1
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Chatzimichail S, Turner P, Feehily C, Farrar A, Crook D, Andersson M, Oakley S, Barrett L, El Sayyed H, Kyropoulos J, Nellåker C, Stoesser N, Kapanidis AN. Rapid identification of bacterial isolates using microfluidic adaptive channels and multiplexed fluorescence microscopy. LAB ON A CHIP 2024; 24:4843-4858. [PMID: 39291847 PMCID: PMC11409657 DOI: 10.1039/d4lc00325j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 09/04/2024] [Indexed: 09/19/2024]
Abstract
We demonstrate the rapid capture, enrichment, and identification of bacterial pathogens using Adaptive Channel Bacterial Capture (ACBC) devices. Using controlled tuning of device backpressure in polydimethylsiloxane (PDMS) devices, we enable the controlled formation of capture regions capable of trapping bacteria from low cell density samples with near 100% capture efficiency. The technical demands to prepare such devices are much lower compared to conventional methods for bacterial trapping and can be achieved with simple benchtop fabrication methods. We demonstrate the capture and identification of seven species of bacteria with bacterial concentrations lower than 1000 cells per mL, including common Gram-negative and Gram-positive pathogens such as Escherichia coli and Staphylococcus aureus. We further demonstrate that species identification of the trapped bacteria can be undertaken in the order of one-hour using multiplexed 16S rRNA-FISH with identification accuracies of 70-98% with unsupervised classification methods across 7 species of bacteria. Finally, by using the bacterial capture capabilities of the ACBC chip with an ultra-rapid antimicrobial susceptibility testing method employing fluorescence imaging and convolutional neural network (CNN) classification, we demonstrate that we can use the ACBC chip as an imaging flow cytometer that can predict the antibiotic susceptibility of E. coli cells after identification.
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Affiliation(s)
- Stelios Chatzimichail
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Piers Turner
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Conor Feehily
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Alison Farrar
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Monique Andersson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Sarah Oakley
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Lucinda Barrett
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Hafez El Sayyed
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jingwen Kyropoulos
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
| | - Christoffer Nellåker
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Big Data Institute, Oxford, OX3 7LF, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Achillefs N Kapanidis
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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2
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Hu X, van Sluijs B, García-Blay Ó, Huck WTS, Hansen MMK. Protocol for simultaneous detection of mRNAs and (phospho-)proteins with ARTseq-FISH in mouse embryonic stem cells. STAR Protoc 2024; 5:103336. [PMID: 39356640 DOI: 10.1016/j.xpro.2024.103336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 08/01/2024] [Accepted: 09/03/2024] [Indexed: 10/04/2024] Open
Abstract
Understanding the molecular signatures of individual cells within complex biological systems is crucial for deciphering cellular heterogeneity and uncovering regulatory mechanisms. Here, we present a protocol for simultaneous multiplexed detection of selected mRNAs and (phospho-)proteins in mouse embryonic stem cells using spatial single-cell profiling. We describe steps for employing single-stranded DNA (ssDNA)-labeled antibo'dies, padlock probes, and rolling circle amplification to achieve simultaneous visualization of mRNAs and (phospho-)proteins at subcellular resolution. This protocol has potential application in identifying cells in heterogeneous biological microenvironments. For complete details on the use and execution of this protocol, please refer to Hu et al.1.
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Affiliation(s)
- Xinyu Hu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands
| | - Bob van Sluijs
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Óscar García-Blay
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands.
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3
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Zhou Y, Bi K, Ge Q, Lu Z. Advances and Challenges in Random Access Techniques for In Vitro DNA Data Storage. ACS APPLIED MATERIALS & INTERFACES 2024; 16:43102-43113. [PMID: 39110103 DOI: 10.1021/acsami.4c07235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
With digital transformation and the general application of new technologies, data storage is facing new challenges with the demand for high-density loading of massive information. In response, DNA storage technology has emerged as a promising research direction. Efficient and reliable data retrieval is critical for DNA storage, and the development of random access technology plays a key role in its practicality and reliability. However, achieving fast and accurate random access functions has proven difficult for existing DNA storage efforts, which limits its practical applications in industry. In this review, we summarize the recent advances in DNA storage technology that enable random access functionality, as well as the challenges that need to be overcome and the current solutions. This review aims to help researchers in the field of DNA storage better understand the importance of the random access step and its impact on the overall development of DNA storage. Furthermore, the remaining challenges and future research trends in random access technology of DNA storage are discussed, with the goal of providing a solid foundation for achieving random access in DNA storage under large-scale data conditions.
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Affiliation(s)
- Ying Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Kun Bi
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
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4
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Steinek C, Guirao-Ortiz M, Stumberger G, Tölke AJ, Hörl D, Carell T, Harz H, Leonhardt H. Generation of densely labeled oligonucleotides for the detection of small genomic elements. CELL REPORTS METHODS 2024; 4:100840. [PMID: 39137784 PMCID: PMC11384094 DOI: 10.1016/j.crmeth.2024.100840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/16/2024] [Accepted: 07/22/2024] [Indexed: 08/15/2024]
Abstract
The genome contains numerous regulatory elements that may undergo complex interactions and contribute to the establishment, maintenance, and change of cellular identity. Three-dimensional genome organization can be explored with fluorescence in situ hybridization (FISH) at the single-cell level, but the detection of small genomic loci remains challenging. Here, we provide a rapid and simple protocol for the generation of bright FISH probes suited for the detection of small genomic elements. We systematically optimized probe design and synthesis, screened polymerases for their ability to incorporate dye-labeled nucleotides, and streamlined purification conditions to yield nanoscopy-compatible oligonucleotides with dyes in variable arrays (NOVA probes). With these probes, we detect genomic loci ranging from genome-wide repetitive regions down to non-repetitive loci below the kilobase scale. In conclusion, we introduce a simple workflow to generate densely labeled oligonucleotide pools that facilitate detection and nanoscopic measurements of small genomic elements in single cells.
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Affiliation(s)
- Clemens Steinek
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 81377 Munich, Germany.
| | - Miguel Guirao-Ortiz
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Gabriela Stumberger
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Annika J Tölke
- Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - David Hörl
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Hartmann Harz
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 81377 Munich, Germany.
| | - Heinrich Leonhardt
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 81377 Munich, Germany.
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5
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Gowri G, Sheng K, Yin P. Scalable design of orthogonal DNA barcode libraries. NATURE COMPUTATIONAL SCIENCE 2024; 4:423-428. [PMID: 38849559 PMCID: PMC11208133 DOI: 10.1038/s43588-024-00646-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/15/2024] [Indexed: 06/09/2024]
Abstract
Orthogonal DNA barcode library design is an essential task in bioengineering. Here we present seqwalk, an efficient method for designing barcode libraries that satisfy a sequence symmetry minimization (SSM) heuristic for orthogonality, with theoretical guarantees of maximal or near-maximal library size under certain design constraints. Seqwalk encodes SSM constraints in a de Bruijn graph representation of sequence space, enabling the application of recent advances in discrete mathematics1 to the problem of orthogonal sequence design. We demonstrate the scalability of seqwalk by designing a library of >106 SSM-satisfying barcode sequences in less than 20 s on a standard laptop.
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Affiliation(s)
- Gokul Gowri
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
| | - Kuanwei Sheng
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Peng Yin
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
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6
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Rasool A, Hong J, Hong Z, Li Y, Zou C, Chen H, Qu Q, Wang Y, Jiang Q, Huang X, Dai J. An Effective DNA-Based File Storage System for Practical Archiving and Retrieval of Medical MRI Data. SMALL METHODS 2024:e2301585. [PMID: 38807543 DOI: 10.1002/smtd.202301585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/29/2024] [Indexed: 05/30/2024]
Abstract
DNA-based data storage is a new technology in computational and synthetic biology, that offers a solution for long-term, high-density data archiving. Given the critical importance of medical data in advancing human health, there is a growing interest in developing an effective medical data storage system based on DNA. Data integrity, accuracy, reliability, and efficient retrieval are all significant concerns. Therefore, this study proposes an Effective DNA Storage (EDS) approach for archiving medical MRI data. The EDS approach incorporates three key components (i) a novel fraction strategy to address the critical issue of rotating encoding, which often leads to data loss due to single base error propagation; (ii) a novel rule-based quaternary transcoding method that satisfies bio-constraints and ensure reliable mapping; and (iii) an indexing technique designed to simplify random search and access. The effectiveness of this approach is validated through computer simulations and biological experiments, confirming its practicality. The EDS approach outperforms existing methods, providing superior control over bio-constraints and reducing computational time. The results and code provided in this study open new avenues for practical DNA storage of medical MRI data, offering promising prospects for the future of medical data archiving and retrieval.
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Affiliation(s)
- Abdur Rasool
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jingwei Hong
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- College of Mathematics and Information Science, Hebei University, Baoding, 071002, China
| | - Zhiling Hong
- Quanzhou Development Group Co., Ltd, Quanzhou, 362000, China
| | - Yuanzhen Li
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen, 518055, China
| | - Chao Zou
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Hui Chen
- Shenzhen Polytechnic University, Shenzhen, 518055, China
| | - Qiang Qu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yang Wang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qingshan Jiang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaoluo Huang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen, 518055, China
| | - Junbiao Dai
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518055, China
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7
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Berleant JD, Banal JL, Rao DK, Bathe M. Scalable search of massively pooled nucleic acid samples enabled by a molecular database query language. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.12.24305660. [PMID: 38699348 PMCID: PMC11064994 DOI: 10.1101/2024.04.12.24305660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
The surge in nucleic acid analytics requires scalable storage and retrieval systems akin to electronic databases used to organize digital data. Such a system could transform disease diagnosis, ecological preservation, and molecular surveillance of biothreats. Current storage systems use individual containers for nucleic acid samples, requiring single-sample retrieval that falls short compared with digital databases that allow complex and combinatorial data retrieval on aggregated data. Here, we leverage protective microcapsules with combinatorial DNA labeling that enables arbitrary retrieval on pooled biosamples analogous to Structured Query Languages. Ninety-six encapsulated pooled mock SARS-CoV-2 genomic samples barcoded with patient metadata are used to demonstrate queries with simultaneous matches to sample collection date ranges, locations, and patient health statuses, illustrating how such flexible queries can be used to yield immunological or epidemiological insights. The approach applies to any biosample database labeled with orthogonal barcodes, enabling complex post-hoc analysis, for example, to study global biothreat epidemiology.
