 DOI: 10.1038/s41597-024-03064-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
High-content image-based screening is widely used in Drug Discovery and Systems Biology. However, sample preparation artefacts may significantly deteriorate the quality of image-based screening assays. While detection and circumvention of such artefacts could be addressed using modern-day machine learning and deep learning algorithms, this is widely impeded by the lack of suitable datasets. To address this, here we present a purpose-created open dataset of high-content microscopy sample preparation artefact. It consists of high-content microscopy of laboratory dust titrated on fixed cell culture specimens imaged with fluorescence filters covering the complete spectral range. To ensure this dataset is suitable for supervised machine learning tasks like image classification or segmentation we propose rule-based annotation strategies on categorical and pixel levels. We demonstrate the applicability of our dataset for deep learning by training a convolutional-neural-network-based classifier.
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Affiliation(s)
- Vaibhav Sharma
- Center for Advanced Systems Understanding (CASUS), Görlitz, Germany
- Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany
| | - Artur Yakimovich
- Center for Advanced Systems Understanding (CASUS), Görlitz, Germany.
- Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany.
- Artificial Intelligence for Life Sciences CIC, Dorset, UK.
- Institute of Computer Science, University of Wroclaw, Wroclaw, Poland.
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50
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Ding D, Shaw AY, Sinai S, Rollins N, Prywes N, Savage DF, Laub MT, Marks DS. Protein design using structure-based residue preferences. Nat Commun 2024; 15:1639. [PMID: 38388493 PMCID: PMC10884402 DOI: 10.1038/s41467-024-45621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Recent developments in protein design rely on large neural networks with up to 100s of millions of parameters, yet it is unclear which residue dependencies are critical for determining protein function. Here, we show that amino acid preferences at individual residues-without accounting for mutation interactions-explain much and sometimes virtually all of the combinatorial mutation effects across 8 datasets (R2 ~ 78-98%). Hence, few observations (~100 times the number of mutated residues) enable accurate prediction of held-out variant effects (Pearson r > 0.80). We hypothesized that the local structural contexts around a residue could be sufficient to predict mutation preferences, and develop an unsupervised approach termed CoVES (Combinatorial Variant Effects from Structure). Our results suggest that CoVES outperforms not just model-free methods but also similarly to complex models for creating functional and diverse protein variants. CoVES offers an effective alternative to complicated models for identifying functional protein mutations.
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Affiliation(s)
- David Ding
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
| | - Ada Y Shaw
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sam Sinai
- Dyno Therapeutics, Watertown, MA, 02472, USA
| | - Nathan Rollins
- Seismic Therapeutics, Lab Central, Cambridge, MA, 02142, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
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