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Pessoa Rodrigues C, Collins JM, Yang S, Martinez C, Kim JW, Lama C, Nam AS, Alt C, Lin C, Zon LI. Transcripts of repetitive DNA elements signal to block phagocytosis of hematopoietic stem cells. Science 2024; 385:eadn1629. [PMID: 39264994 DOI: 10.1126/science.adn1629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 04/09/2024] [Accepted: 07/04/2024] [Indexed: 09/14/2024]
Abstract
Macrophages maintain hematopoietic stem cell (HSC) quality by assessing cell surface Calreticulin (Calr), an "eat-me" signal induced by reactive oxygen species (ROS). Using zebrafish genetics, we identified Beta-2-microglobulin (B2m) as a crucial "don't eat-me" signal on blood stem cells. A chemical screen revealed inducers of surface Calr that promoted HSC proliferation without triggering ROS or macrophage clearance. Whole-genome CRISPR-Cas9 screening showed that Toll-like receptor 3 (Tlr3) signaling regulated b2m expression. Targeting b2m or tlr3 reduced the HSC clonality. Elevated B2m levels correlated with high expression of repetitive element (RE) transcripts. Overall, our data suggest that RE-associated double-stranded RNA could interact with TLR3 to stimulate surface expression of B2m on hematopoietic stem and progenitor cells. These findings suggest that the balance of Calr and B2m regulates macrophage-HSC interactions and defines hematopoietic clonality.
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Affiliation(s)
- Cecilia Pessoa Rodrigues
- Howard Hughes Medical Institute, Boston Children's Hospital Boston, MA, USA
- Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Joseph M Collins
- Howard Hughes Medical Institute, Boston Children's Hospital Boston, MA, USA
- Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Song Yang
- Howard Hughes Medical Institute, Boston Children's Hospital Boston, MA, USA
| | - Catherine Martinez
- Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Ji Wook Kim
- Howard Hughes Medical Institute, Boston Children's Hospital Boston, MA, USA
- Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Chhiring Lama
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Anna S Nam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Clemens Alt
- Wellman Center for Photomedicine, Mass General Research Institute, Boston, MA, USA
| | - Charles Lin
- Wellman Center for Photomedicine, Mass General Research Institute, Boston, MA, USA
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Leonard I Zon
- Howard Hughes Medical Institute, Boston Children's Hospital Boston, MA, USA
- Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
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2
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Bogacheva MS, Kuivanen S, Potdar S, Hassinen A, Huuskonen S, Pöhner I, Luck TJ, Turunen L, Feodoroff M, Szirovicza L, Savijoki K, Saarela J, Tammela P, Paavolainen L, Poso A, Varjosalo M, Kallioniemi O, Pietiäinen V, Vapalahti O. Drug repurposing platform for deciphering the druggable SARS-CoV-2 interactome. Antiviral Res 2024; 223:105813. [PMID: 38272320 DOI: 10.1016/j.antiviral.2024.105813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has heavily challenged the global healthcare system. Despite the vaccination programs, the new virus variants are circulating. Further research is required for understanding of the biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and for discovery of therapeutic agents against the virus. Here, we took advantage of drug repurposing to identify if existing drugs could inhibit SARS-CoV-2 infection. We established an open high throughput platform for in vitro screening of drugs against SARS-CoV-2 infection. We screened ∼1000 drugs for their ability to inhibit SARS-CoV-2-induced cell death in the African green monkey kidney cell line (Vero-E6), analyzed how the hit compounds affect the viral N (nucleocapsid) protein expression in human cell lines using high-content microscopic imaging and analysis, determined the hit drug targets in silico, and assessed their ability to cause phospholipidosis, which can interfere with the viral replication. Duvelisib was found by in silico interaction assay as a potential drug targeting virus-host protein interactions. The predicted interaction between PARP1 and S protein, affected by Duvelisib, was further validated by immunoprecipitation. Our results represent a rapidly applicable platform for drug repurposing and evaluation of the new emerging viruses' responses to the drugs. Further in silico studies help us to discover the druggable host pathways involved in the infectious cycle of SARS-CoV-2.