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Affiliation(s)
- Joseph D. Berleant
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James L. Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Present address: Cache DNA, Inc. 733 Industrial Rd., San Carlos, CA 94070 USA
| | | | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139 USA
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8
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Kristensen NP, Dionisio E, Bentzen AK, Tamhane T, Kemming JS, Nos G, Voss LF, Hansen UK, Lauer GM, Hadrup SR. Simultaneous analysis of pMHC binding and reactivity unveils virus-specific CD8 T cell immunity to a concise epitope set. SCIENCE ADVANCES 2024; 10:eadm8951. [PMID: 38608022 PMCID: PMC11014448 DOI: 10.1126/sciadv.adm8951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/12/2024] [Indexed: 04/14/2024]
Abstract
CD8 T cells provide immunity to virus infection through recognition of epitopes presented by peptide major histocompatibility complexes (pMHCs). To establish a concise panel of widely recognized T cell epitopes from common viruses, we combined analysis of TCR down-regulation upon stimulation with epitope-specific enumeration based on barcode-labeled pMHC multimers. We assess CD8 T cell binding and reactivity for 929 previously reported epitopes in the context of 1 of 25 HLA alleles representing 29 viruses. The prevalence and magnitude of CD8 T cell responses were evaluated in 48 donors and reported along with 137 frequently recognized virus epitopes, many of which were underrepresented in the public domain. Eighty-four percent of epitope-specific CD8 T cell populations demonstrated reactivity to peptide stimulation, which was associated with effector and long-term memory phenotypes. Conversely, nonreactive T cell populations were associated primarily with naive phenotypes. Our analysis provides a reference map of epitopes for characterizing CD8 T cell responses toward common human virus infections.
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Affiliation(s)
- Nikolaj Pagh Kristensen
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Edoardo Dionisio
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Amalie Kai Bentzen
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Tripti Tamhane
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Janine Sophie Kemming
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Grigorii Nos
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Lasse Frank Voss
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Ulla Kring Hansen
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Georg Michael Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Sine Reker Hadrup
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
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9
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Im J, Kim S, Park S, Wang SX, Lee JR. Evaluation of restriction and Cas endonuclease kinetics using matrix-insensitive magnetic biosensors. Biosens Bioelectron 2024; 249:116017. [PMID: 38262299 PMCID: PMC10867820 DOI: 10.1016/j.bios.2024.116017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/02/2024] [Accepted: 01/07/2024] [Indexed: 01/25/2024]
Abstract
The enzymatic actions of endonucleases in vivo can be altered due to bound substrates and differences in local environments, including enzyme concentration, pH, salinity, ionic strength, and temperature. Thus, accurate estimation of enzymatic reactions in vivo using matrix-dependent methods in solution can be challenging. Here, we report a matrix-insensitive magnetic biosensing platform that enables the measurement of endonuclease activity under different conditions with varying pH, salinity, ionic strength, and temperature. Using biosensor arrays and orthogonal pairs of oligonucleotides, we quantitatively characterized the enzymatic activity of EcoRI under different buffer conditions and in the presence of inhibitors. To mimic a more physiological environment, we monitored the sequence-dependent star activity of EcoRI under unconventional conditions. Furthermore, enzymatic activity was measured in cell culture media, saliva, and serum. Last, we estimated the effective cleavage rates of Cas12a on anchored single-strand DNAs using this platform, which more closely resembles in vivo settings. This platform will facilitate precise characterization of restriction and Cas endonucleases under various conditions.
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Affiliation(s)
- Jisoo Im
- Division of Mechanical and Biomedical Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea; Graduate Program in Smart Factory, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Songeun Kim
- Division of Mechanical and Biomedical Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea; Graduate Program in Smart Factory, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Suhyeon Park
- Division of Mechanical and Biomedical Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea; Graduate Program in Smart Factory, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Shan X Wang
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, 94305, USA; Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Jung-Rok Lee
- Division of Mechanical and Biomedical Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea; Graduate Program in Smart Factory, Ewha Womans University, Seoul, 03760, Republic of Korea.
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10
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Unterauer EM, Shetab Boushehri S, Jevdokimenko K, Masullo LA, Ganji M, Sograte-Idrissi S, Kowalewski R, Strauss S, Reinhardt SCM, Perovic A, Marr C, Opazo F, Fornasiero EF, Jungmann R. Spatial proteomics in neurons at single-protein resolution. Cell 2024; 187:1785-1800.e16. [PMID: 38552614 DOI: 10.1016/j.cell.2024.02.045] [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: 05/17/2023] [Revised: 11/28/2023] [Accepted: 02/29/2024] [Indexed: 04/02/2024]
Abstract
To understand biological processes, it is necessary to reveal the molecular heterogeneity of cells by gaining access to the location and interaction of all biomolecules. Significant advances were achieved by super-resolution microscopy, but such methods are still far from reaching the multiplexing capacity of proteomics. Here, we introduce secondary label-based unlimited multiplexed DNA-PAINT (SUM-PAINT), a high-throughput imaging method that is capable of achieving virtually unlimited multiplexing at better than 15 nm resolution. Using SUM-PAINT, we generated 30-plex single-molecule resolved datasets in neurons and adapted omics-inspired analysis for data exploration. This allowed us to reveal the complexity of synaptic heterogeneity, leading to the discovery of a distinct synapse type. We not only provide a resource for researchers, but also an integrated acquisition and analysis workflow for comprehensive spatial proteomics at single-protein resolution.
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Affiliation(s)
- Eduard M Unterauer
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sayedali Shetab Boushehri
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Data & Analytics, Roche Pharma Research and Early Development, Roche Innovation Center Munich, Munich, Germany; Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Kristina Jevdokimenko
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Mahipal Ganji
- Max Planck Institute of Biochemistry, Planegg, Germany; Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Shama Sograte-Idrissi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany; Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Rafal Kowalewski
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sebastian Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Susanne C M Reinhardt
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Ana Perovic
- Max Planck Institute of Biochemistry, Planegg, Germany
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany; Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany; NanoTag Biotechnologies GmbH, Göttingen, Germany
| | - Eugenio F Fornasiero
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany; Department of Life Sciences, University of Trieste, Trieste, Italy.
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany.
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11
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Zong DM, Sadeghpour M, Molinari S, Alnahhas RN, Hirning AJ, Giannitsis C, Ott W, Josić K, Bennett MR. Tunable Dynamics in a Multistrain Transcriptional Pulse Generator. ACS Synth Biol 2023; 12:3531-3543. [PMID: 38016068 DOI: 10.1021/acssynbio.3c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
One challenge in synthetic biology is the tuning of regulatory components within gene circuits to elicit a specific behavior. This challenge becomes more difficult in synthetic microbial consortia since each strain's circuit must function at the intracellular level and their combination must operate at the population level. Here we demonstrate that circuit dynamics can be tuned in synthetic consortia through the manipulation of strain fractions within the community. To do this, we construct a microbial consortium comprised of three strains of engineered Escherichia coli that, when cocultured, use homoserine lactone-mediated intercellular signaling to create a multistrain incoherent type-1 feedforward loop (I1-FFL). Like naturally occurring I1-FFL motifs in gene networks, this engineered microbial consortium acts as a pulse generator of gene expression. We demonstrate that the amplitude of the pulse can be easily tuned by adjusting the relative population fractions of the strains. We also develop a mathematical model for the temporal dynamics of the microbial consortium. This model allows us to identify population fractions that produced desired pulse characteristics, predictions that were confirmed for all but extreme fractions. Our work demonstrates that intercellular gene circuits can be effectively tuned simply by adjusting the starting fractions of each strain in the consortium.
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Affiliation(s)
- David M Zong
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Mehdi Sadeghpour
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Mathematics, University of Houston, Houston, Texas 77004, United States
| | - Sara Molinari
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Razan N Alnahhas
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Andrew J Hirning
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Charilaos Giannitsis
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - William Ott
- Department of Mathematics, University of Houston, Houston, Texas 77004, United States
| | - Krešimir Josić
- Department of Mathematics, University of Houston, Houston, Texas 77004, United States
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
- Rice Synthetic Biology Institute, Rice University, Houston, Texas 77005, United States
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12
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Liu S, Zheng P, Wang CY, Jia BB, Zemke NR, Ren B, Zhuang X. Cell-type-specific 3D-genome organization and transcription regulation in the brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.570024. [PMID: 38105994 PMCID: PMC10723369 DOI: 10.1101/2023.12.04.570024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
3D organization of the genome plays a critical role in regulating gene expression. However, it remains unclear how chromatin organization differs among different cell types in the brain. Here we used genome-scale DNA and RNA imaging to investigate 3D-genome organization in transcriptionally distinct cell types in the primary motor cortex of the mouse brain. We uncovered a wide spectrum of differences in the nuclear architecture and 3D-genome organization among different cell types, ranging from the physical size of the cell nucleus to the active-inactive chromatin compartmentalization and radial positioning of chromatin loci within the nucleus. These cell-type-dependent variations in nuclear architecture and chromatin organization exhibited strong correlation with both total transcriptional activity of the cell and transcriptional regulation of cell-type-specific marker genes. Moreover, we found that the methylated-DNA-binding protein MeCP2 regulates transcription in a divergent manner, depending on the nuclear radial positions of chromatin loci, through modulating active-inactive chromatin compartmentalization.
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Affiliation(s)
- Shiwei Liu
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Pu Zheng
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Cosmos Yuqi Wang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Bojing Blair Jia
- Bioinformatics and Systems Biology Graduate Program, Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
| | - Nathan R. Zemke
- Department of Cellular and Molecular Medicine and Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine and Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
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13
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Hsu FM, Chang YL, Chen CY, Lin SR, Cheng JCH. Hybridization Protection Reaction for Sensitive and Robust Gene Expression Profiling of Clinical Formalin-Fixed Paraffin-Embedded Samples. Clin Chem 2023; 69:1385-1395. [PMID: 37964418 DOI: 10.1093/clinchem/hvad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 10/03/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND RNA profiling of formalin-fixed paraffin-embedded (FFPE) tumor tissues for the molecular diagnostics of disease prognosis or treatment response is often irreproducible and limited to a handful of biomarkers. This has led to an unmet need for robust multiplexed assays that can profile several RNA biomarkers of interest using a limited amount of specimen. Here, we describe hybridization protection reaction (HPR), which is a novel RNA profiling approach with high reproducibility. METHODS HPR assays were designed for multiple genes, including 10 radiosensitivity-associated genes, and compared with TaqMan assays. Performance was tested with synthetic RNA fragments, and the ability to analyze RNA was investigated in FPPE samples from 20 normal lung tissues, 40 lung cancer, and 30 esophageal cancer biopsies. RESULTS Experiments performed on 3 synthetic RNA fragments demonstrated a linear dynamic range of over 1000-fold with a replicate correlation coefficient of 0.99 and high analytical sensitivity between 3.2 to 10 000 pM. Comparison of HPR with standard quantitative reverse transcription polymerase chain reaction on FFPE specimens shows nonsignificant differences with > 99% confidence interval between 2 assays in transcript profiling of 91.7% of test transcripts. In addition, HPR was effectively applied to quantify transcript levels of 10 radiosensitivity-associated genes. CONCLUSIONS Overall, HPR is an alternative approach for RNA profiling with high sensitivity, reproducibility, robustness, and capability for molecular diagnostics in FFPE tumor biopsy specimens of lung and esophageal cancer.
