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Lee MB, Blue B, Muir M, Kaeberlein M. The million-molecule challenge: a moonshot project to rapidly advance longevity intervention discovery. GeroScience 2023; 45:3103-3113. [PMID: 37432607 PMCID: PMC10643437 DOI: 10.1007/s11357-023-00867-6] [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: 05/16/2023] [Accepted: 06/30/2023] [Indexed: 07/12/2023] Open
Abstract
Targeting aging is the future of twenty-first century preventative medicine. Small molecule interventions that promote healthy longevity are known, but few are well-developed and discovery of novel, robust interventions has stagnated. To accelerate longevity intervention discovery and development, high-throughput systems are needed that can perform unbiased drug screening and directly measure lifespan and healthspan metrics in whole animals. C. elegans is a powerful model system for this type of drug discovery. Combined with automated data capture and analysis technologies, truly high-throughput longevity drug discovery is possible. In this perspective, we propose the "million-molecule challenge", an effort to quantitatively assess 1,000,000 interventions for longevity within five years. The WormBot-AI, our best-in-class robotics and AI data analysis platform, provides a tool to achieve the million-molecule challenge for pennies per animal tested.
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Affiliation(s)
- Mitchell B Lee
- Ora Biomedical, Inc., 12101 Tukwila International Blvd Suite 210, Seattle, WA, 98168, USA.
| | - Benjamin Blue
- Ora Biomedical, Inc., 12101 Tukwila International Blvd Suite 210, Seattle, WA, 98168, USA
| | - Michael Muir
- Ora Biomedical, Inc., 12101 Tukwila International Blvd Suite 210, Seattle, WA, 98168, USA
| | - Matt Kaeberlein
- Ora Biomedical, Inc., 12101 Tukwila International Blvd Suite 210, Seattle, WA, 98168, USA
- Optispan Geroscience, Seattle, WA, USA
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2
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Jushaj A, Churgin M, De La Torre M, Kieswetter A, Driesschaert B, Dhondt I, Braeckman BP, Fang-Yen C, Temmerman L. Adult-restricted gene knock-down reveals candidates that affect locomotive healthspan in C. elegans. Biogerontology 2023; 24:225-233. [PMID: 36662373 DOI: 10.1007/s10522-022-10009-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/25/2022] [Indexed: 01/21/2023]
Abstract
Understanding how we can age healthily is a challenge at the heart of biogerontological interest. Whereas myriad genes are known to affect the lifespan of model organisms, effects of such interventions on healthspan-the period of life where an animal is considered healthy, rather than merely alive-are less clear. To understand relationships between life- and healthspan, in recent years several platforms were developed with the purpose of assessing both readouts simultaneously. We here relied on one such platform, the WorMotel, to study effects of adulthood-restricted knock-down of 130 Caenorhabditis elegans genes on the locomotive health of the animals along their lifespans. We found that knock-down of six genes affected healthspan while lifespan remained unchanged. For two of these, F26A3.4 and chn-1, knock-down resulted in an improvement of healthspan. In follow-up experiments we showed that knockdown of F26A3.4 indeed improves locomotive health and muscle structure at old age.
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Affiliation(s)
- Areta Jushaj
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Matthew Churgin
- Department of Bioengineering, University of Pennsylvania, Philadelphia, USA
| | - Miguel De La Torre
- Department of Bioengineering, University of Pennsylvania, Philadelphia, USA
| | - Amanda Kieswetter
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Brecht Driesschaert
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Ineke Dhondt
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, Ghent, Belgium
| | - Bart P Braeckman
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, Ghent, Belgium
| | | | - Liesbet Temmerman
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium.
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3
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Kerr RA, Roux AE, Goudeau J, Kenyon C. The C. elegans Observatory: High-throughput exploration of behavioral aging. FRONTIERS IN AGING 2022; 3:932656. [PMID: 36105851 PMCID: PMC9466599 DOI: 10.3389/fragi.2022.932656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022]
Abstract
Organisms undergo a variety of characteristic changes as they age, suggesting a substantial commonality in the mechanistic basis of aging. Experiments in model organisms have revealed a variety of cellular systems that impact lifespan, but technical challenges have prevented a comprehensive evaluation of how these components impact the trajectory of aging, and many components likely remain undiscovered. To facilitate the deeper exploration of aging trajectories at a sufficient scale to enable primary screening, we have created the Caenorhabditis elegans Observatory, an automated system for monitoring the behavior of group-housed C. elegans throughout their lifespans. One Observatory consists of a set of computers running custom software to control an incubator containing custom imaging and motion-control hardware. In its standard configuration, the Observatory cycles through trays of standard 6 cm plates, running four assays per day on up to 576 plates per incubator. High-speed image processing captures a range of behavioral metrics, including movement speed and stimulus-induced turning, and a data processing pipeline continuously computes summary statistics. The Observatory software includes a web interface that allows the user to input metadata and view graphs of the trajectory of behavioral aging as the experiment unfolds. Compared to the manual use of a plate-based C. elegans tracker, the Observatory reduces the effort required by close to two orders of magnitude. Within the Observatory, reducing the function of known lifespan genes with RNA interference (RNAi) gives the expected phenotypic changes, including extended motility in daf-2(RNAi) and progeria in hsf-1(RNAi). Lifespans scored manually from worms raised in conventional conditions match those scored from images captured by the Observatory. We have used the Observatory for a small candidate-gene screen and identified an extended youthful vigor phenotype for tank-1(RNAi) and a progeric phenotype for cdc-42(RNAi). By utilizing the Observatory, it is now feasible to conduct whole-genome screens for an aging-trajectory phenotype, thus greatly increasing our ability to discover and analyze new components of the aging program.