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Affiliation(s)
- Mariia S Bogacheva
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland.
| | - Suvi Kuivanen
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Antti Hassinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Sini Huuskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ina Pöhner
- Faculty of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Tamara J Luck
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Laura Turunen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Michaela Feodoroff
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Leonora Szirovicza
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Kirsi Savijoki
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Päivi Tammela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Lassi Paavolainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Antti Poso
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland; Department of Internal Medicine VIII, University Hospital Tubingen, Tubingen, Germany
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland; Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland; HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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Liu Z, Du J, Lin Z, Li Z, Liu B, Cui Z, Fang J, Xie L. DenovoProfiling: A webserver for de novo generated molecule library profiling. Comput Struct Biotechnol J 2022; 20:4082-4097. [PMID: 36016718 PMCID: PMC9379519 DOI: 10.1016/j.csbj.2022.07.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 01/10/2023] Open
Abstract
Various deep learning-based architectures for molecular generation have been proposed for de novo drug design. The flourish of the de novo molecular generation methods and applications has created a great demand for the visualization and functional profiling for the de novo generated molecules. An increasing number of publicly available chemogenomic databases sets good foundations and creates good opportunities for comprehensive profiling of the de novo library. In this paper, we present DenovoProfiling, a webserver dedicated to de novo library visualization and functional profiling. Currently, DenovoProfiling contains six modules: (1) identification & visualization module for chemical structure visualization and identify the reported structures, (2) chemical space module for chemical space exploration using similarity maps, principal components analysis (PCA), drug-like properties distribution, and scaffold-based clustering, (3) ADMET prediction module for predicting the ADMET properties of the de novo molecules, (4) molecular alignment module for three dimensional molecular shape analysis, (5) drugs mapping module for identifying structural similar drugs, and (6) target & pathway module for identifying the reported targets and corresponding functional pathways. DenovoProfiling could provide structural identification, chemical space exploration, drug mapping, and target & pathway information. The comprehensive annotated information could give users a clear picture of their de novo library and could guide the further selection of candidates for chemical synthesis and biological confirmation. DenovoProfiling is freely available at http://denovoprofiling.xielab.net.
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Key Words
- DDR1, Discovered potent discoidin domain receptor 1
- De novo drug design
- De novo molecule library
- Deep learning
- FBDD, Fragment-based drug design
- FDR, False discovery rate
- GAN, Generative adversarial networks
- HTS, High throughput screening
- LSTM, Long short-term memory
- Library profiling
- PCA, Principal components analysis
- RNN, Recurrent neural networks
- SCA, Scaffold-based classification approach
- VAE, Variational autoencoders
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Affiliation(s)
- Zhihong Liu
- School of Public Health, Xinxiang Medical University, Xinxiang, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jiewen Du
- Beijing Jingpai Technology Co., Ltd., 1500-1, Hailong Building Z-Park, Beijing 100090, China
| | - Ziying Lin
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Ze Li
- School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Bingdong Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zongbin Cui
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jiansong Fang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- Corresponding authors at: School of Public Health, Xinxiang Medical University, Xinxiang, China (L. Xie). Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China (J. Fang).
| | - Liwei Xie
- School of Public Health, Xinxiang Medical University, Xinxiang, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Corresponding authors at: School of Public Health, Xinxiang Medical University, Xinxiang, China (L. Xie). Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China (J. Fang).