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Affiliation(s)
- Feng-Ming Hsu
- Division of Radiation Oncology, Department of Oncology, National Taiwan University Hospital, Taipei 100225, Taiwan
- Graduate Institute of Oncology and Cancer Research Center, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Yih-Leong Chang
- Department of Pathology, National Taiwan University Hospital, Taipei 100225, Taiwan
| | - Chung-Yung Chen
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli District, Taoyuan 320314, Taiwan
- Center for Nanotechnology and Center for Biomedical Technology, Chung Yuan Christian University, Taoyuan 320314, Taiwan
| | - Shu-Rung Lin
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli District, Taoyuan 320314, Taiwan
- Center for Nanotechnology and Center for Biomedical Technology, Chung Yuan Christian University, Taoyuan 320314, Taiwan
| | - Jason Chia-Hsien Cheng
- Division of Radiation Oncology, Department of Oncology, National Taiwan University Hospital, Taipei 100225, Taiwan
- Graduate Institute of Oncology and Cancer Research Center, National Taiwan University College of Medicine, Taipei 100025, Taiwan
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14
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Cheng Y, Hu M, Yang B, Jensen TB, Yang T, Yu R, Ma Z, Radda JSD, Jin S, Zang C, Wang S. Perturb-tracing enables high-content screening of multiscale 3D genome regulators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.525983. [PMID: 36778402 PMCID: PMC9915657 DOI: 10.1101/2023.01.31.525983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Three-dimensional (3D) genome organization becomes altered during development, aging, and disease1-23, but the factors regulating chromatin topology are incompletely understood and currently no technology can efficiently screen for new regulators of multiscale chromatin organization. Here, we developed an image-based high-content screening platform (Perturb-tracing) that combines pooled CRISPR screen, a new cellular barcode readout method (BARC-FISH), and chromatin tracing. We performed a loss-of-function screen in human cells, and visualized alterations to their genome organization from 13,000 imaging target-perturbation combinations, alongside perturbation-paired barcode readout in the same single cells. Using 1.4 million 3D positions along chromosome traces, we discovered tens of new regulators of chromatin folding at different length scales, ranging from chromatin domains and compartments to chromosome territory. A subset of the regulators exhibited 3D genome effects associated with loop-extrusion and A-B compartmentalization mechanisms, while others were largely unrelated to these known 3D genome mechanisms. We found that the ATP-dependent helicase CHD7, the loss of which causes the congenital neural crest syndrome CHARGE24 and a chromatin remodeler previously shown to promote local chromatin openness25-27, counter-intuitively compacts chromatin over long range in different genomic contexts and cell backgrounds including neural crest cells, and globally represses gene expression. The DNA compaction effect of CHD7 is independent of its chromatin remodeling activity and does not require other protein partners. Finally, we identified new regulators of nuclear architectures and found a functional link between chromatin compaction and nuclear shape. Altogether, our method enables scalable, high-content identification of chromatin and nuclear topology regulators that will stimulate new insights into the 3D genome functions, such as global gene and nuclear regulation, in health and disease.
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Affiliation(s)
- Yubao Cheng
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Mengwei Hu
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Bing Yang
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Tyler B Jensen
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
- M.D.-Ph.D. Program, Yale University, New Haven, CT 06510, USA
| | - Tianqi Yang
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Ruihuan Yu
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Zhaoxia Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jonathan S D Radda
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Shengyan Jin
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA, 22908, USA
| | - Siyuan Wang
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06510, USA
- Molecular Cell Biology, Genetics and Development Program, Yale University, New Haven, CT 06510, USA
- Biochemistry, Quantitative Biology, Biophysics, and Structural Biology Program, Yale University, New Haven, CT 06510, USA
- M.D.-Ph.D. Program, Yale University, New Haven, CT 06510, USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Liver Center, Yale University School of Medicine, New Haven, CT 06510, USA
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15
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Shi H, He Y, Zhou Y, Huang J, Maher K, Wang B, Tang Z, Luo S, Tan P, Wu M, Lin Z, Ren J, Thapa Y, Tang X, Chan KY, Deverman BE, Shen H, Liu A, Liu J, Wang X. Spatial atlas of the mouse central nervous system at molecular resolution. Nature 2023; 622:552-561. [PMID: 37758947 PMCID: PMC10709140 DOI: 10.1038/s41586-023-06569-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/22/2023] [Indexed: 09/29/2023]
Abstract
Spatially charting molecular cell types at single-cell resolution across the 3D volume is critical for illustrating the molecular basis of brain anatomy and functions. Single-cell RNA sequencing has profiled molecular cell types in the mouse brain1,2, but cannot capture their spatial organization. Here we used an in situ sequencing method, STARmap PLUS3,4, to profile 1,022 genes in 3D at a voxel size of 194 × 194 × 345 nm3, mapping 1.09 million high-quality cells across the adult mouse brain and spinal cord. We developed computational pipelines to segment, cluster and annotate 230 molecular cell types by single-cell gene expression and 106 molecular tissue regions by spatial niche gene expression. Joint analysis of molecular cell types and molecular tissue regions enabled a systematic molecular spatial cell-type nomenclature and identification of tissue architectures that were undefined in established brain anatomy. To create a transcriptome-wide spatial atlas, we integrated STARmap PLUS measurements with a published single-cell RNA-sequencing atlas1, imputing single-cell expression profiles of 11,844 genes. Finally, we delineated viral tropisms of a brain-wide transgene delivery tool, AAV-PHP.eB5,6. Together, this annotated dataset provides a single-cell resource that integrates the molecular spatial atlas, brain anatomy and the accessibility to genetic manipulation of the mammalian central nervous system.
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Affiliation(s)
- Hailing Shi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yichun He
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
| | - Yiming Zhou
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jiahao Huang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kamal Maher
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computational and Systems Biology PhD Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brandon Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zefang Tang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shuchen Luo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peng Tan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Morgan Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zuwan Lin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jingyi Ren
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yaman Thapa
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xin Tang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
| | - Ken Y Chan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin E Deverman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hao Shen
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
| | - Albert Liu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jia Liu
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA.
| | - Xiao Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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16
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Poisson W, Bastien A, Gilbert I, Carrier A, Prunier J, Robert C. Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding. Genet Sel Evol 2023; 55:47. [PMID: 37430194 DOI: 10.1186/s12711-023-00819-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND The frequency of chromosomal rearrangements in Canadian breeding boars has been estimated at 0.91 to 1.64%. These abnormalities are widely recognized as a potential cause of subfertility in livestock production. Since artificial insemination is practiced in almost all intensive pig production systems, the use of elite boars carrying cytogenetic defects that have an impact on fertility can lead to major economic losses. To avoid keeping subfertile boars in artificial insemination centres and spreading chromosomal defects within populations, cytogenetic screening of boars is crucial. Different techniques are used for this purpose, but several issues are frequently encountered, i.e. environmental factors can influence the quality of results, the lack of genomic information outputted by these techniques, and the need for prior cytogenetic skills. The aim of this study was to develop a new pig karyotyping method based on fluorescent banding patterns. RESULTS The use of 207,847 specific oligonucleotides generated 96 fluorescent bands that are distributed across the 18 autosomes and the sex chromosomes. Tested alongside conventional G-banding, this oligo-banding method allowed us to identify four chromosomal translocations and a rare unbalanced chromosomal rearrangement that was not detected by conventional banding. In addition, this method allowed us to investigate chromosomal imbalance in spermatozoa. CONCLUSIONS The use of oligo-banding was found to be appropriate for detecting chromosomal aberrations in a Canadian pig nucleus and its convenient design and use make it an interesting tool for livestock karyotyping and cytogenetic studies.
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Affiliation(s)
- William Poisson
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Québec, QC, Canada
| | - Alexandre Bastien
- Plateforme d'imagerie et microscopie, Institut de biologie intégrative et des systèmes, Université Laval, Québec, QC, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Québec, QC, Canada
| | - Alexandra Carrier
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Québec, QC, Canada
| | - Julien Prunier
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Claude Robert
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada.
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Québec, QC, Canada.
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17
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Poisson W, Prunier J, Carrier A, Gilbert I, Mastromonaco G, Albert V, Taillon J, Bourret V, Droit A, Côté SD, Robert C. Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights. BMC Genomics 2023; 24:142. [PMID: 36959567 PMCID: PMC10037892 DOI: 10.1186/s12864-023-09189-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Genome assembly into chromosomes facilitates several analyses including cytogenetics, genomics and phylogenetics. Despite rapid development in bioinformatics, however, assembly beyond scaffolds remains challenging, especially in species without closely related well-assembled and available reference genomes. So far, four draft genomes of Rangifer tarandus (caribou or reindeer, a circumpolar distributed cervid species) have been published, but none with chromosome-level assembly. This emblematic northern species is of high interest in ecological studies and conservation since most populations are declining. RESULTS We have designed specific probes based on Oligopaint FISH technology to upgrade the latest published reindeer and caribou chromosome-level genomes. Using this oligonucleotide-based method, we found six mis-assembled scaffolds and physically mapped 68 of the largest scaffolds representing 78% of the most recent R. tarandus genome assembly. Combining physical mapping and comparative genomics, it was possible to document chromosomal evolution among Cervidae and closely related bovids. CONCLUSIONS Our results provide validation for the current chromosome-level genome assembly as well as resources to use chromosome banding in studies of Rangifer tarandus.
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Affiliation(s)
- William Poisson
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Québec, QC, Canada
- Réseau Québécois en reproduction, QC, Saint-Hyacinthe, Canada
| | - Julien Prunier
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada
| | - Alexandra Carrier
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Québec, QC, Canada
- Réseau Québécois en reproduction, QC, Saint-Hyacinthe, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Québec, QC, Canada
- Réseau Québécois en reproduction, QC, Saint-Hyacinthe, Canada
| | | | - Vicky Albert
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Québec, QC, Canada
| | - Joëlle Taillon
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Québec, QC, Canada
| | - Vincent Bourret
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Québec, QC, Canada
| | - Arnaud Droit
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Steeve D Côté
- Caribou Ungava, Département de biologie and Centre d'études nordiques, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada
| | - Claude Robert
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada.
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Québec, QC, Canada.
- Réseau Québécois en reproduction, QC, Saint-Hyacinthe, Canada.
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18
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Chauvel M, Bachellier-Bassi S, Guérout AM, Lee KK, Maufrais C, Permal E, Da Fonseca JP, Znaidi S, Mazel D, Munro CA, d'Enfert C, Legrand M. High-throughput functional profiling of the human fungal pathogen Candida albicans genome. Res Microbiol 2023; 174:104025. [PMID: 36587858 DOI: 10.1016/j.resmic.2022.104025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022]
Abstract
Candida albicans is a major fungal pathogen of humans. Although its genome has been sequenced more than two decades ago, there are still over 4300 uncharacterized C. albicans genes. We previously generated an ORFeome as well as a collection of destination vectors to facilitate overexpression of C. albicans ORFs. Here, we report the construction of ∼2500 overexpression mutants and their evaluation by in vitro spotting on rich medium and in a liquid pool experiment in rich medium, allowing the identification of genes whose overexpression has a fitness cost. The candidates were further validated at the individual strain level. This new resource allows large-scale screens in different growth conditions to be performed routinely. Altogether, based on the concept of identifying functionally related genes by cluster analysis, the availability of this overexpression mutant collection will facilitate the characterization of gene functions in C. albicans.
