1
|
Moreno-Campos R, Singleton EW, Uribe RA. A targeted CRISPR-Cas9 mediated F0 screen identifies genes involved in establishment of the enteric nervous system. PLoS One 2024; 19:e0303914. [PMID: 38809858 DOI: 10.1371/journal.pone.0303914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
The vertebrate enteric nervous system (ENS) is a crucial network of enteric neurons and glia resident within the entire gastrointestinal tract (GI). Overseeing essential GI functions such as gut motility and water balance, the ENS serves as a pivotal bidirectional link in the gut-brain axis. During early development, the ENS is primarily derived from enteric neural crest cells (ENCCs). Disruptions to ENCC development, as seen in conditions like Hirschsprung disease (HSCR), lead to the absence of ENS in the GI, particularly in the colon. In this study, using zebrafish, we devised an in vivo F0 CRISPR-based screen employing a robust, rapid pipeline integrating single-cell RNA sequencing, CRISPR reverse genetics, and high-content imaging. Our findings unveil various genes, including those encoding opioid receptors, as possible regulators of ENS establishment. In addition, we present evidence that suggests opioid receptor involvement in the neurochemical coding of the larval ENS. In summary, our work presents a novel, efficient CRISPR screen targeting ENS development, facilitating the discovery of previously unknown genes, and increasing knowledge of nervous system construction.
Collapse
Affiliation(s)
- Rodrigo Moreno-Campos
- Biosciences Department, Rice University, Houston, Texas, United States of America
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, Texas, United States of America
| | - Eileen W Singleton
- Biosciences Department, Rice University, Houston, Texas, United States of America
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, Texas, United States of America
| | - Rosa A Uribe
- Biosciences Department, Rice University, Houston, Texas, United States of America
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, Texas, United States of America
| |
Collapse
|
2
|
Pacesa M, Pelea O, Jinek M. Past, present, and future of CRISPR genome editing technologies. Cell 2024; 187:1076-1100. [PMID: 38428389 DOI: 10.1016/j.cell.2024.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes and treat the underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency and easy programmability, stand at the forefront of this revolution. In this Review, we discuss the current state of CRISPR gene editing technologies in both research and therapy, highlighting limitations that constrain them and the technological innovations that have been developed in recent years to address them. Additionally, we examine and summarize the current landscape of gene editing applications in the context of human health and therapeutics. Finally, we outline potential future developments that could shape gene editing technologies and their applications in the coming years.
Collapse
Affiliation(s)
- Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Station 19, CH-1015 Lausanne, Switzerland
| | - Oana Pelea
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| |
Collapse
|
3
|
Brooks A, Zhang Y, Chen J, Zhao CX. Cancer Metastasis-on-a-Chip for Modeling Metastatic Cascade and Drug Screening. Adv Healthc Mater 2024:e2302436. [PMID: 38224141 DOI: 10.1002/adhm.202302436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 01/06/2024] [Indexed: 01/16/2024]
Abstract
Microfluidic chips are valuable tools for studying intricate cellular and cell-microenvironment interactions. Traditional in vitro cancer models lack accuracy in mimicking the complexities of in vivo tumor microenvironment. However, cancer-metastasis-on-a-chip (CMoC) models combine the advantages of 3D cultures and microfluidic technology, serving as powerful platforms for exploring cancer mechanisms and facilitating drug screening. These chips are able to compartmentalize the metastatic cascade, deepening the understanding of its underlying mechanisms. This article provides an overview of current CMoC models, focusing on distinctive models that simulate invasion, intravasation, circulation, extravasation, and colonization, and their applications in drug screening. Furthermore, challenges faced by CMoC and microfluidic technologies are discussed, while exploring promising future directions in cancer research. The ongoing development and integration of these models into cancer studies are expected to drive transformative advancements in the field.
Collapse
Affiliation(s)
- Anastasia Brooks
- School of Chemical Engineering, University of Adelaide, Adelaide, 5005, Australia
| | - Yali Zhang
- School of Chemical Engineering, University of Adelaide, Adelaide, 5005, Australia
| | - Jiezhong Chen
- School of Chemical Engineering, University of Adelaide, Adelaide, 5005, Australia
| | - Chun-Xia Zhao
- School of Chemical Engineering, University of Adelaide, Adelaide, 5005, Australia
| |
Collapse
|
4
|
Parvez S, Zhang T, Peterson RT. Scalable CRISPR Screens in Zebrafish Using MIC-Drop. Methods Mol Biol 2024; 2707:319-334. [PMID: 37668922 DOI: 10.1007/978-1-0716-3401-1_21] [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: 09/06/2023]
Abstract
CRISPR-Cas9 is a powerful tool to interrogate gene function in a targeted and systematic manner. Although the technology has been scaled up for large-scale genetic screens in cell culture, similar scale screens in vivo have been extremely challenging due to the cost, labor, and time required to generate and keep track of thousands of mutant animals. We reported the development of Multiplexed Intermixed CRISPR Droplets (MIC-Drop), a platform that makes large-scale reverse genetic screens possible in zebrafish. In this chapter, we provide a detailed protocol to conduct large-scale genetic screens using this novel platform.
Collapse
Affiliation(s)
- Saba Parvez
- Department of Pharmacology & Toxicology, University of Utah, Salt Lake City, UT, USA
| | - Tejia Zhang
- Department of Pharmacology & Toxicology, University of Utah, Salt Lake City, UT, USA
| | - Randall T Peterson
- Department of Pharmacology & Toxicology, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
5
|
Moreno-Campos R, Singleton EW, Uribe RA. A targeted CRISPR-Cas9 mediated F0 screen identifies genes involved in establishment of the enteric nervous system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.28.573581. [PMID: 38234831 PMCID: PMC10793464 DOI: 10.1101/2023.12.28.573581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The vertebrate enteric nervous system (ENS) is a crucial network of enteric neurons and glia resident within the entire gastrointestinal tract (GI). Overseeing essential GI functions such as gut motility and water balance, the ENS serves as a pivotal bidirectional link in the gut-brain axis. During early development, the ENS is primarily derived from enteric neural crest cells (ENCCs). Disruptions to ENCC development, as seen in conditions like Hirschsprung disease (HSCR), lead to absence of ENS in the GI, particularly in the colon. In this study, using zebrafish, we devised an in vivo F0 CRISPR-based screen employing a robust, rapid pipeline integrating single-cell RNA sequencing, CRISPR reverse genetics, and high-content imaging. Our findings unveil various genes, including those encoding for opioid receptors, as possible regulators of ENS establishment. In addition, we present evidence that suggests opioid receptor involvement in neurochemical coding of the larval ENS. In summary, our work presents a novel, efficient CRISPR screen targeting ENS development, facilitating the discovery of previously unknown genes, and increasing knowledge of nervous system construction.