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Affiliation(s)
- Rex A. Kerr
- Calico Life Sciences LLC, South San Francisco, CA, United States
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4
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Sinha DB, Pincus ZS. High temporal resolution measurements of movement reveal novel early-life physiological decline in C. elegans. PLoS One 2022; 17:e0257591. [PMID: 35108272 PMCID: PMC8809618 DOI: 10.1371/journal.pone.0257591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/16/2022] [Indexed: 11/19/2022] Open
Abstract
Age-related physiological changes are most notable and best-studied late in life, while the nature of aging in early- or middle-aged individuals has not been explored as thoroughly. In C. elegans, many studies of movement vs. age generally focus on three distinct phases: sustained, youthful movement; onset of rapidly progressing impairment; and gross immobility. We investigated whether this first period of early-life adult movement is a sustained “healthy” level of high function followed by a discrete “movement catastrophe”—or whether there are early-life changes in movement that precede future physiological declines. To determine how movement varies during early adult life, we followed isolated individuals throughout life with a previously unachieved combination of duration and temporal resolution. By tracking individuals across the first six days of adulthood, we observed declines in movement starting as early as the first two days of adult life, as well as high interindividual variability in total daily movement. These findings suggest that movement is a highly dynamic behavior early in life, and that factors driving movement decline may begin acting as early as the first day of adulthood. Using simulation studies based on acquired data, we suggest that too-infrequent sampling in common movement assays limits observation of early-adult changes in motility, and we propose feasible strategies and a framework for designing assays with increased sensitivity for early movement declines.
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Affiliation(s)
- Drew Benjamin Sinha
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Departments from Genetics and Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Zachary Scott Pincus
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Departments from Genetics and Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail: ,
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5
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Han X, Su Y, White H, O'Neill KM, Morgan NY, Christensen R, Potarazu D, Vishwasrao HD, Xu S, Sun Y, Huang SY, Moyle MW, Dai Q, Pommier Y, Giniger E, Albrecht DR, Probst R, Shroff H. A polymer index-matched to water enables diverse applications in fluorescence microscopy. LAB ON A CHIP 2021; 21:1549-1562. [PMID: 33629685 PMCID: PMC8058278 DOI: 10.1039/d0lc01233e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We demonstrate diffraction-limited and super-resolution imaging through thick layers (tens-hundreds of microns) of BIO-133, a biocompatible, UV-curable, commercially available polymer with a refractive index (RI) matched to water. We show that cells can be directly grown on BIO-133 substrates without the need for surface passivation and use this capability to perform extended time-lapse volumetric imaging of cellular dynamics 1) at isotropic resolution using dual-view light-sheet microscopy, and 2) at super-resolution using instant structured illumination microscopy. BIO-133 also enables immobilization of 1) Drosophila tissue, allowing us to track membrane puncta in pioneer neurons, and 2) Caenorhabditis elegans, which allows us to image and inspect fine neural structure and to track pan-neuronal calcium activity over hundreds of volumes. Finally, BIO-133 is compatible with other microfluidic materials, enabling optical and chemical perturbation of immobilized samples, as we demonstrate by performing drug and optogenetic stimulation on cells and C. elegans.
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Affiliation(s)
- Xiaofei Han
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA. and Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA. and Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hamilton White
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA. and Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Kate M O'Neill
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA and Institute for Physical Science and Technology, University of Maryland College Park, College Park, MD 20742, USA
| | - Nicole Y Morgan
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan Christensen
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Deepika Potarazu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen Xu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shar-Yin Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark W Moyle
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dirk R Albrecht
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA. and Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Roland Probst
- ACUITYnano, Innovation in Biomedical Imaging, North Bethesda, MD 20850, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA. and Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA and Marine Biological Laboratory Fellows Program, Woods Hole, MA 02543, USA
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6
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Kinser HE, Mosley MC, Plutzer IB, Pincus Z. Global, cell non-autonomous gene regulation drives individual lifespan among isogenic C. elegans. eLife 2021; 10:e65026. [PMID: 33522488 PMCID: PMC7864635 DOI: 10.7554/elife.65026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/13/2021] [Indexed: 01/04/2023] Open
Abstract
Across species, lifespan is highly variable among individuals within a population. Even genetically identical Caenorhabditis elegans reared in homogeneous environments are as variable in lifespan as outbred human populations. We hypothesized that persistent inter-individual differences in expression of key regulatory genes drives this lifespan variability. As a test, we examined the relationship between future lifespan and the expression of 22 microRNA promoter::GFP constructs. Surprisingly, expression of nearly half of these reporters, well before death, could effectively predict lifespan. This indicates that prospectively long- vs. short-lived individuals have highly divergent patterns of transgene expression and transcriptional regulation. The gene-regulatory processes reported on by two of the most lifespan-predictive transgenes do not require DAF-16, the FOXO transcription factor that is a principal effector of insulin/insulin-like growth factor (IGF-1) signaling. Last, we demonstrate a hierarchy of redundancy in lifespan-predictive ability among three transgenes expressed in distinct tissues, suggesting that they collectively report on an organism-wide, cell non-autonomous process that acts to set each individual's lifespan.