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Affiliation(s)
- Murielle Chauvel
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France.
| | - Sophie Bachellier-Bassi
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France.
| | - Anne-Marie Guérout
- Institut Pasteur, Université Paris Cité, UMR3525 CNRS, Unité Plasticité du Génome Bactérien, F-75015 Paris, France.
| | - Keunsook K Lee
- Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK; NGeneBio, 307 Daerung Post-tower 1, 288 Digital-ro, Guro-gu, Seoul 08390, Republic of Korea.
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France; Institut Pasteur, Université Paris Cité, Hub de Bioinformatique, F-75015 Paris, France.
| | - Emmanuelle Permal
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France; Institut Pasteur, Université Paris Cité, UMR3525 CNRS, Unité Plasticité du Génome Bactérien, F-75015 Paris, France; Institut Pasteur, Université Paris Cité, Hub de Bioinformatique, F-75015 Paris, France.
| | - Juliana Pipoli Da Fonseca
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques (C2RT), F-75015 Paris, France.
| | - Sadri Znaidi
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France; Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis-Belvédère, Tunisia.
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, UMR3525 CNRS, Unité Plasticité du Génome Bactérien, F-75015 Paris, France.
| | - Carol A Munro
- Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK.
| | - Christophe d'Enfert
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France.
| | - Melanie Legrand
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France.
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19
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Einhaus J, Rochwarger A, Mattern S, Gaudillière B, Schürch CM. High-multiplex tissue imaging in routine pathology-are we there yet? Virchows Arch 2023; 482:801-812. [PMID: 36757500 PMCID: PMC10156760 DOI: 10.1007/s00428-023-03509-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/22/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023]
Abstract
High-multiplex tissue imaging (HMTI) approaches comprise several novel immunohistological methods that enable in-depth, spatial single-cell analysis. Over recent years, studies in tumor biology, infectious diseases, and autoimmune conditions have demonstrated the information gain accessible when mapping complex tissues with HMTI. Tumor biology has been a focus of innovative multiparametric approaches, as the tumor microenvironment (TME) contains great informative value for accurate diagnosis and targeted therapeutic approaches: unraveling the cellular composition and structural organization of the TME using sophisticated computational tools for spatial analysis has produced histopathologic biomarkers for outcomes in breast cancer, predictors of positive immunotherapy response in melanoma, and histological subgroups of colorectal carcinoma. Integration of HMTI technologies into existing clinical workflows such as molecular tumor boards will contribute to improve patient outcomes through personalized treatments tailored to the specific heterogeneous pathological fingerprint of cancer, autoimmunity, or infection. Here, we review the advantages and limitations of existing HMTI technologies and outline how spatial single-cell data can improve our understanding of pathological disease mechanisms and determinants of treatment success. We provide an overview of the analytic processing and interpretation and discuss how HMTI can improve future routine clinical diagnostic and therapeutic processes.
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Affiliation(s)
- Jakob Einhaus
- Department of Anaesthesiology, Perioperative & Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Alexander Rochwarger
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Sven Mattern
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Brice Gaudillière
- Department of Anaesthesiology, Perioperative & Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian M Schürch
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany.
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20
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Urban EA, Chernoff C, Layng KV, Han J, Anderson C, Konzman D, Johnston RJ. Activating and repressing gene expression between chromosomes during stochastic fate specification. Cell Rep 2023; 42:111910. [PMID: 36640351 PMCID: PMC9976292 DOI: 10.1016/j.celrep.2022.111910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/28/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
DNA elements act across long genomic distances to regulate gene expression. During transvection in Drosophila, DNA elements on one allele of a gene act between chromosomes to regulate expression of the other allele. Little is known about the biological roles and developmental regulation of transvection. Here, we study the stochastic expression of spineless (ss) in photoreceptors in the fly eye to understand transvection. We determine a biological role for transvection in regulating expression of naturally occurring ss alleles. We identify DNA elements required for activating and repressing transvection. Different enhancers participate in transvection at different times during development to promote gene expression and specify cell fates. Bringing a silencer element on a heterologous chromosome into proximity with the ss locus "reconstitutes" the gene, leading to repression. Our studies show that transvection regulates gene expression via distinct DNA elements at specific timepoints in development, with implications for genome organization and architecture.
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Affiliation(s)
- Elizabeth A. Urban
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA,These authors contributed equally
| | - Chaim Chernoff
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA,Present address: Harvard Stem Cell Institute, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA,These authors contributed equally
| | - Kayla Viets Layng
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Jeong Han
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Caitlin Anderson
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Daniel Konzman
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Robert J. Johnston
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA,Lead contact,Correspondence:
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21
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HT-smFISH: a cost-effective and flexible workflow for high-throughput single-molecule RNA imaging. Nat Protoc 2023; 18:157-187. [PMID: 36280749 DOI: 10.1038/s41596-022-00750-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 07/04/2022] [Indexed: 01/14/2023]
Abstract
The ability to visualize RNA in its native subcellular environment by using single-molecule fluorescence in situ hybridization (smFISH) has reshaped our understanding of gene expression and cellular functions. A major hindrance of smFISH is the difficulty to perform systematic experiments in medium- or high-throughput formats, principally because of the high cost of generating the individual fluorescent probe sets. Here, we present high-throughput smFISH (HT-smFISH), a simple and cost-efficient method for imaging hundreds to thousands of single endogenous RNA molecules in 96-well plates. HT-smFISH uses RNA probes transcribed in vitro from a large pool of unlabeled oligonucleotides. This allows the generation of individual probes for many RNA species, replacing commercial DNA probe sets. HT-smFISH thus reduces costs per targeted RNA compared with many smFISH methods and is easily scalable and flexible in design. We provide a protocol that combines oligo pool design, probe set generation, optimized hybridization conditions and guidelines for image acquisition and analysis. The pipeline requires knowledge of standard molecular biology tools, cell culture and fluorescence microscopy. It is achievable in ~20 d. In brief, HT-smFISH is tailored for medium- to high-throughput screens that image RNAs at single-molecule sensitivity.
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22
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Voortman L, Anderson C, Urban E, Yuan L, Tran S, Neuhaus-Follini A, Derrick J, Gregor T, Johnston RJ. Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies. Dev Cell 2022; 57:1817-1832.e5. [PMID: 35835116 PMCID: PMC9378680 DOI: 10.1016/j.devcel.2022.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 01/12/2023]
Abstract
Stochastic mechanisms diversify cell fates during development. How cells randomly choose between two or more fates remains poorly understood. In the Drosophila eye, the random mosaic of two R7 photoreceptor subtypes is determined by expression of the transcription factor Spineless (Ss). We investigated how cis-regulatory elements and trans factors regulate nascent transcriptional activity and chromatin compaction at the ss gene locus during R7 development. The ss locus is in a compact state in undifferentiated cells. An early enhancer drives transcription in all R7 precursors, and the locus opens. In differentiating cells, transcription ceases and the ss locus stochastically remains open or compacts. In SsON R7s, ss is open and competent for activation by a late enhancer, whereas in SsOFF R7s, ss is compact, and repression prevents expression. Our results suggest that a temporally dynamic antagonism, in which transcription drives large-scale decompaction and then compaction represses transcription, controls stochastic fate specification.
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Affiliation(s)
- Lukas Voortman
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Caitlin Anderson
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elizabeth Urban
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Luorongxin Yuan
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sang Tran
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Josh Derrick
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Thomas Gregor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Joseph Henry Laboratories of Physics, the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Developmental and Stem Cell Biology, UMR3738, Institut Pasteur, 75015 Paris, France
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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23
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Bugeon S, Duffield J, Dipoppa M, Ritoux A, Prankerd I, Nicoloutsopoulos D, Orme D, Shinn M, Peng H, Forrest H, Viduolyte A, Reddy CB, Isogai Y, Carandini M, Harris KD. A transcriptomic axis predicts state modulation of cortical interneurons. Nature 2022; 607:330-338. [PMID: 35794483 PMCID: PMC9279161 DOI: 10.1038/s41586-022-04915-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/27/2022] [Indexed: 12/14/2022]
Abstract
Transcriptomics has revealed that cortical inhibitory neurons exhibit a great diversity of fine molecular subtypes1-6, but it is not known whether these subtypes have correspondingly diverse patterns of activity in the living brain. Here we show that inhibitory subtypes in primary visual cortex (V1) have diverse correlates with brain state, which are organized by a single factor: position along the main axis of transcriptomic variation. We combined in vivo two-photon calcium imaging of mouse V1 with a transcriptomic method to identify mRNA for 72 selected genes in ex vivo slices. We classified inhibitory neurons imaged in layers 1-3 into a three-level hierarchy of 5 subclasses, 11 types and 35 subtypes using previously defined transcriptomic clusters3. Responses to visual stimuli differed significantly only between subclasses, with cells in the Sncg subclass uniformly suppressed, and cells in the other subclasses predominantly excited. Modulation by brain state differed at all hierarchical levels but could be largely predicted from the first transcriptomic principal component, which also predicted correlations with simultaneously recorded cells. Inhibitory subtypes that fired more in resting, oscillatory brain states had a smaller fraction of their axonal projections in layer 1, narrower spikes, lower input resistance and weaker adaptation as determined in vitro7, and expressed more inhibitory cholinergic receptors. Subtypes that fired more during arousal had the opposite properties. Thus, a simple principle may largely explain how diverse inhibitory V1 subtypes shape state-dependent cortical processing.
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Affiliation(s)
- Stéphane Bugeon
- UCL Queen Square Institute of Neurology, University College London, London, UK.
| | - Joshua Duffield
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Mario Dipoppa
- UCL Queen Square Institute of Neurology, University College London, London, UK
- Center for Theoretical Neuroscience, Columbia University, New York, NY, USA
| | - Anne Ritoux
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Isabelle Prankerd
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | | | - David Orme
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Maxwell Shinn
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Han Peng
- Department of Physics, University of Oxford, Oxford, UK
| | - Hamish Forrest
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Aiste Viduolyte
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Charu Bai Reddy
- UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Yoh Isogai
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London, UK
| | - Matteo Carandini
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Kenneth D Harris
- UCL Queen Square Institute of Neurology, University College London, London, UK.