Collapse
Affiliation(s)
- Rodrigo Moreno-Campos
- Biosciences Department, Rice University, Houston, Texas, 77005, U.S.A
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, Texas, 77005, U.S.A
| | - Eileen W. Singleton
- Biosciences Department, Rice University, Houston, Texas, 77005, U.S.A
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, Texas, 77005, U.S.A
| | - Rosa A. Uribe
- Biosciences Department, Rice University, Houston, Texas, 77005, U.S.A
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, Texas, 77005, U.S.A
| |
Collapse
|
6
|
Sur A, Wang Y, Capar P, Margolin G, Prochaska MK, Farrell JA. Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development. Dev Cell 2023; 58:3028-3047.e12. [PMID: 37995681 DOI: 10.1016/j.devcel.2023.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/24/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
During development, animals generate distinct cell populations with specific identities, functions, and morphologies. We mapped transcriptionally distinct populations across 489,686 cells from 62 stages during wild-type zebrafish embryogenesis and early larval development (3-120 h post-fertilization). Using these data, we identified the limited catalog of gene expression programs reused across multiple tissues and their cell-type-specific adaptations. We also determined the duration each transcriptional state is present during development and identify unexpected long-term cycling populations. Focused clustering and transcriptional trajectory analyses of non-skeletal muscle and endoderm identified transcriptional profiles and candidate transcriptional regulators of understudied cell types and subpopulations, including the pneumatic duct, individual intestinal smooth muscle layers, spatially distinct pericyte subpopulations, and recently discovered best4+ cells. To enable additional discoveries, we make this comprehensive transcriptional atlas of early zebrafish development available through our website, Daniocell.
Collapse
Affiliation(s)
- Abhinav Sur
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Yiqun Wang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Paulina Capar
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Gennady Margolin
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Morgan Kathleen Prochaska
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Jeffrey A Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA.
| |
Collapse
|
7
|
Lillesaar C, Norton W, Liedtke D, Tsuda S. Understanding disorders of the human nervous system: How fish models reveal disease mechanisms from single molecules to behavior (part 1). Dev Growth Differ 2023; 65:432-433. [PMID: 37881022 DOI: 10.1111/dgd.12894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2023] [Indexed: 10/27/2023]
Affiliation(s)
- Christina Lillesaar
- Department of Child and Adolescent Psychiatry, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany
| | - William Norton
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Daniel Liedtke
- Department of Human Genetics, Würzburg University, Würzburg, Germany
| | - Sachiko Tsuda
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| |
Collapse
|
8
|
Raza MH, Desai S, Aravamudhan S, Zadegan R. An outlook on the current challenges and opportunities in DNA data storage. Biotechnol Adv 2023; 66:108155. [PMID: 37068530 PMCID: PMC11060094 DOI: 10.1016/j.biotechadv.2023.108155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/23/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023]
Abstract
Silicon is the gold standard for information storage systems. The exponential generation of digital information will exhaust the global supply of refined silicon. Therefore, investing in alternative information storage materials such as DNA has gained momentum. DNA as a memory material possesses several advantages over silicon-based data storage, including higher storage capacity, data retention, and lower operational energy. Routine DNA data storage approaches encode data into chemically synthesized nucleotide sequences. The scalability of DNA data storage depends on factors such as the cost and the generation of hazardous waste during DNA synthesis, latency of writing and reading, and limited rewriting capacity. Here, we review the current status of DNA data storage encoding, writing, storing, retrieving and reading, and discuss the technology's challenges and opportunities.
Collapse
Affiliation(s)
- Muhammad Hassan Raza
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, Greensboro, NC 27401, USA
| | - Salil Desai
- Department of Industrial & Systems Engineering, North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA; Center of Excellence in Product Design and Advanced Manufacturing (CEPDAM), North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, Greensboro, NC 27401, USA; Center of Excellence in Product Design and Advanced Manufacturing (CEPDAM), North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, Greensboro, NC 27401, USA; Center of Excellence in Product Design and Advanced Manufacturing (CEPDAM), North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA.
| |
Collapse
|
9
|
Gable SM, Mendez JM, Bushroe NA, Wilson A, Byars MI, Tollis M. The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order. Genes (Basel) 2023; 14:1387. [PMID: 37510292 PMCID: PMC10379679 DOI: 10.3390/genes14071387] [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: 06/06/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade.
Collapse
Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jasmine M Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Nicholas A Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Michael I Byars
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| |
Collapse
|
10
|
Zhu Y, Auer F, Gelnaw H, Davis SN, Hamling KR, May CE, Ahamed H, Ringstad N, Nagel KI, Schoppik D. SAMPL is a high-throughput solution to study unconstrained vertical behavior in small animals. Cell Rep 2023; 42:112573. [PMID: 37267107 PMCID: PMC10592459 DOI: 10.1016/j.celrep.2023.112573] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/27/2023] [Accepted: 05/11/2023] [Indexed: 06/04/2023] Open
Abstract
Balance and movement are impaired in many neurological disorders. Recent advances in behavioral monitoring provide unprecedented access to posture and locomotor kinematics but without the throughput and scalability necessary to screen candidate genes/potential therapeutics. Here, we present a scalable apparatus to measure posture and locomotion (SAMPL). SAMPL includes extensible hardware and open-source software with real-time processing and can acquire data from D. melanogaster, C. elegans, and D. rerio as they move vertically. Using SAMPL, we define how zebrafish balance as they navigate vertically and discover small but systematic variations among kinematic parameters between genetic backgrounds. We demonstrate SAMPL's ability to resolve differences in posture and navigation as a function of effect size and data gathered, providing key data for screens. SAMPL is therefore both a tool to model balance and locomotor disorders and an exemplar of how to scale apparatus to support screens.
Collapse
Affiliation(s)
- Yunlu Zhu
- Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Franziska Auer
- Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Hannah Gelnaw
- Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Samantha N Davis
- Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kyla R Hamling
- Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Christina E May
- The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Hassan Ahamed
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Niels Ringstad
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Katherine I Nagel
- The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - David Schoppik
- Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
11
|
Parvez S, Brandt ZJ, Peterson RT. Large-scale F0 CRISPR screens in vivo using MIC-Drop. Nat Protoc 2023; 18:1841-1865. [PMID: 37069311 PMCID: PMC10419324 DOI: 10.1038/s41596-023-00821-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/26/2023] [Indexed: 04/19/2023]
Abstract
The zebrafish is a powerful model system for studying animal development, for modeling genetic diseases, and for large-scale in vivo functional genetics. Because of its ease of use and its high efficiency in targeted gene perturbation, CRISPR-Cas9 has recently gained prominence as the tool of choice for genetic manipulation in zebrafish. However, scaling up the technique for high-throughput in vivo functional genetics has been a challenge. We recently developed a method, Multiplexed Intermixed CRISPR Droplets (MIC-Drop), that makes large-scale CRISPR screening in zebrafish possible. Here, we outline the step-by-step protocol for performing functional genetic screens in zebrafish by using MIC-Drop. MIC-Drop uses multiplexed single-guide RNAs to generate biallelic mutations in injected zebrafish embryos, allowing genetic screens to be performed in F0 animals. Combining microfluidics and DNA barcoding enables simultaneous targeting of tens to hundreds of genes from a single injection needle, while also enabling retrospective and rapid identification of the genotype responsible for an observed phenotype. The primary target audiences for MIC-Drop are developmental biologists, zebrafish geneticists, and researchers interested in performing in vivo functional genetic screens in a vertebrate model system. MIC-Drop will also prove useful in the hands of chemical biologists seeking to identify targets of small molecules that cause phenotypic changes in zebrafish. By using MIC-Drop, a typical screen of 100 genes can be conducted within 2-3 weeks by a single user.