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Hedgpeth B, Missall R, Bambaci A, Smolen M, Yavuz S, Cottrell J, Chu T, Chang SL. A Review of Bioinformatics Tools to Understand Acetaminophen-Alcohol Interaction. MEDICINES (BASEL, SWITZERLAND) 2019; 6:E79. [PMID: 31349598 PMCID: PMC6789846 DOI: 10.3390/medicines6030079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/15/2019] [Accepted: 07/23/2019] [Indexed: 01/17/2023]
Abstract
Background: Drug-ethanol interaction can result in hepatotoxicity. The liver is capable of metabolizing both acetaminophen and ethanol; however, severe acute or moderate chronic simultaneous exposure can cause cell and tissue damage. Therapeutic doses can become harmful if gene activity is altered via competition for metabolic pathways. Simultaneous intake of ethanol and acetaminophen results in overactive CYP2E1 and depletion of glutathione, leaving NAPQI to build up in the liver. NAPQI is a hepatotoxic substance typically neutralized by glutathione. Methods: Bioinformatics tools including PharmGKB, Chemical Annotation Retrieval Toolkit, Transcriptome Analysis Console 4.0 (TAC), wikipathways, STRING, and Ingenuity Pathway Analysis (IPA) were used to explore interactive metabolic pathways of ethanol-acetaminophen exposure as a proof of concept for assessing drug-drug or drug-alcohol interactions. Results: As the ethanol-acetaminophen comparison indicates, bioinformatics tools may be used to understand interactive pathways following exposure to ethanol and acetaminophen, with potential extrapolation to other drug-drug/drug-ethanol interactions. Conclusions: Direct interactive effects were not able to be confirmed through this bioinformatics study due to the lack of existing ethanol-acetaminophen simultaneous exposure data. This work suggests that a battery of software applications should be used to assess interactive effects.
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Affiliation(s)
- Bryan Hedgpeth
- Department of Biological Science, Seton Hall University, South Orange, NJ 07079, USA
| | - Roy Missall
- Department of Biological Science, Seton Hall University, South Orange, NJ 07079, USA
| | - Anna Bambaci
- Department of Biological Science, Seton Hall University, South Orange, NJ 07079, USA
| | - Matthew Smolen
- Department of Biological Science, Seton Hall University, South Orange, NJ 07079, USA
| | - Sevgi Yavuz
- Department of Biological Science, Seton Hall University, South Orange, NJ 07079, USA
| | - Jessica Cottrell
- Department of Biological Science, Seton Hall University, South Orange, NJ 07079, USA
| | - Tinchun Chu
- Department of Biological Science, Seton Hall University, South Orange, NJ 07079, USA.
| | - Sulie L Chang
- Department of Biological Science, Seton Hall University, South Orange, NJ 07079, USA.
- The Institute of NeuroImmune Pharmacology (I-NIP), Seton Hall University, South Orange, NJ 07079, USA.
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Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 2018; 555:623-628. [PMID: 29555994 PMCID: PMC6108420 DOI: 10.1038/nature25979] [Citation(s) in RCA: 1160] [Impact Index Per Article: 193.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 02/08/2018] [Indexed: 12/13/2022]
Abstract
A few commonly used non-antibiotic drugs have recently been associated with changes in gut microbiome composition, but the extent of this phenomenon is unknown. Here, we screened more than 1,000 marketed drugs against 40 representative gut bacterial strains, and found that 24% of the drugs with human targets, including members of all therapeutic classes, inhibited the growth of at least one strain in vitro. Particular classes, such as the chemically diverse antipsychotics, were overrepresented in this group. The effects of human-targeted drugs on gut bacteria are reflected on their antibiotic-like side effects in humans and are concordant with existing human cohort studies. Susceptibility to antibiotics and human-targeted drugs correlates across bacterial species, suggesting common resistance mechanisms, which we verified for some drugs. The potential risk of non-antibiotics promoting antibiotic resistance warrants further exploration. Our results provide a resource for future research on drug-microbiome interactions, opening new paths for side effect control and drug repurposing, and broadening our view of antibiotic resistance.
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Affiliation(s)
- Lisa Maier
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Mihaela Pruteanu
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Michael Kuhn
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Georg Zeller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Anja Telzerow
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Exene Erin Anderson
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Ana Rita Brochado
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | | | - Hitomi Dose
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Hirotada Mori
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Kiran Raosaheb Patil
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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