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24
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Rensen E, Pietropaoli S, Mueller F, Weber C, Souquere S, Sommer S, Isnard P, Rabant M, Gibier JB, Terzi F, Simon-Loriere E, Rameix-Welti MA, Pierron G, Barba-Spaeth G, Zimmer C. Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH. Life Sci Alliance 2022; 5:e202101124. [PMID: 34996842 PMCID: PMC8742873 DOI: 10.26508/lsa.202101124] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 01/22/2023] Open
Abstract
The current COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The positive-sense single-stranded RNA virus contains a single linear RNA segment that serves as a template for transcription and replication, leading to the synthesis of positive and negative-stranded viral RNA (vRNA) in infected cells. Tools to visualize vRNA directly in infected cells are critical to analyze the viral replication cycle, screen for therapeutic molecules, or study infections in human tissue. Here, we report the design, validation, and initial application of FISH probes to visualize positive or negative RNA of SARS-CoV-2 (CoronaFISH). We demonstrate sensitive visualization of vRNA in African green monkey and several human cell lines, in patient samples and human tissue. We further demonstrate the adaptation of CoronaFISH probes to electron microscopy. We provide all required oligonucleotide sequences, source code to design the probes, and a detailed protocol. We hope that CoronaFISH will complement existing techniques for research on SARS-CoV-2 biology and COVID-19 pathophysiology, drug screening, and diagnostics.
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Affiliation(s)
- Elena Rensen
- Institut Pasteur, Université de Paris, CNRS UMR 3691, Imaging and Modeling Unit, Paris, France
| | - Stefano Pietropaoli
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Florian Mueller
- Institut Pasteur, Université de Paris, CNRS UMR 3691, Imaging and Modeling Unit, Paris, France
| | - Christian Weber
- Institut Pasteur, Université de Paris, CNRS UMR 3691, Imaging and Modeling Unit, Paris, France
| | | | - Sina Sommer
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Pierre Isnard
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département "Croissance et Signalisation," Paris, France
- Service d'Anatomo-Pathologie, AP-HP, Hôpital Necker Enfants Malades, AP-HP Centre, Paris, France
| | - Marion Rabant
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département "Croissance et Signalisation," Paris, France
- Service d'Anatomo-Pathologie, AP-HP, Hôpital Necker Enfants Malades, AP-HP Centre, Paris, France
| | - Jean-Baptiste Gibier
- Service d'Anatomo-Pathologie, Centre de Biologie Pathologie, CHU Lille, Lille, France
| | - Fabiola Terzi
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département "Croissance et Signalisation," Paris, France
| | - Etienne Simon-Loriere
- Institut Pasteur, Université de Paris, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Marie-Anne Rameix-Welti
- Université Paris-Saclay, INSERM, Université de Versailles St. Quentin, UMR 1173 (2I), Montigny-le-Bretonneux, France
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | | | - Giovanna Barba-Spaeth
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Christophe Zimmer
- Institut Pasteur, Université de Paris, CNRS UMR 3691, Imaging and Modeling Unit, Paris, France
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25
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Lin Z, Yang Y, Jagota A, Zheng M. Machine Learning-Guided Systematic Search of DNA Sequences for Sorting Carbon Nanotubes. ACS NANO 2022; 16:4705-4713. [PMID: 35213805 DOI: 10.1021/acsnano.1c11448] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The prerequisite of utilizing DNA in sequence-dependent applications is to search specific sequences. Developing a strategy for efficient DNA sequence screening represents a grand challenge due to the countless possibilities of sequence combination. Herein, relying on sequence-dependent recognition between DNA and single-wall carbon nanotubes (SWCNTs), we demonstrate a method for systematic search of DNA sequences for sorting single-chirality SWCNTs. Different from previously documented empirical search, which has a low efficiency and accuracy, our approach combines machine learning and experimental investigation. The number of resolving sequences and the success rate of finding them are improved from ∼102 to ∼103 and from ∼10% to >90%, respectively. Moreover, the resolving sequence patterns determined from 5-mer and 6-mer short sequences can be extended to sequence search in longer DNA subspaces.
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Affiliation(s)
- Zhiwei Lin
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Yoona Yang
- Department of Chemical & Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Anand Jagota
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Ming Zheng
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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26
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Vu T, Vallmitjana A, Gu J, La K, Xu Q, Flores J, Zimak J, Shiu J, Hosohama L, Wu J, Douglas C, Waterman ML, Ganesan A, Hedde PN, Gratton E, Zhao W. Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis. Nat Commun 2022; 13:169. [PMID: 35013281 PMCID: PMC8748653 DOI: 10.1038/s41467-021-27798-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/15/2021] [Indexed: 12/14/2022] Open
Abstract
Multiplexed mRNA profiling in the spatial context provides new information enabling basic research and clinical applications. Unfortunately, existing spatial transcriptomics methods are limited due to either low multiplexing or complexity. Here, we introduce a spatialomics technology, termed Multi Omic Single-scan Assay with Integrated Combinatorial Analysis (MOSAICA), that integrates in situ labeling of mRNA and protein markers in cells or tissues with combinatorial fluorescence spectral and lifetime encoded probes, spectral and time-resolved fluorescence imaging, and machine learning-based decoding. We demonstrate MOSAICA's multiplexing scalability in detecting 10-plex targets in fixed colorectal cancer cells using combinatorial labeling of five fluorophores with facile error-detection and removal of autofluorescence. MOSAICA's analysis is strongly correlated with sequencing data (Pearson's r = 0.96) and was further benchmarked using RNAscopeTM and LGC StellarisTM. We further apply MOSAICA for multiplexed analysis of clinical melanoma Formalin-Fixed Paraffin-Embedded (FFPE) tissues. We finally demonstrate simultaneous co-detection of protein and mRNA in cancer cells.
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Affiliation(s)
- Tam Vu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA
| | - Alexander Vallmitjana
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA, 92697, USA
| | - Joshua Gu
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Kieu La
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
| | - Qi Xu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jesus Flores
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA
- CIRM Stem Cell Research Biotechnology Training Program at California State University, Long Beach, Long Beach, CA, 90840, USA
| | - Jan Zimak
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jessica Shiu
- Department of Dermatology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Linzi Hosohama
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA
| | - Christopher Douglas
- Department of Pathology & Laboratory Medicine, University of California, Irvine, Irvine, CA, 92617, USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA
| | - Anand Ganesan
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Dermatology, University of California, Irvine, Irvine, CA, 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA
| | - Per Niklas Hedde
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
- Beckman Laser Institute & Medical Clinic, University of California, Irvine, Irvine, CA, 92697, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA.
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA, 92697, USA.
- Beckman Laser Institute & Medical Clinic, University of California, Irvine, Irvine, CA, 92697, USA.
| | - Weian Zhao
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA.
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA.
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA.
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27
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Kristensen NP, Heeke C, Tvingsholm SA, Borch A, Draghi A, Crowther MD, Carri I, Munk KK, Holm JS, Bjerregaard AM, Bentzen AK, Marquard AM, Szallasi Z, McGranahan N, Andersen R, Nielsen M, Jönsson GB, Donia M, Svane IM, Hadrup SR. Neoantigen-reactive CD8+ T cells affect clinical outcome of adoptive transfer with tumor-infiltrating lymphocytes in melanoma. J Clin Invest 2021; 132:150535. [PMID: 34813506 PMCID: PMC8759789 DOI: 10.1172/jci150535] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Neoantigen-driven recognition and T cell-mediated killing contribute to tumor clearance following adoptive cell therapy (ACT) with Tumor-Infiltrating Lymphocytes (TILs). Yet, how diversity, frequency, and persistence of expanded neoepitope-specific CD8+ T cells derived from TIL infusion products affect patient outcome is not fully determined. METHODS Using barcoded pMHC multimers, we provide a comprehensive mapping of CD8+ T cells recognizing neoepitopes in TIL infusion products and blood samples from 26 metastatic mela-noma patients who received ACT. RESULTS We identified 106 neoepitopes within TIL infusion products corresponding to 1.8% of all predicted neoepitopes. We observed neoepitope-specific recognition to be virtually devoid in TIL infusion products given to patients with progressive disease outcome. Moreover, we found that the frequency of neoepitope-specific CD8+ T cells in TIL infusion products correlated with in-creased survival, and that detection of engrafted CD8+ T cells in post-treatment (i.e. originating from the TIL infusion product) were unique to responders of TIL-ACT. Finally, we found that a transcriptional signature for lymphocyte activity within the tumor microenvironment was associated with a higher frequency of neoepitope-specific CD8+ T cells in the infusion product. CONCLUSIONS These data support previous case studies of neoepitope-specific CD8+ T cells in melanoma, and indicate that successful TIL-ACT is associated with an expansion of neoepitope-specific CD8+ T cells. FUNDING NEYE Foundation; European Research Council; Lundbeck Foundation Fellowship; Carlsberg Foundation.
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Affiliation(s)
- Nikolaj Pagh Kristensen
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Christina Heeke
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Siri A Tvingsholm
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Annie Borch
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Arianna Draghi
- Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | | | - Ibel Carri
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Kamilla K Munk
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Jeppe Sejerø Holm
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Anne-Mette Bjerregaard
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Amalie Kai Bentzen
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Andrea M Marquard
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | | | - Rikke Andersen
- Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Morten Nielsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Göran B Jönsson
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Marco Donia
- Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Inge Marie Svane
- Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
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28
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Banal JL, Bathe M. Scalable Nucleic Acid Storage and Retrieval Using Barcoded Microcapsules. ACS APPLIED MATERIALS & INTERFACES 2021; 13:49729-49736. [PMID: 34652142 DOI: 10.1021/acsami.1c14985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rapid advances in nucleic acid sequencing and synthesis technologies have spurred a major need to collect, store, and sequence the DNA and RNA from viral, bacterial, and mammalian sources and organisms. However, current approaches to storing nucleic acids rely on a low-temperature environment and require robotics for access, posing challenges for scalable and low-cost nucleic acid storage. Here, we present an alternative method for storing nucleic acids, termed Preservation and Access of Nucleic aciDs using barcOded micRocApsules (PANDORA). Nucleic acids spanning kilobases to gigabases and from different sources, including animals, bacteria, and viruses, are encapsulated into silica microcapsules to protect them from environmental denaturants at room temperature. Molecular barcodes attached to each microcapsule enable sample pooling and subsequent identification and retrieval using fluorescence-activated sorting. We demonstrate quantitative storage and rapid access to targeted nucleic acids from a pool emulating standard retrieval operations implemented in conventional storage systems, including recovery of 100,000-200,000 samples and Boolean logic selection using four unique barcodes. Quantitative polymerase chain reaction and short-read sequencing of the retrieved samples validated the sorting experiments and the integrity of the released nucleic acids. Our proposed approach offers a scalable long-term, room-temperature storage and retrieval of nucleic acids with high sample fidelity.