Collapse
Affiliation(s)
- Saba Parvez
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Zachary J Brandt
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Randall T Peterson
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
12
|
Rutkove SB, Callegari S, Concepcion H, Mourey T, Widrick J, Nagy JA, Nath AK. Electrical impedance myography detects age-related skeletal muscle atrophy in adult zebrafish. Sci Rep 2023; 13:7191. [PMID: 37137956 PMCID: PMC10156759 DOI: 10.1038/s41598-023-34119-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/25/2023] [Indexed: 05/05/2023] Open
Abstract
Age-related deficits in skeletal muscle function, termed sarcopenia, are due to loss of muscle mass and changes in the intrinsic mechanisms underlying contraction. Sarcopenia is associated with falls, functional decline, and mortality. Electrical impedance myography (EIM)-a minimally invasive, rapid electrophysiological tool-can be applied to animals and humans to monitor muscle health, thereby serving as a biomarker in both preclinical and clinical studies. EIM has been successfully employed in several species; however, the application of EIM to the assessment of zebrafish-a model organism amenable to high-throughput experimentation-has not been reported. Here, we demonstrated differences in EIM measures between the skeletal muscles of young (6 months of age) and aged (33 months of age) zebrafish. For example, EIM phase angle and reactance at 2 kHz showed significantly decreased phase angle (5.3 ± 2.1 versus 10.7 ± 1.5°; p = 0.001) and reactance (89.0 ± 3.9 versus 172.2 ± 54.8 ohms; p = 0.007) in aged versus young animals. Total muscle area, in addition to other morphometric features, was also strongly correlated to EIM 2 kHz phase angle across both groups (r = 0.7133, p = 0.01). Moreover, there was a strong correlation between 2 kHz phase angle and established metrics of zebrafish swimming performance, including turn angle, angular velocity, and lateral motion (r = 0.7253, r = 0.7308, r = 0.7857, respectively, p < 0.01 for all). In addition, the technique was shown to have high reproducibility between repeated measurements with a mean percentage difference of 5.34 ± 1.17% for phase angle. These relationships were also confirmed in a separate replication cohort. Together, these findings establish EIM as a fast, sensitive method for quantifying zebrafish muscle function and quality. Moreover, identifying the abnormalities in the bioelectrical properties of sarcopenic zebrafish provides new opportunities to evaluate potential therapeutics for age-related neuromuscular disorders and to interrogate the disease mechanisms of muscle degeneration.
Collapse
Affiliation(s)
- Seward B Rutkove
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA.
- Harvard Medical School, Boston, MA, 02215, USA.
| | - Santiago Callegari
- Department of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Holly Concepcion
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Tyler Mourey
- Zebrafish Core Facility, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Jeffrey Widrick
- Harvard Medical School, Boston, MA, 02215, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Janice A Nagy
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Anjali K Nath
- Harvard Medical School, Boston, MA, 02215, USA.
- Department of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA.
- Broad Institute, Cambridge, MA, 02142, USA.
| |
Collapse
|
13
|
Sur A, Wang Y, Capar P, Margolin G, Farrell JA. Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533545. [PMID: 36993555 PMCID: PMC10055256 DOI: 10.1101/2023.03.20.533545] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
During development, animals generate distinct cell populations with specific identities, functions, and morphologies. We mapped transcriptionally distinct populations across 489,686 cells from 62 stages during wild-type zebrafish embryogenesis and early larval development (3-120 hours post-fertilization). Using these data, we identified the limited catalog of gene expression programs reused across multiple tissues and their cell-type-specific adaptations. We also determined the duration each transcriptional state is present during development and suggest new long-term cycling populations. Focused analyses of non-skeletal muscle and the endoderm identified transcriptional profiles of understudied cell types and subpopulations, including the pneumatic duct, individual intestinal smooth muscle layers, spatially distinct pericyte subpopulations, and homologs of recently discovered human best4+ enterocytes. The transcriptional regulators of these populations remain unknown, so we reconstructed gene expression trajectories to suggest candidates. To enable additional discoveries, we make this comprehensive transcriptional atlas of early zebrafish development available through our website, Daniocell.
Collapse
Affiliation(s)
- Abhinav Sur
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814
| | - Yiqun Wang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Paulina Capar
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814
| | - Gennady Margolin
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland 20814
| | - Jeffrey A. Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814
| |
Collapse
|
14
|
Shan H, Fei T. CRISPR screening in cardiovascular research. Front Cell Dev Biol 2023; 11:1175849. [PMID: 37123412 PMCID: PMC10130668 DOI: 10.3389/fcell.2023.1175849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Abstract
The recent advent and widespread application of CRISPR-based genome editing tools have revolutionized biomedical research and beyond. Taking advantage of high perturbation efficiency and scalability, CRISPR screening has been regarded as one of the most powerful technologies in functional genomics which allows investigation of different genetic subjects at a large scale in parallel. Significant progress has been made using various CRISPR screening tools especially in cancer research, however, fewer attempts and less success are reported in other contexts. In this mini-review, we discuss how CRISPR screening has been implemented in studies on cardiovascular research and related metabolic disorders, highlight the scientific progress utilizing CRISPR screening, and further envision how to fully unleash the power of this technique to expedite scientific discoveries in these fields.
Collapse
Affiliation(s)
- Haihuan Shan
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang, China
- Key Laboratory of Data Analytics and Optimization for Smart Industry (Northeastern University), Ministry of Education, Shenyang, China
| | - Teng Fei
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang, China
- Key Laboratory of Data Analytics and Optimization for Smart Industry (Northeastern University), Ministry of Education, Shenyang, China
| |
Collapse
|
15
|
Zhu Y, Auer F, Gelnaw H, Davis SN, Hamling KR, May CE, Ahamed H, Ringstad N, Nagel KI, Schoppik D. Scalable Apparatus to Measure Posture and Locomotion (SAMPL): a high-throughput solution to study unconstrained vertical behavior in small animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.07.523102. [PMID: 36712122 PMCID: PMC9881893 DOI: 10.1101/2023.01.07.523102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Balance and movement are impaired in a wide variety of neurological disorders. Recent advances in behavioral monitoring provide unprecedented access to posture and locomotor kinematics, but without the throughput and scalability necessary to screen candidate genes / potential therapeutics. We present a powerful solution: a Scalable Apparatus to Measure Posture and Locomotion (SAMPL). SAMPL includes extensible imaging hardware and low-cost open-source acquisition software with real-time processing. We first demonstrate that SAMPL's hardware and acquisition software can acquire data from from D. melanogaster, C. elegans, and D. rerio as they move vertically. Next, we leverage SAMPL's throughput to rapidly (two weeks) gather a new zebrafish dataset. We use SAMPL's analysis and visualization tools to replicate and extend our current understanding of how zebrafish balance as they navigate through a vertical environment. Next, we discover (1) that key kinematic parameters vary systematically with genetic background, and (2) that such background variation is small relative to the changes that accompany early development. Finally, we simulate SAMPL's ability to resolve differences in posture or vertical navigation as a function of affect size and data gathered -- key data for screens. Taken together, our apparatus, data, and analysis provide a powerful solution for labs using small animals to investigate balance and locomotor disorders at scale. More broadly, SAMPL is both an adaptable resource for labs looking process videographic measures of behavior in real-time, and an exemplar of how to scale hardware to enable the throughput necessary for screening.
Collapse
Affiliation(s)
- Yunlu Zhu
- Department. of Otolaryngology, New York University Grossman School of Medicine
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - Franziska Auer
- Department. of Otolaryngology, New York University Grossman School of Medicine
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - Hannah Gelnaw
- Department. of Otolaryngology, New York University Grossman School of Medicine
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - Samantha N. Davis
- Department. of Otolaryngology, New York University Grossman School of Medicine
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - Kyla R. Hamling
- Department. of Otolaryngology, New York University Grossman School of Medicine
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - Christina E. May
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - Hassan Ahamed
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine
| | - Niels Ringstad
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine
| | - Katherine I. Nagel
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - David Schoppik
- Department. of Otolaryngology, New York University Grossman School of Medicine
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
- Lead Contact
| |
Collapse
|
16
|
Using Zebrafish Animal Model to Study the Genetic Underpinning and Mechanism of Arrhythmogenic Cardiomyopathy. Int J Mol Sci 2023; 24:ijms24044106. [PMID: 36835518 PMCID: PMC9966228 DOI: 10.3390/ijms24044106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Arrhythmogenic cardiomyopathy (ACM) is largely an autosomal dominant genetic disorder manifesting fibrofatty infiltration and ventricular arrhythmia with predominantly right ventricular involvement. ACM is one of the major conditions associated with an increased risk of sudden cardiac death, most notably in young individuals and athletes. ACM has strong genetic determinants, and genetic variants in more than 25 genes have been identified to be associated with ACM, accounting for approximately 60% of ACM cases. Genetic studies of ACM in vertebrate animal models such as zebrafish (Danio rerio), which are highly amenable to large-scale genetic and drug screenings, offer unique opportunities to identify and functionally assess new genetic variants associated with ACM and to dissect the underlying molecular and cellular mechanisms at the whole-organism level. Here, we summarize key genes implicated in ACM. We discuss the use of zebrafish models, categorized according to gene manipulation approaches, such as gene knockdown, gene knock-out, transgenic overexpression, and CRISPR/Cas9-mediated knock-in, to study the genetic underpinning and mechanism of ACM. Information gained from genetic and pharmacogenomic studies in such animal models can not only increase our understanding of the pathophysiology of disease progression, but also guide disease diagnosis, prognosis, and the development of innovative therapeutic strategies.
Collapse
|
17
|
Cheng J, Lin G, Wang T, Wang Y, Guo W, Liao J, Yang P, Chen J, Shao X, Lu X, Zhu L, Wang Y, Fan X. Massively Parallel CRISPR-Based Genetic Perturbation Screening at Single-Cell Resolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204484. [PMID: 36504444 PMCID: PMC9896079 DOI: 10.1002/advs.202204484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/09/2022] [Indexed: 06/17/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-based genetic screening has been demonstrated as a powerful approach for unbiased functional genomics research. Single-cell CRISPR screening (scCRISPR) techniques, which result from the combination of single-cell toolkits and CRISPR screening, allow dissecting regulatory networks in complex biological systems at unprecedented resolution. These methods allow cells to be perturbed en masse using a pooled CRISPR library, followed by high-content phenotyping. This is technically accomplished by annotating cells with sgRNA-specific barcodes or directly detectable sgRNAs. According to the integration of distinct single-cell technologies, these methods principally fall into four categories: scCRISPR with RNA-seq, scCRISPR with ATAC-seq, scCRISPR with proteome probing, and imaging-based scCRISPR. scCRISPR has deciphered genotype-phenotype relationships, genetic regulations, tumor biological issues, and neuropathological mechanisms. This review provides insight into the technical breakthrough of scCRISPR by systematically summarizing the advancements of various scCRISPR methodologies and analyzing their merits and limitations. In addition, an application-oriented approach guide is offered to meet researchers' individualized demands.
Collapse
Affiliation(s)
- Junyun Cheng
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Gaole Lin
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Tianhao Wang
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Yunzhu Wang
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Wenbo Guo
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Jie Liao
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Penghui Yang
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Jie Chen
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Xin Shao
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Xiaoyan Lu
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
- State Key Laboratory of Component‐Based Chinese MedicineInnovation Center in Zhejiang UniversityHangzhou310058China
- Jinhua Institute of Zhejiang UniversityJinhua321016China
| | - Ling Zhu
- The Save Sight InstituteFaculty of Medicine and Healththe University of SydneySydneyNSW2000Australia
| | - Yi Wang
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
- State Key Laboratory of Component‐Based Chinese MedicineInnovation Center in Zhejiang UniversityHangzhou310058China
- Future Health LaboratoryInnovation Center of Yangtze River DeltaZhejiang UniversityJiaxing314100China
| | - Xiaohui Fan
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
- State Key Laboratory of Component‐Based Chinese MedicineInnovation Center in Zhejiang UniversityHangzhou310058China
- Jinhua Institute of Zhejiang UniversityJinhua321016China
- The Save Sight InstituteFaculty of Medicine and Healththe University of SydneySydneyNSW2000Australia
- Future Health LaboratoryInnovation Center of Yangtze River DeltaZhejiang UniversityJiaxing314100China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
| |
Collapse
|
18
|
Richardson C, Kelsh RN, J. Richardson R. New advances in CRISPR/Cas-mediated precise gene-editing techniques. Dis Model Mech 2023; 16:dmm049874. [PMID: 36847161 PMCID: PMC10003097 DOI: 10.1242/dmm.049874] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Over the past decade, CRISPR/Cas-based gene editing has become a powerful tool for generating mutations in a variety of model organisms, from Escherichia coli to zebrafish, rodents and large mammals. CRISPR/Cas-based gene editing effectively generates insertions or deletions (indels), which allow for rapid gene disruption. However, a large proportion of human genetic diseases are caused by single-base-pair substitutions, which result in more subtle alterations to protein function, and which require more complex and precise editing to recreate in model systems. Precise genome editing (PGE) methods, however, typically have efficiencies of less than a tenth of those that generate less-specific indels, and so there has been a great deal of effort to improve PGE efficiency. Such optimisations include optimal guide RNA and mutation-bearing donor DNA template design, modulation of DNA repair pathways that underpin how edits result from Cas-induced cuts, and the development of Cas9 fusion proteins that introduce edits via alternative mechanisms. In this Review, we provide an overview of the recent progress in optimising PGE methods and their potential for generating models of human genetic disease.