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Affiliation(s)
- James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142 United States
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29
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Barber KW, Shrock E, Elledge SJ. CRISPR-based peptide library display and programmable microarray self-assembly for rapid quantitative protein binding assays. Mol Cell 2021; 81:3650-3658.e5. [PMID: 34390675 DOI: 10.1016/j.molcel.2021.07.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/25/2021] [Accepted: 07/21/2021] [Indexed: 01/08/2023]
Abstract
CRISPR-inspired systems have been extensively developed for applications in genome editing and nucleic acid detection. Here, we introduce a CRISPR-based peptide display technology to facilitate customized, high-throughput in vitro protein interaction studies. We show that bespoke peptide libraries fused to catalytically inactive Cas9 (dCas9) and barcoded with unique single guide RNA (sgRNA) molecules self-assemble from a single mixed pool to programmable positions on a DNA microarray surface for rapid, multiplexed binding assays. We develop dCas9-displayed saturation mutagenesis libraries to characterize antibody-epitope binding for a commercial anti-FLAG monoclonal antibody and human serum antibodies. We also show that our platform can be used for viral epitope mapping and exhibits promise as a multiplexed diagnostics tool. Our CRISPR-based peptide display platform and the principles of complex library self-assembly using dCas9 could be adapted for rapid interrogation of varied customized protein libraries or biological materials assembly using DNA scaffolding.
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Affiliation(s)
- Karl W Barber
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen Shrock
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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30
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Xu M, Mehl L, Zhang T, Thakur R, Sowards H, Myers T, Jessop L, Chesi A, Johnson ME, Wells AD, Michael HT, Bunda P, Jones K, Higson H, Hennessey RC, Jermusyk A, Kovacs MA, Landi MT, Iles MM, Goldstein AM, Choi J, Chanock SJ, Grant SF, Chari R, Merlino G, Law MH, Brown KM, Brown KM. A UVB-responsive common variant at chromosome band 7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor, AHR. Am J Hum Genet 2021; 108:1611-1630. [PMID: 34343493 DOI: 10.1016/j.ajhg.2021.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified a melanoma-associated locus on chromosome band 7p21.1 with rs117132860 as the lead SNP and a secondary independent signal marked by rs73069846. rs117132860 is also associated with tanning ability and cutaneous squamous cell carcinoma (cSCC). Because ultraviolet radiation (UVR) is a key environmental exposure for all three traits, we investigated the mechanisms by which this locus contributes to melanoma risk, focusing on cellular response to UVR. Fine-mapping of melanoma GWASs identified four independent sets of candidate causal variants. A GWAS region-focused Capture-C study of primary melanocytes identified physical interactions between two causal sets and the promoter of the aryl hydrocarbon receptor (AHR). Subsequent chromatin state annotation, eQTL, and luciferase assays identified rs117132860 as a functional variant and reinforced AHR as a likely causal gene. Because AHR plays critical roles in cellular response to dioxin and UVR, we explored links between this SNP and AHR expression after both 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and ultraviolet B (UVB) exposure. Allele-specific AHR binding to rs117132860-G was enhanced following both, consistent with predicted weakened AHR binding to the risk/poor-tanning rs117132860-A allele, and allele-preferential AHR expression driven from the protective rs117132860-G allele was observed following UVB exposure. Small deletions surrounding rs117132860 introduced via CRISPR abrogates AHR binding, reduces melanocyte cell growth, and prolongs growth arrest following UVB exposure. These data suggest AHR is a melanoma susceptibility gene at the 7p21.1 risk locus and rs117132860 is a functional variant within a UVB-responsive element, leading to allelic AHR expression and altering melanocyte growth phenotypes upon exposure.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
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31
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Banal JL, Shepherd TR, Berleant J, Huang H, Reyes M, Ackerman CM, Blainey PC, Bathe M. Random access DNA memory using Boolean search in an archival file storage system. NATURE MATERIALS 2021; 20:1272-1280. [PMID: 34112975 PMCID: PMC8564878 DOI: 10.1038/s41563-021-01021-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 04/26/2021] [Indexed: 05/03/2023]
Abstract
DNA is an ultrahigh-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and if random access of files within exabyte-to-yottabyte-scale DNA data pools were feasible. Here, we demonstrate a path to overcome the second barrier by encapsulating data-encoding DNA file sequences within impervious silica capsules that are surface labelled with single-stranded DNA barcodes. Barcodes are chosen to represent file metadata, enabling selection of sets of files with Boolean logic directly, without use of amplification. We demonstrate random access of image files from a prototypical 2-kilobyte image database using fluorescence sorting with selection sensitivity of one in 106 files, which thereby enables one in 106N selection capability using N optical channels. Our strategy thereby offers a scalable concept for random access of archival files in large-scale molecular datasets.
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Affiliation(s)
- James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joseph Berleant
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Miguel Reyes
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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32
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Sinyakov AN, Ryabinin VA, Kostina EV. Application of Array-Based Oligonucleotides for Synthesis of Genetic Designs. Mol Biol 2021. [DOI: 10.1134/s0026893321030109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Chalapati S, Crosbie CA, Limbachiya D, Pinnamaneni N. Direct oligonucleotide sequencing with nanopores. OPEN RESEARCH EUROPE 2021; 1:47. [PMID: 37645114 PMCID: PMC10445935 DOI: 10.12688/openreseurope.13578.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/13/2021] [Indexed: 08/31/2023]
Abstract
Third-generation DNA sequencing has enabled sequencing of long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insights like base-level modifications, phosphoramidite synthesis yield estimates and strand quality analysis, without the need to add the complimentary strand. Direct sequencing of single-stranded nucleic acid species is challenging as they are non-compatible to the double-stranded sequencing adapters used by manufacturers. The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through a layer of biological nanopore sensors; although sequencing is performed on single-strands, the recommended template by the manufacturer is double-stranded. We have identified that the MinION platform can perform sequencing of short, single-strand oligonucleotides directly without amplification or second-strand synthesis by performing a single annealing step before library preparation. Short 5' phosphorylated oligos when annealed to an adapter sequence can be directly sequenced in the 5' to 3' direction via nanopores. Adapter sequences were designed to bind to the 5' end of the oligos and to leave a 3' adenosine overhang after binding to their target. The 3' adenosine overhang of the adapter and the terminal phosphate makes the 5' end of the oligo analogous to an end-prepared dsDNA, rendering it compatible with ligation-based library preparation for sequencing. An oligo-pool containing 42,000, 120 nt orthogonal sequences was phosphorylated and sequenced using this method and ~90% of these sequences were recovered with high accuracy using BLAST. In the nanopore raw data, we have identified that empty signals can be wrongly identified as a valid read by the MinION platform and sometimes multiple signals containing several strands can be fused into a single raw sequence file due to segmentation faults in the software. This direct oligonucleotide sequencing method enables novel applications in DNA data storage systems where short oligonucleotides are the primary information carriers.
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Affiliation(s)
- Sachin Chalapati
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Conor A Crosbie
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Dixita Limbachiya
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Nimesh Pinnamaneni
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
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34
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Chalapati S, Crosbie CA, Limbachiya D, Pinnamaneni N. Direct oligonucleotide sequencing with nanopores. OPEN RESEARCH EUROPE 2021; 1:47. [PMID: 37645114 PMCID: PMC10445935 DOI: 10.12688/openreseurope.13578.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/13/2021] [Indexed: 09/27/2023]
Abstract
Third-generation DNA sequencing has enabled sequencing of long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insights like base-level modifications, phosphoramidite synthesis yield estimates and strand quality analysis, without the need to add the complimentary strand. Direct sequencing of single-stranded nucleic acid species is challenging as they are non-compatible to the double-stranded sequencing adapters used by manufacturers. The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through a layer of biological nanopore sensors; although sequencing is performed on single-strands, the recommended template by the manufacturer is double-stranded. We have identified that the MinION platform can perform sequencing of short, single-strand oligonucleotides directly without amplification or second-strand synthesis by performing a single annealing step before library preparation. Short 5' phosphorylated oligos when annealed to an adapter sequence can be directly sequenced in the 5' to 3' direction via nanopores. Adapter sequences were designed to bind to the 5' end of the oligos and to leave a 3' adenosine overhang after binding to their target. The 3' adenosine overhang of the adapter and the terminal phosphate makes the 5' end of the oligo analogous to an end-prepared dsDNA, rendering it compatible with ligation-based library preparation for sequencing. An oligo-pool containing 42,000, 120 nt orthogonal sequences was phosphorylated and sequenced using this method and ~90% of these sequences were recovered with high accuracy using BLAST. In the nanopore raw data, we have identified that empty signals can be wrongly identified as a valid read by the MinION platform and sometimes multiple signals containing several strands can be fused into a single raw sequence file due to segmentation faults in the software. This direct oligonucleotide sequencing method enables novel applications in DNA data storage systems where short oligonucleotides are the primary information carriers.
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Affiliation(s)
- Sachin Chalapati
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Conor A Crosbie
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Dixita Limbachiya
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Nimesh Pinnamaneni
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
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35
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Tomov ML, O'Neil A, Abbasi HS, Cimini BA, Carpenter AE, Rubin LL, Bathe M. Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging. Commun Biol 2021; 4:786. [PMID: 34168275 PMCID: PMC8225800 DOI: 10.1038/s42003-021-02276-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/28/2021] [Indexed: 12/30/2022] Open
Abstract
Human induced pluripotent stem cell-derived (iPSC) neural cultures offer clinically relevant models of human diseases, including Amyotrophic Lateral Sclerosis, Alzheimer’s, and Autism Spectrum Disorder. In situ characterization of the spatial-temporal evolution of cell state in 3D culture and subsequent 2D dissociated culture models based on protein expression levels and localizations is essential to understanding neural cell differentiation, disease state phenotypes, and sample-to-sample variability. Here, we apply PRobe-based Imaging for Sequential Multiplexing (PRISM) to facilitate multiplexed imaging with facile, rapid exchange of imaging probes to analyze iPSC-derived cortical and motor neuron cultures that are relevant to psychiatric and neurodegenerative disease models, using over ten protein targets. Our approach permits analysis of cell differentiation, cell composition, and functional marker expression in complex stem-cell derived neural cultures. Furthermore, our approach is amenable to automation, offering in principle the ability to scale-up to dozens of protein targets and samples. Tomov et al. utilize DNA-PRISM to allow for multiplexed imaging of cultured cells using antibodies modified with oligonucleotide probes. The differentiation of iPSCs to cortical and motor neurons is characterized in model cultures, relevant for use in disease research and drug screening.