Collapse
Affiliation(s)
- Chris Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Robert N. Kelsh
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Rebecca J. Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
| |
Collapse
|
19
|
Henke K, Farmer DT, Niu X, Kraus JM, Galloway JL, Youngstrom DW. Genetically engineered zebrafish as models of skeletal development and regeneration. Bone 2023; 167:116611. [PMID: 36395960 PMCID: PMC11080330 DOI: 10.1016/j.bone.2022.116611] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
Zebrafish (Danio rerio) are aquatic vertebrates with significant homology to their terrestrial counterparts. While zebrafish have a centuries-long track record in developmental and regenerative biology, their utility has grown exponentially with the onset of modern genetics. This is exemplified in studies focused on skeletal development and repair. Herein, the numerous contributions of zebrafish to our understanding of the basic science of cartilage, bone, tendon/ligament, and other skeletal tissues are described, with a particular focus on applications to development and regeneration. We summarize the genetic strengths that have made the zebrafish a powerful model to understand skeletal biology. We also highlight the large body of existing tools and techniques available to understand skeletal development and repair in the zebrafish and introduce emerging methods that will aid in novel discoveries in skeletal biology. Finally, we review the unique contributions of zebrafish to our understanding of regeneration and highlight diverse routes of repair in different contexts of injury. We conclude that zebrafish will continue to fill a niche of increasing breadth and depth in the study of basic cellular mechanisms of skeletal biology.
Collapse
Affiliation(s)
- Katrin Henke
- Department of Orthopaedics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - D'Juan T Farmer
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA.
| | - Xubo Niu
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Jessica M Kraus
- Department of Orthopaedic Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA.
| | - Jenna L Galloway
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel W Youngstrom
- Department of Orthopaedic Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA.
| |
Collapse
|
20
|
MacRae CA, Peterson RT. Zebrafish as a Mainstream Model for In Vivo Systems Pharmacology and Toxicology. Annu Rev Pharmacol Toxicol 2023; 63:43-64. [PMID: 36151053 DOI: 10.1146/annurev-pharmtox-051421-105617] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Pharmacology and toxicology are part of a much broader effort to understand the relationship between chemistry and biology. While biomedicine has necessarily focused on specific cases, typically of direct human relevance, there are real advantages in pursuing more systematic approaches to characterizing how health and disease are influenced by small molecules and other interventions. In this context, the zebrafish is now established as the representative screenable vertebrate and, through ongoing advances in the available scale of genome editing and automated phenotyping, is beginning to address systems-level solutions to some biomedical problems. The addition of broader efforts to integrate information content across preclinical model organisms and the incorporation of rigorous analytics, including closed-loop deep learning, will facilitate efforts to create systems pharmacology and toxicology with the ability to continuously optimize chemical biological interactions around societal needs. In this review, we outline progress toward this goal.
Collapse
Affiliation(s)
- Calum A MacRae
- Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA;
| | | |
Collapse
|
21
|
Djannatian M, Radha S, Weikert U, Safaiyan S, Wrede C, Deichsel C, Kislinger G, Rhomberg A, Ruhwedel T, Campbell DS, van Ham T, Schmid B, Hegermann J, Möbius W, Schifferer M, Simons M. Myelination generates aberrant ultrastructure that is resolved by microglia. J Biophys Biochem Cytol 2023; 222:213804. [PMID: 36637807 PMCID: PMC9856851 DOI: 10.1083/jcb.202204010] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 10/18/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023] Open
Abstract
To enable rapid propagation of action potentials, axons are ensheathed by myelin, a multilayered insulating membrane formed by oligodendrocytes. Most of the myelin is generated early in development, resulting in the generation of long-lasting stable membrane structures. Here, we explored structural and dynamic changes in central nervous system myelin during development. To achieve this, we performed an ultrastructural analysis of mouse optic nerves by serial block face scanning electron microscopy (SBF-SEM) and confocal time-lapse imaging in the zebrafish spinal cord. We found that myelin undergoes extensive ultrastructural changes during early postnatal development. Myelin degeneration profiles were engulfed and phagocytosed by microglia using exposed phosphatidylserine as one "eat me" signal. In contrast, retractions of entire myelin sheaths occurred independently of microglia and involved uptake of myelin by the oligodendrocyte itself. Our findings show that the generation of myelin early in development is an inaccurate process associated with aberrant ultrastructural features that require substantial refinement.
Collapse
Affiliation(s)
- Minou Djannatian
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany,https://ror.org/043j0f473German Center for Neurodegenerative Diseases, Munich, Germany,Department of Neurology, Klinikum rechts der Isar, TUM School of Medicine, Technical University of Munich, Munich, Germany,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany,Minou Djannatian:
| | - Swathi Radha
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany,https://ror.org/043j0f473German Center for Neurodegenerative Diseases, Munich, Germany
| | - Ulrich Weikert
- Max-Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Shima Safaiyan
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany,https://ror.org/043j0f473German Center for Neurodegenerative Diseases, Munich, Germany
| | - Christoph Wrede
- https://ror.org/00f2yqf98Institute of Functional and Applied Anatomy, Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, Germany
| | - Cassandra Deichsel
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany,https://ror.org/043j0f473German Center for Neurodegenerative Diseases, Munich, Germany
| | - Georg Kislinger
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany,https://ror.org/043j0f473German Center for Neurodegenerative Diseases, Munich, Germany
| | - Agata Rhomberg
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany,https://ror.org/043j0f473German Center for Neurodegenerative Diseases, Munich, Germany
| | - Torben Ruhwedel
- Max-Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Douglas S. Campbell
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany,https://ror.org/043j0f473German Center for Neurodegenerative Diseases, Munich, Germany
| | - Tjakko van Ham
- https://ror.org/018906e22Department of Clinical Genetics, Erasmus University Medical Center, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Bettina Schmid
- https://ror.org/043j0f473German Center for Neurodegenerative Diseases, Munich, Germany
| | - Jan Hegermann
- https://ror.org/00f2yqf98Institute of Functional and Applied Anatomy, Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, Germany
| | - Wiebke Möbius
- Max-Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Martina Schifferer
- https://ror.org/043j0f473German Center for Neurodegenerative Diseases, Munich, Germany,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Mikael Simons
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany,https://ror.org/043j0f473German Center for Neurodegenerative Diseases, Munich, Germany,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany,Institute for Stroke and Dementia Research, University Hospital of Munich, Ludwig Maximilian University of Munich, Munich, Germany,Correspondence to Mikael Simons:
| |
Collapse
|
22
|
Wu J, Lin X, Wu D, Yan B, Bao M, Zheng P, Wang J, Yang C, Li Z, Jin X, Jiang K. Poly(I:C)-exposed zebrafish shows autism-like behaviors which are ameliorated by fabp2 gene knockout. Front Mol Neurosci 2023; 15:1068019. [PMID: 36683854 PMCID: PMC9849760 DOI: 10.3389/fnmol.2022.1068019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/12/2022] [Indexed: 01/07/2023] Open
Abstract
Introduction Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders mainly representing impaired social communication. The etiology of ASD includes genetic and environmental risk factors. Rodent models containing ASD risk gene mutations or environmental risk factors, such as exposure to maternal inflammation, show abnormal behavior. Although zebrafish conserves many important brain structures of humans and has sophisticated and fine behaviors in social interaction, it is unknown whether the social behaviors of their offspring would be impaired due to exposure to maternal inflammation. Methods We exposed zebrafish to maternal immune activation (MIA) by injection with polyinosinic:polycytidylic acid [poly(I:C)], and screened their behaviors through social behavioral tests such as social preference and shoaling behavior tests. We compared phenotypes resulted from different ways of poly(I:C) exposure. RNA sequencing was performed to explore the differential expression genes (DEGs). Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction (PPI) network analysis was performed with the detected DEGs to find the concentrated pathways. Finally, we knocked out the fatty acid-binding protein 2 (fabp2), a key node of the concentrated PPI network, to find its rescues on the altered social behavior. Results We reported here that MIA offspring born to mothers injected with poly(I:C) exhibited impaired social approach and social cohesion that mimicked human ASD phenotypes. Both maternal exposure and direct embryo exposure to poly(I:C) resulted in activations of the innate immune system through toll-like receptors 3 and 4. RNA-sequencing results from MIA brain tissues illustrated that the numbers of overexpressed genes were significantly more than that of underexpressed genes. GO and KEGG analyses found that MIA-induced DEGs were mainly concentrated in complement and coagulation cascade pathways. PPI network analyses suggested that villin-1 (vil1) pathway might play a key role in MIA-induced ASD. Knockout of fabp2 in F0 zebrafish rescued the social behavior deficits in MIA offspring. Conclusions Overall, our work established an ASD model with assessable behavior phenotype in zebrafish and provided key insights into environmental risk factor in ASD etiology and the influence of fabp2 gene on ASD-like behavior.
Collapse
Affiliation(s)
- Jing Wu
- Department of Child Psychology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Xueting Lin
- Department of Child Psychology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Dian Wu
- Department of Child Psychology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Binhong Yan
- Department of Biobank Center, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Mengyi Bao
- Department of Child Psychology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Peilei Zheng
- Department of Biobank Center, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Jiangping Wang
- Department of Child Psychology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Cuiwei Yang
- Department of Neurology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Zhongxia Li
- Department of Pediatrics, The Seventh Affiliated Hospital of Guangxi Medical University (Wuzhou GongRen Hospital), Wuzhou, Guangxi, China
| | - Xiaoming Jin
- Indiana Spinal Cord and Brain Injury Research Group, Stark Neurosciences Research Institute, Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, United States,Stark Neuroscience Research Institute, Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kewen Jiang
- Department of Child Psychology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China,Department of Biobank Center, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China,*Correspondence: Kewen Jiang,
| |
Collapse
|
23
|
Wu M, Xu J, Zhang Y, Wen Z. Learning from Zebrafish Hematopoiesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:137-157. [PMID: 38228963 DOI: 10.1007/978-981-99-7471-9_9] [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: 01/18/2024]
Abstract
Hematopoiesis is a complex process that tightly regulates the generation, proliferation, differentiation, and maintenance of hematopoietic cells. Disruptions in hematopoiesis can lead to various diseases affecting both hematopoietic and non-hematopoietic systems, such as leukemia, anemia, thrombocytopenia, rheumatoid arthritis, and chronic granuloma. The zebrafish serves as a powerful vertebrate model for studying hematopoiesis, offering valuable insights into both hematopoietic regulation and hematopoietic diseases. In this chapter, we present a comprehensive overview of zebrafish hematopoiesis, highlighting its distinctive characteristics in hematopoietic processes. We discuss the ontogeny and modulation of both primitive and definitive hematopoiesis, as well as the microenvironment that supports hematopoietic stem/progenitor cells. Additionally, we explore the utility of zebrafish as a disease model and its potential in drug discovery, which not only advances our understanding of the regulatory mechanisms underlying hematopoiesis but also facilitates the exploration of novel therapeutic strategies for hematopoietic diseases.
Collapse
Affiliation(s)
- Mei Wu
- Affiliated Hospital of Guangdong Medical University and Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Jin Xu
- South China University of Technology, School of Medicine, Guangzhou, Guangdong, China.
| | - Yiyue Zhang
- South China University of Technology, School of Medicine, Guangzhou, Guangdong, China.
| | - Zilong Wen
- Southern University of Science and Technology, School of Life Sciences, Shenzhen, Guangdong, China.
| |
Collapse
|
24
|
Xie Y, Li H, Chen F, Udayakumar S, Arora K, Chen H, Lan Y, Hu Q, Zhou X, Guo X, Xiu L, Yin K. Clustered Regularly Interspaced short palindromic repeats-Based Microfluidic System in Infectious Diseases Diagnosis: Current Status, Challenges, and Perspectives. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2204172. [PMID: 36257813 PMCID: PMC9731715 DOI: 10.1002/advs.202204172] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/16/2022] [Indexed: 06/02/2023]
Abstract
Mitigating the spread of global infectious diseases requires rapid and accurate diagnostic tools. Conventional diagnostic techniques for infectious diseases typically require sophisticated equipment and are time consuming. Emerging clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) detection systems have shown remarkable potential as next-generation diagnostic tools to achieve rapid, sensitive, specific, and field-deployable diagnoses of infectious diseases, based on state-of-the-art microfluidic platforms. Therefore, a review of recent advances in CRISPR-based microfluidic systems for infectious diseases diagnosis is urgently required. This review highlights the mechanisms of CRISPR/Cas biosensing and cutting-edge microfluidic devices including paper, digital, and integrated wearable platforms. Strategies to simplify sample pretreatment, improve diagnostic performance, and achieve integrated detection are discussed. Current challenges and future perspectives contributing to the development of more effective CRISPR-based microfluidic diagnostic systems are also proposed.