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Affiliation(s)
- Martin L Tomov
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Alison O'Neil
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Hamdah S Abbasi
- Imaging Platform at Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Beth A Cimini
- Imaging Platform at Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform at Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lee L Rubin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Mark Bathe
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
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36
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Tang D, Zhao H, Wu Y, Peng B, Gao Z, Sun Y, Duan J, Qi Y, Li Y, Zhou Z, Guo G, Zhang Y, Li C, Sui J, Li W. Transcriptionally inactive hepatitis B virus episome DNA preferentially resides in the vicinity of chromosome 19 in 3D host genome upon infection. Cell Rep 2021; 35:109288. [PMID: 34192543 DOI: 10.1016/j.celrep.2021.109288] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 03/07/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
The hepatitis B virus (HBV) infects 257 million people worldwide. HBV infection requires establishment and persistence of covalently closed circular (ccc) DNA, a viral episome, in nucleus. Here, we study cccDNA spatial localization in the 3D host genome by using chromosome conformation capture-based sequencing analysis and fluorescence in situ hybridization (FISH). We show that transcriptionally inactive cccDNA is not randomly distributed in host nucleus. Rather, it is preferentially accumulated at specialized areas, including regions close to chromosome 19 (chr.19). Activation of the cccDNA is apparently associated with its re-localization, from a pre-established heterochromatin hub formed by 5 regions of chr.19 to transcriptionally active regions formed by chr.19 and nearby chromosomes including chr.16, 17, 20, and 22. This active versus inactive positioning at discrete regions of the host genome is primarily controlled by the viral HBx protein and by host factors including the structural maintenance of chromosomes protein 5/6 (SMC5/6) complex.
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Affiliation(s)
- Dingbin Tang
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing, China; National Institute of Biological Sciences, Beijing, China
| | - Hanqing Zhao
- National Institute of Biological Sciences, Beijing, China
| | - Yumeng Wu
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing, China; National Institute of Biological Sciences, Beijing, China
| | - Bo Peng
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing, China; National Institute of Biological Sciences, Beijing, China
| | - Zhenchao Gao
- National Institute of Biological Sciences, Beijing, China
| | - Yinyan Sun
- National Institute of Biological Sciences, Beijing, China
| | - Jinzhi Duan
- National Institute of Biological Sciences, Beijing, China
| | - Yonghe Qi
- National Institute of Biological Sciences, Beijing, China
| | - Yunfei Li
- National Institute of Biological Sciences, Beijing, China
| | - Zhongmin Zhou
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing, China
| | - Guilan Guo
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing, China
| | - Yu Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Cheng Li
- School of Life Sciences, Center for Statistical Science, Center for Bioinformatics, Peking University, Beijing, China
| | - Jianhua Sui
- National Institute of Biological Sciences, Beijing, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Wenhui Li
- National Institute of Biological Sciences, Beijing, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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37
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Xin L, Duan X, Liu N. Dimerization and oligomerization of DNA-assembled building blocks for controlled multi-motion in high-order architectures. Nat Commun 2021; 12:3207. [PMID: 34050157 PMCID: PMC8163789 DOI: 10.1038/s41467-021-23532-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 04/19/2021] [Indexed: 01/01/2023] Open
Abstract
In living organisms, proteins are organized prevalently through a self-association mechanism to form dimers and oligomers, which often confer new functions at the intermolecular interfaces. Despite the progress on DNA-assembled artificial systems, endeavors have been largely paid to achieve monomeric nanostructures that mimic motor proteins for a single type of motion. Here, we demonstrate a DNA-assembled building block with rotary and walking modules, which can introduce new motion through dimerization and oligomerization. The building block is a chiral system, comprising two interacting gold nanorods to perform rotation and walking, respectively. Through dimerization, two building blocks can form a dimer to yield coordinated sliding. Further oligomerization leads to higher-order structures, containing alternating rotation and sliding dimer interfaces to impose structural twisting. Our hierarchical assembly scheme offers a design blueprint to construct DNA-assembled advanced architectures with high degrees of freedom to tailor the optical responses and regulate multi-motion on the nanoscale. Creation of high-order architectures using DNA devices is of interest for increasing the complexity of synthetic systems. Here, the authors, inspired by biological oligomers, create DNA dimers and oligomers that combining rotation and walking to make high-order systems with more complex conformational changes.
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Affiliation(s)
- Ling Xin
- 2. Physics Institute, University of Stuttgart, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Stuttgart, Germany
| | - Xiaoyang Duan
- Max Planck Institute for Solid State Research, Stuttgart, Germany
| | - Na Liu
- 2. Physics Institute, University of Stuttgart, Stuttgart, Germany. .,Max Planck Institute for Solid State Research, Stuttgart, Germany.
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38
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Wang Y, Cottle WT, Wang H, Feng XA, Mallon J, Gavrilov M, Bailey S, Ha T. Genome oligopaint via local denaturation fluorescence in situ hybridization. Mol Cell 2021; 81:1566-1577.e8. [PMID: 33657402 PMCID: PMC8026568 DOI: 10.1016/j.molcel.2021.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/22/2020] [Accepted: 02/04/2021] [Indexed: 12/26/2022]
Abstract
Cas9 in complex with a programmable guide RNA targets specific double-stranded DNA for cleavage. By harnessing Cas9 as a programmable loader of superhelicase to genomic DNA, we report a physiological-temperature DNA fluorescence in situ hybridization (FISH) method termed genome oligopaint via local denaturation (GOLD) FISH. Instead of global denaturation as in conventional DNA FISH, loading a superhelicase at a Cas9-generated nick allows for local DNA denaturation, reducing nonspecific binding of probes and avoiding harsh treatments such as heat denaturation. GOLD FISH relies on Cas9 cleaving target DNA sequences and avoids the high nuclear background associated with other genome labeling methods that rely on Cas9 binding. The excellent signal brightness and specificity enable us to image nonrepetitive genomic DNA loci and analyze the conformational differences between active and inactive X chromosomes. Finally, GOLD FISH could be used for rapid identification of HER2 gene amplification in patient tissue.
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Affiliation(s)
- Yanbo Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Wayne Taylor Cottle
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Haobo Wang
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xinyu Ashlee Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - John Mallon
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Momcilo Gavrilov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Scott Bailey
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
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39
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Nedrud D, Coyote-Maestas W, Schmidt D. A large-scale survey of pairwise epistasis reveals a mechanism for evolutionary expansion and specialization of PDZ domains. Proteins 2021; 89:899-914. [PMID: 33620761 DOI: 10.1002/prot.26067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/02/2021] [Accepted: 02/18/2021] [Indexed: 12/21/2022]
Abstract
Deep mutational scanning (DMS) facilitates data-driven models of protein structure and function. Here, we adapted Saturated Programmable Insertion Engineering (SPINE) as a programmable DMS technique. We validate SPINE with a reference single mutant dataset in the PSD95 PDZ3 domain and then characterize most pairwise double mutants to study epistasis. We observe wide-spread proximal negative epistasis, which we attribute to mutations affecting thermodynamic stability, and strong long-range positive epistasis, which is enriched in an evolutionarily conserved and function-defining network of "sector" and clade-specifying residues. Conditional neutrality of mutations in clade-specifying residues compensates for deleterious mutations in sector positions. This suggests that epistatic interactions between these position pairs facilitated the evolutionary expansion and specialization of PDZ domains. We propose that SPINE provides easy experimental access to reveal epistasis signatures in proteins that will improve our understanding of the structural basis for protein function and adaptation.
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Affiliation(s)
- David Nedrud
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Willow Coyote-Maestas
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Daniel Schmidt
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, Minnesota, USA
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40
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A comprehensive phenotypic CRISPR-Cas9 screen of the ubiquitin pathway uncovers roles of ubiquitin ligases in mitosis. Mol Cell 2021; 81:1319-1336.e9. [PMID: 33539788 DOI: 10.1016/j.molcel.2021.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 10/20/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
The human ubiquitin proteasome system, composed of over 700 ubiquitin ligases (E3s) and deubiquitinases (DUBs), has been difficult to characterize systematically and phenotypically. We performed chemical-genetic CRISPR-Cas9 screens to identify E3s/DUBs whose loss renders cells sensitive or resistant to 41 compounds targeting a broad range of biological processes, including cell cycle progression, genome stability, metabolism, and vesicular transport. Genes and compounds clustered functionally, with inhibitors of related pathways interacting similarly with E3s/DUBs. Some genes, such as FBXW7, showed interactions with many of the compounds. Others, such as RNF25 and FBXO42, showed interactions primarily with a single compound (methyl methanesulfonate for RNF25) or a set of related compounds (the mitotic cluster for FBXO42). Mutation of several E3s with sensitivity to mitotic inhibitors led to increased aberrant mitoses, suggesting a role for these genes in cell cycle regulation. Our comprehensive CRISPR-Cas9 screen uncovered 466 gene-compound interactions covering 25% of the interrogated E3s/DUBs.
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41
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Alon S, Goodwin DR, Sinha A, Wassie AT, Chen F, Daugharthy ER, Bando Y, Kajita A, Xue AG, Marrett K, Prior R, Cui Y, Payne AC, Yao CC, Suk HJ, Wang R, Yu CCJ, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman RE, Miller JA, Lein ES, Lako A, Cullen N, Rodig S, Helvie K, Abravanel DL, Wagle N, Johnson BE, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rozenblatt-Rosen O, Regev A, Church GM, Marblestone AH, Boyden ES. Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Science 2021; 371:eaax2656. [PMID: 33509999 PMCID: PMC7900882 DOI: 10.1126/science.aax2656] [Citation(s) in RCA: 193] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/13/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022]
Abstract
Methods for highly multiplexed RNA imaging are limited in spatial resolution and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to the mouse brain, which yielded the readout of thousands of genes, including splice variants. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in the neurons of the mouse hippocampus, revealing patterns across multiple cell types, layer-specific cell types across the mouse visual cortex, and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus, ExSeq enables highly multiplexed mapping of RNAs from nanoscale to system scale.
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Affiliation(s)
- Shahar Alon
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Faculty of Engineering, Gonda Brain Research Center and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Daniel R Goodwin
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Anubhav Sinha
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Asmamaw T Wassie
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Fei Chen
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Evan R Daugharthy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Yosuke Bando
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Kioxia Corporation, Minato-ku, Tokyo, Japan
| | | | - Andrew G Xue
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
| | | | | | - Yi Cui
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Andrew C Payne
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chun-Chen Yao
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ho-Jun Suk
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Ru Wang
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Chih-Chieh Jay Yu
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Paul Tillberg
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
| | - Paul Reginato
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Nikita Pak
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA, USA
| | - Songlei Liu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Sukanya Punthambaker
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Eswar P R Iyer
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Richie E Kohman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ana Lako
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicole Cullen
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott Rodig
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karla Helvie
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Daniel L Abravanel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Nikhil Wagle
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bruce E Johnson
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Michal Slyper
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | | | - Edward S Boyden
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA.
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
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42
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Marshall JL, Doughty BR, Subramanian V, Guckelberger P, Wang Q, Chen LM, Rodriques SG, Zhang K, Fulco CP, Nasser J, Grinkevich EJ, Noel T, Mangiameli S, Bergman DT, Greka A, Lander ES, Chen F, Engreitz JM. HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes. Proc Natl Acad Sci U S A 2020; 117:33404-33413. [PMID: 33376219 PMCID: PMC7776864 DOI: 10.1073/pnas.2010738117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of hundreds of chosen genes in single cells. HyPR-seq involves hybridizing DNA probes to RNA, distributing cells into nanoliter droplets, amplifying the probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell-type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome single-cell RNA-sequencing, making HyPR-seq a powerful method for targeted RNA profiling in single cells.