Collapse
Affiliation(s)
- Yi Xie
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Huimin Li
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Fumin Chen
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Srisruthi Udayakumar
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02139USA
| | - Khyati Arora
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02139USA
| | - Hui Chen
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02139USA
| | - Yang Lan
- Centre for Nature‐Inspired EngineeringDepartment of Chemical EngineeringUniversity College LondonLondonWC1E 7JEUK
| | - Qinqin Hu
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Xiaonong Zhou
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Xiaokui Guo
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Leshan Xiu
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Kun Yin
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| |
Collapse
|
25
|
McLean B, Istadi A, Clack T, Vankan M, Schramek D, Neely GG, Pajic M. A CRISPR Path to Finding Vulnerabilities and Solving Drug Resistance: Targeting the Diverse Cancer Landscape and Its Ecosystem. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2200014. [PMID: 36911295 PMCID: PMC9993475 DOI: 10.1002/ggn2.202200014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Cancer is the second leading cause of death globally, with therapeutic resistance being a major cause of treatment failure in the clinic. The dynamic signaling that occurs between tumor cells and the diverse cells of the surrounding tumor microenvironment actively promotes disease progression and therapeutic resistance. Improving the understanding of how tumors evolve following therapy and the molecular mechanisms underpinning de novo or acquired resistance is thus critical for the identification of new targets and for the subsequent development of more effective combination regimens. Simultaneously targeting multiple hallmark capabilities of cancer to circumvent adaptive or evasive resistance may lead to significantly improved treatment response in the clinic. Here, the latest applications of functional genomics tools, such as clustered regularly interspaced short palindromic repeats (CRISPR) editing, to characterize the dynamic cancer resistance mechanisms, from improving the understanding of resistance to classical chemotherapeutics, to deciphering unique mechanisms that regulate tumor responses to new targeted agents and immunotherapies, are discussed. Potential avenues of future research in combating therapeutic resistance, the contribution of tumor-stroma signaling in this setting, and how advanced functional genomics tools can help streamline the identification of key molecular determinants of drug response are explored.
Collapse
Affiliation(s)
- Benjamin McLean
- The Kinghorn Cancer Centre The Garvan Institute of Medical Research 384 Victoria St, Darlinghurst Sydney New South Wales 2010 Australia
| | - Aji Istadi
- The Kinghorn Cancer Centre The Garvan Institute of Medical Research 384 Victoria St, Darlinghurst Sydney New South Wales 2010 Australia
| | - Teleri Clack
- Dr. John and Anne Chong Lab for Functional Genomics Charles Perkins Centre Centenary Institute University of Sydney Camperdown New South Wales 2006 Australia
| | - Mezzalina Vankan
- Dr. John and Anne Chong Lab for Functional Genomics Charles Perkins Centre Centenary Institute University of Sydney Camperdown New South Wales 2006 Australia
| | - Daniel Schramek
- Centre for Molecular and Systems Biology Lunenfeld-Tanenbaum Research Institute Mount Sinai Hospital Toronto Ontario M5G 1X5 Canada.,Department of Molecular Genetics Faculty of Medicine University of Toronto Toronto Ontario M5S 1A8 Canada
| | - G Gregory Neely
- Dr. John and Anne Chong Lab for Functional Genomics Charles Perkins Centre Centenary Institute University of Sydney Camperdown New South Wales 2006 Australia
| | - Marina Pajic
- The Kinghorn Cancer Centre The Garvan Institute of Medical Research 384 Victoria St, Darlinghurst Sydney New South Wales 2010 Australia.,St Vincent's Clinical School Faculty of Medicine University of NSW Sydney Sydney New South Wales 2052 Australia
| |
Collapse
|
26
|
Hu Y, Ewen-Campen B, Comjean A, Rodiger J, Mohr SE, Perrimon N. Paralog Explorer: A resource for mining information about paralogs in common research organisms. Comput Struct Biotechnol J 2022; 20:6570-6577. [PMID: 36467589 PMCID: PMC9712503 DOI: 10.1016/j.csbj.2022.11.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Paralogs are genes which arose via gene duplication, and when such paralogs retain overlapping or redundant function, this poses a challenge to functional genetics research. Recent technological advancements have made it possible to systematically probe gene function for redundant genes using dual or multiplex gene perturbation, and there is a need for a simple bioinformatic tool to identify putative paralogs of a gene(s) of interest. We have developed Paralog Explorer (https://www.flyrnai.org/tools/paralogs/), an online resource that allows researchers to quickly and accurately identify candidate paralogous genes in the genomes of the model organisms D. melanogaster, C. elegans, D. rerio, M. musculus, and H. sapiens. Paralog Explorer deploys an effective between-species ortholog prediction software, DIOPT, to analyze within-species paralogs. Paralog Explorer allows users to identify candidate paralogs, and to navigate relevant databases regarding gene co-expression, protein-protein and genetic interaction, as well as gene ontology and phenotype annotations. Altogether, this tool extends the value of current ortholog prediction resources by providing sophisticated features useful for identification and study of paralogous genes.
Collapse
Affiliation(s)
- Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA,Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA,Corresponding authors at: Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
| | - Ben Ewen-Campen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA,Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jonathan Rodiger
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA,Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Stephanie E. Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA,Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA,Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA,Howard Hughes Medical Institute, Boston, MA 02138, USA,Corresponding authors at: Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
| |
Collapse
|
27
|
Kunisaki J, Quinlan A, Aston KI, Hotaling J. Integrating Precision Medicine into the Standard of Care for Male Infertility: What Will it Take? Eur Urol 2022; 82:339-340. [PMID: 35811191 PMCID: PMC10914127 DOI: 10.1016/j.eururo.2022.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 11/04/2022]
Affiliation(s)
- Jason Kunisaki
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Aaron Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA; Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | - Kenneth I Aston
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - James Hotaling
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA.
| |
Collapse
|
28
|
Alper SR, Dorsky RI. Unique advantages of zebrafish larvae as a model for spinal cord regeneration. Front Mol Neurosci 2022; 15:983336. [PMID: 36157068 PMCID: PMC9489991 DOI: 10.3389/fnmol.2022.983336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/18/2022] [Indexed: 11/30/2022] Open
Abstract
The regenerative capacity of the spinal cord in mammals ends at birth. In contrast, teleost fish and amphibians retain this capacity throughout life, leading to the use of the powerful zebrafish model system to identify novel mechanisms that promote spinal cord regeneration. While adult zebrafish offer an effective comparison with non-regenerating mammals, they lack the complete array of experimental approaches that have made this animal model so successful. In contrast, the optical transparency, simple anatomy and complex behavior of zebrafish larvae, combined with the known conservation of pro-regenerative signals and cell types between larval and adult stages, suggest that they may hold even more promise as a system for investigating spinal cord regeneration. In this review, we highlight characteristics and advantages of the larval model that underlie its potential to provide future therapeutic approaches for treating human spinal cord injury.
Collapse
|
29
|
Nishiga M, Liu C, Qi LS, Wu JC. The use of new CRISPR tools in cardiovascular research and medicine. Nat Rev Cardiol 2022; 19:505-521. [PMID: 35145236 PMCID: PMC10283450 DOI: 10.1038/s41569-021-00669-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 02/07/2023]
Abstract
Many novel CRISPR-based genome-editing tools, with a wide variety of applications, have been developed in the past few years. The original CRISPR-Cas9 system was developed as a tool to alter genomic sequences in living organisms in a simple way. However, the functions of new CRISPR tools are not limited to conventional genome editing mediated by non-homologous end-joining or homology-directed repair but expand into gene-expression control, epigenome editing, single-nucleotide editing, RNA editing and live-cell imaging. Furthermore, genetic perturbation screening by multiplexing guide RNAs is gaining popularity as a method to identify causative genes and pathways in an unbiased manner. New CRISPR tools can also be applied to ex vivo or in vivo therapeutic genome editing for the treatment of conditions such as hyperlipidaemia. In this Review, we first provide an overview of the diverse new CRISPR tools that have been developed to date. Second, we summarize how these new CRISPR tools are being used to study biological processes and disease mechanisms in cardiovascular research and medicine. Finally, we discuss the prospect of therapeutic genome editing by CRISPR tools to cure genetic cardiovascular diseases.
Collapse
Affiliation(s)
- Masataka Nishiga
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
| | - Chun Liu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
30
|
Abstract
Heart disease is the leading cause of death worldwide. Despite decades of research, most heart pathologies have limited treatments, and often the only curative approach is heart transplantation. Thus, there is an urgent need to develop new therapeutic approaches for treating cardiac diseases. Animal models that reproduce the human pathophysiology are essential to uncovering the biology of diseases and discovering therapies. Traditionally, mammals have been used as models of cardiac disease, but the cost of generating and maintaining new models is exorbitant, and the studies have very low throughput. In the last decade, the zebrafish has emerged as a tractable model for cardiac diseases, owing to several characteristics that made this animal popular among developmental biologists. Zebrafish fertilization and development are external; embryos can be obtained in high numbers, are cheap and easy to maintain, and can be manipulated to create new genetic models. Moreover, zebrafish exhibit an exceptional ability to regenerate their heart after injury. This review summarizes 25 years of research using the zebrafish to study the heart, from the classical forward screenings to the contemporary methods to model mutations found in patients with cardiac disease. We discuss the advantages and limitations of this model organism and introduce the experimental approaches exploited in zebrafish, including forward and reverse genetics and chemical screenings. Last, we review the models used to induce cardiac injury and essential ideas derived from studying natural regeneration. Studies using zebrafish have the potential to accelerate the discovery of new strategies to treat cardiac diseases.
Collapse
Affiliation(s)
- Juan Manuel González-Rosa
- Cardiovascular Research Center, Massachusetts General Hospital Research Institute, Harvard Medical School, Charlestown, MA
| |
Collapse
|
31
|
Siedlik MJ, Issadore D. Pico-washing: simultaneous liquid addition and removal for continuous-flow washing of microdroplets. MICROSYSTEMS & NANOENGINEERING 2022; 8:46. [PMID: 35498338 PMCID: PMC9050730 DOI: 10.1038/s41378-022-00381-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/02/2022] [Accepted: 03/07/2022] [Indexed: 05/19/2023]
Abstract
Droplet microfluidics is based on a toolbox of several established unit operations, including droplet generation, incubation, mixing, pico-injection, and sorting. In the last two decades, the development of droplet microfluidic systems, which incorporate these multiple unit operations into a workflow, has demonstrated unique capabilities in fields ranging from single-cell transcriptomic analyses to materials optimization. One unit operation that is sorely underdeveloped in droplet microfluidics is washing, exchange of the fluid in a droplet with a different fluid. Here, we demonstrate what we name the "pico-washer," a unit operation capable of simultaneously adding fluid to and removing fluid from droplets in flow while requiring only a small footprint on a microfluidic chip. We describe the fabrication strategy, device architecture, and process parameters required for stable operation of this technology, which is capable of operating with kHz droplet throughput. Furthermore, we provide an image processing workflow to characterize the washing process with microsecond and micrometer resolution. Finally, we demonstrate the potential for integrated droplet workflows by arranging two of these unit operations in series with a droplet generator, describe a design rule for stable operation of the pico-washer when integrated into a system, and validate this design rule experimentally. We anticipate that this technology will contribute to continued development of the droplet microfluidics toolbox and the realization of novel droplet-based, multistep biological and chemical assays.
Collapse
Affiliation(s)
- Michael J. Siedlik
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 United States
| | - David Issadore
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 United States
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104 United States
| |
Collapse
|
32
|
Abstract
In the past few years, the CRISPR (clustered regularly interspaced short palindromic repeats) applications in medicine and molecular biology have broadened. CRISPR has also been integrated with microfluidic-based biosensors to enhance the sensitivity and selectivity of medical diagnosis due to its great potentials. The CRISPR-powered microfluidics can help quantify DNAs and RNAs for different diseases such as cancer, and viral or bacterial diseases among others. Here in this review, we discussed the main applications of such tools along with their advantages and limitations.
Collapse
|
33
|
CRISPR-SID: Identifying EZH2 as a druggable target for desmoid tumors via in vivo dependency mapping. Proc Natl Acad Sci U S A 2021; 118:2115116118. [PMID: 34789568 DOI: 10.1073/pnas.2115116118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer precision medicine implies identification of tumor-specific vulnerabilities associated with defined oncogenic pathways. Desmoid tumors are soft-tissue neoplasms strictly driven by Wnt signaling network hyperactivation. Despite this clearly defined genetic etiology and the strict and unique implication of the Wnt/β-catenin pathway, no specific molecular targets for these tumors have been identified. To address this caveat, we developed fast, efficient, and penetrant genetic Xenopus tropicalis desmoid tumor models to identify and characterize drug targets. We used multiplexed CRISPR/Cas9 genome editing in these models to simultaneously target a tumor suppressor gene (apc) and candidate dependency genes. Our methodology CRISPR/Cas9 selection-mediated identification of dependencies (CRISPR-SID) uses calculated deviations between experimentally observed gene editing outcomes and deep-learning-predicted double-strand break repair patterns to identify genes under negative selection during tumorigenesis. This revealed EZH2 and SUZ12, both encoding polycomb repressive complex 2 components, and the transcription factor CREB3L1 as genetic dependencies for desmoid tumors. In vivo EZH2 inhibition by Tazemetostat induced partial regression of established autochthonous tumors. In vitro models of patient desmoid tumor cells revealed a direct effect of Tazemetostat on Wnt pathway activity. CRISPR-SID represents a potent approach for in vivo mapping of tumor vulnerabilities and drug target identification.
Collapse
|