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Affiliation(s)
| | | | | | - Philine Guckelberger
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Qingbo Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA 02115
| | - Linlin M Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Samuel G Rodriques
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Kaite Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Teia Noel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | | | - Anna Greka
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142;
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142;
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142;
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Basic Science and Engineering Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA 94305
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43
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RNA structure-wide discovery of functional interactions with multiplexed RNA motif library. Nat Commun 2020; 11:6275. [PMID: 33293523 PMCID: PMC7723054 DOI: 10.1038/s41467-020-19699-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 10/16/2020] [Indexed: 12/30/2022] Open
Abstract
Biochemical assays and computational analyses have discovered RNA structures throughout various transcripts. However, the roles of these structures are mostly unknown. Here we develop folded RNA element profiling with structure library (FOREST), a multiplexed affinity assay system to identify functional interactions from transcriptome-wide RNA structure datasets. We generate an RNA structure library by extracting validated or predicted RNA motifs from gene-annotated RNA regions. The RNA structure library with an affinity enrichment assay allows for the comprehensive identification of target-binding RNA sequences and structures in a high-throughput manner. As a proof-of-concept, FOREST discovers multiple RNA-protein interaction networks with quantitative scores, including translational regulatory elements that function in living cells. Moreover, FOREST reveals different binding landscapes of RNA G-quadruplex (rG4) structures-binding proteins and discovers rG4 structures in the terminal loops of precursor microRNAs. Overall, FOREST serves as a versatile platform to investigate RNA structure-function relationships on a large scale. Structured RNA motifs can be obtained by structure probing, duplex capture, and motif prediction. Here the authors develop a multiplexed affinity assay system to identify functional protein interactors from an RNA structure library with validated or predicted RNA motifs.
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44
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Bousbaine D, Ploegh HL. Antigen discovery tools for adaptive immune receptor repertoire research. CURRENT OPINION IN SYSTEMS BIOLOGY 2020; 24:64-70. [PMID: 33195881 PMCID: PMC7665270 DOI: 10.1016/j.coisb.2020.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The adaptive immune system has evolved to recognize with incredible precision a large diversity of molecules. Innovations in high-throughput sequencing and bioinformatics have accelerated large-scale immune repertoire analyses and given us important insights into the behavior of the adaptive immune system. However, establishing a connection between receptor sequence and its antigen-specificity remains a challenge despite its central role in determining T and B cell fate. We discuss recent large-scale antigen discovery technologies which can be combined with adaptive immune receptor repertoire (AIRR) studies. We highlight important discoveries made using repertoire analyses in the field of host-microbe interactions.
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Affiliation(s)
- Djenet Bousbaine
- Department of Bioengineering and ChEM-H, Stanford University, Stanford CA, USA
| | - Hidde L. Ploegh
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston MA, USA
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45
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Thompson MK, Kiourlappou M, Davis I. Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion. RNA (NEW YORK, N.Y.) 2020; 26:1731-1742. [PMID: 32759389 PMCID: PMC7566562 DOI: 10.1261/rna.076562.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
The measurement of RNA abundance derived from massively parallel sequencing experiments is an essential technique. Methods that reduce ribosomal RNA levels are usually required prior to sequencing library construction because ribosomal RNA typically comprises the vast majority of a total RNA sample. For some experiments, ribosomal RNA depletion is favored over poly(A) selection because it offers a more inclusive representation of the transcriptome. However, methods to deplete ribosomal RNA are generally proprietary, complex, inefficient, applicable to only specific species, or compatible with only a narrow range of RNA input levels. Here, we describe Ribo-Pop (ribosomal RNA depletion for popular use), a simple workflow and antisense oligo design strategy that we demonstrate works over a wide input range and can be easily adapted to any organism with a sequenced genome. We provide a computational pipeline for probe selection, a streamlined 20-min protocol, and ready-to-use oligo sequences for several organisms. We anticipate that our simple and generalizable "open source" design strategy would enable virtually any laboratory to pursue full transcriptome sequencing in their organism of interest with minimal time and resource investment.
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Affiliation(s)
- Mary Kay Thompson
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Maria Kiourlappou
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
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46
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Xiao L, Liao R, Guo J. Highly Multiplexed Single-Cell In Situ RNA and DNA Analysis by Consecutive Hybridization. Molecules 2020; 25:molecules25214900. [PMID: 33113917 PMCID: PMC7660199 DOI: 10.3390/molecules25214900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
The ability to comprehensively profile nucleic acids in individual cells in their natural spatial contexts is essential to advance our understanding of biology and medicine. Here, we report a novel method for spatial transcriptomics and genomics analysis. In this method, every nucleic acid molecule is detected as a fluorescent spot at its natural cellular location throughout the cycles of consecutive fluorescence in situ hybridization (C-FISH). In each C-FISH cycle, fluorescent oligonucleotide probes hybridize to the probes applied in the previous cycle, and also introduce the binding sites for the next cycle probes. With reiterative cycles of hybridization, imaging and photobleaching, the identities of the varied nucleic acids are determined by their unique color sequences. To demonstrate the feasibility of this method, we show that transcripts or genomic loci in single cells can be unambiguously quantified with 2 fluorophores and 16 C-FISH cycles or with 3 fluorophores and 9 C-FISH cycles. Without any error correction, the error rates obtained using the raw data are close to zero. These results indicate that C-FISH potentially enables tens of thousands (216 = 65,536 or 39 = 19,683) of different transcripts or genomic loci to be precisely profiled in individual cells in situ.
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Affiliation(s)
| | | | - Jia Guo
- Correspondence: ; Tel.: +1-480-727-2096
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47
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Abstract
T cells respond to threats in an antigen-specific manner using T cell receptors (TCRs) that recognize short peptide antigens presented on major histocompatibility complex (MHC) proteins. The TCR-peptide-MHC interaction mediated between a T cell and its target cell dictates its function and thereby influences its role in disease. A lack of approaches for antigen discovery has limited the fundamental understanding of the antigenic landscape of the overall T cell response. Recent advances in high-throughput sequencing, mass cytometry, microfluidics and computational biology have led to a surge in approaches to address the challenge of T cell antigen discovery. Here, we summarize the scope of this challenge, discuss in depth the recent exciting work and highlight the outstanding questions and remaining technical hurdles in this field.
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48
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Zhou W, Emery SB, Flasch DA, Wang Y, Kwan KY, Kidd JM, Moran JV, Mills RE. Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology. Nucleic Acids Res 2020; 48:1146-1163. [PMID: 31853540 PMCID: PMC7026601 DOI: 10.1093/nar/gkz1173] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/14/2019] [Accepted: 12/05/2019] [Indexed: 11/13/2022] Open
Abstract
Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome sequencing (WGS) data; however, they have limitations in detecting insertions in complex repetitive genomic regions. Here, we developed a computational tool (PALMER) and used it to identify 203 non-reference L1Hs insertions in the NA12878 benchmark genome. Using PacBio long-read sequencing data, we identified L1Hs insertions that were absent in previous short-read studies (90/203). Approximately 81% (73/90) of the L1Hs insertions reside within endogenous LINE-1 sequences in the reference assembly and the analysis of unique breakpoint junction sequences revealed 63% (57/90) of these L1Hs insertions could be genotyped in 1000 Genomes Project sequences. Moreover, we observed that amplification biases encountered in single-cell WGS experiments led to a wide variation in L1Hs insertion detection rates between four individual NA12878 cells; under-amplification limited detection to 32% (65/203) of insertions, whereas over-amplification increased false positive calls. In sum, these data indicate that L1Hs insertions are often missed using standard short-read sequencing approaches and long-read sequencing approaches can significantly improve the detection of L1Hs insertions present in individual genomes.
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Affiliation(s)
- Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Diane A Flasch
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Kenneth Y Kwan
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA.,Molecular and Behavioral Neuroscience Institute, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Jeffrey M Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
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49
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Coyote-Maestas W, Nedrud D, Okorafor S, He Y, Schmidt D. Targeted insertional mutagenesis libraries for deep domain insertion profiling. Nucleic Acids Res 2020; 48:e11. [PMID: 31745561 PMCID: PMC6954442 DOI: 10.1093/nar/gkz1110] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/22/2019] [Accepted: 11/08/2019] [Indexed: 11/21/2022] Open
Abstract
Domain recombination is a key principle in protein evolution and protein engineering, but inserting a donor domain into every position of a target protein is not easily experimentally accessible. Most contemporary domain insertion profiling approaches rely on DNA transposons, which are constrained by sequence bias. Here, we establish Saturated Programmable Insertion Engineering (SPINE), an unbiased, comprehensive, and targeted domain insertion library generation technique using oligo library synthesis and multi-step Golden Gate cloning. Through benchmarking to MuA transposon-mediated library generation on four ion channel genes, we demonstrate that SPINE-generated libraries are enriched for in-frame insertions, have drastically reduced sequence bias as well as near-complete and highly-redundant coverage. Unlike transposon-mediated domain insertion that was severely biased and sparse for some genes, SPINE generated high-quality libraries for all genes tested. Using the Inward Rectifier K+ channel Kir2.1, we validate the practical utility of SPINE by constructing and comparing domain insertion permissibility maps. SPINE is the first technology to enable saturated domain insertion profiling. SPINE could help explore the relationship between domain insertions and protein function, and how this relationship is shaped by evolutionary forces and can be engineered for biomedical applications.
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Affiliation(s)
- Willow Coyote-Maestas
- Dept. of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Nedrud
- Dept. of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Steffan Okorafor
- Dept. of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yungui He
- Dept. of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel Schmidt
- Dept. of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
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50
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Donahue PS, Draut JW, Muldoon JJ, Edelstein HI, Bagheri N, Leonard JN. The COMET toolkit for composing customizable genetic programs in mammalian cells. Nat Commun 2020; 11:779. [PMID: 32034124 PMCID: PMC7005830 DOI: 10.1038/s41467-019-14147-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022] Open
Abstract
Engineering mammalian cells to carry out sophisticated and customizable genetic programs requires a toolkit of multiple orthogonal and well-characterized transcription factors (TFs). To address this need, we develop the COmposable Mammalian Elements of Transcription (COMET)-an ensemble of TFs and promoters that enable the design and tuning of gene expression to an extent not, to the best of our knowledge, previously possible. COMET currently comprises 44 activating and 12 inhibitory zinc-finger TFs and 83 cognate promoters, combined in a framework that readily accommodates new parts. This system can tune gene expression over three orders of magnitude, provides chemically inducible control of TF activity, and enables single-layer Boolean logic. We also develop a mathematical model that provides mechanistic insights into COMET performance characteristics. Altogether, COMET enables the design and construction of customizable genetic programs in mammalian cells.
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Affiliation(s)
- Patrick S Donahue
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Joseph W Draut
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Joseph J Muldoon
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
| | - Hailey I Edelstein
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, 60208, USA
- Biology and Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, 60208, USA.
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