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Affiliation(s)
- Holly E Kinser
- Department of Biomedical Engineering, Washington University in St. LouisSt. LouisUnited States
- Department of Developmental Biology and Department of Genetics, Washington University in St. LouisSt. LouisUnited States
| | - Matthew C Mosley
- Department of Developmental Biology and Department of Genetics, Washington University in St. LouisSt. LouisUnited States
- Program in Developmental, Regenerative, and Stem Cell Biology, Washington University in St. LouisSt. LouisUnited States
| | - Isaac B Plutzer
- Department of Developmental Biology and Department of Genetics, Washington University in St. LouisSt. LouisUnited States
| | - Zachary Pincus
- Department of Developmental Biology and Department of Genetics, Washington University in St. LouisSt. LouisUnited States
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7
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Wan J, Lu H. Enabling high-throughput single-animal gene-expression studies with molecular and micro-scale technologies. LAB ON A CHIP 2020; 20:4528-4538. [PMID: 33237042 PMCID: PMC7769683 DOI: 10.1039/d0lc00881h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Gene expression and regulation play diverse and important roles across all living systems. By quantifying the expression, whether in a sample of single cells, a specific tissue, or in a whole animal, one can gain insights into the underlying biology. Many biological questions now require single-animal and tissue-specific resolution, such as why individuals, even within an isogenic population, have variations in development and aging across different tissues and organs. The popular techniques that quantify the transcriptome (e.g. RNA-sequencing) process populations of animals and cells together and thus, have limitations in both individual and spatial resolution. There are single-animal assays available (e.g. fluorescent reporters); however, they suffer other technical bottlenecks, such as a lack of robust sample-handling methods. Microfluidic technologies have demonstrated various improvements throughout the years, and it is likely they can enhance the impact of these single-animal gene-expression assays. In this perspective, we aim to highlight how the engineering/method-development field have unique opportunities to create new tools that can enable us to robustly answer the next set of important questions in biology that require high-density, high-quality gene expression data.
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Affiliation(s)
- Jason Wan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA.
| | - Hang Lu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA. and School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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8
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Rahman M, Edwards H, Birze N, Gabrilska R, Rumbaugh KP, Blawzdziewicz J, Szewczyk NJ, Driscoll M, Vanapalli SA. NemaLife chip: a micropillar-based microfluidic culture device optimized for aging studies in crawling C. elegans. Sci Rep 2020; 10:16190. [PMID: 33004810 PMCID: PMC7530743 DOI: 10.1038/s41598-020-73002-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 09/10/2020] [Indexed: 01/23/2023] Open
Abstract
In this study, we report a microfluidic device for the whole-life culture of the nematode Caenorhabditis elegans that allows the scoring of animal survival and health measures. This device referred to as the NemaLife chip features: (1) an optimized micropillar arena in which animals can crawl, (2) sieve channels that separate progeny and prevent the loss of adults from the arena during culture maintenance, and (3) ports that allow rapid accessibility for feeding the adult-only population and introducing reagents as needed. The pillar arena geometry was optimized to accommodate the growing body size during culture and emulate the body gait and locomotion of animals reared on agar. Likewise, feeding protocols were optimized to recapitulate longevity outcomes typical of standard plate growth. Key benefits of the NemaLife Chip include eliminating the need to perform repeated manual transfers of adults during survival assays, negating the need for progeny-blocking chemical interventions, and avoiding the swim-induced stress across lifespan in animals reared in liquid. We also show that the culture of animals in pillar-less microfluidic chambers reduces lifespan and introduces physiological stress by increasing the occurrence of age-related vulval integrity disorder. We validated our pillar-based device with longevity analyses of classical aging mutants (daf-2, age-1, eat-2, and daf-16) and animals subjected to RNAi knockdown of age-related genes (age-1 and daf-16). We also showed that healthspan measures such as pharyngeal pumping and tap-induced stimulated reversals can be scored across the lifespan in the NemaLife chip. Overall, the capacity to generate reliable lifespan and physiological data underscores the potential of the NemaLife chip to accelerate healthspan and lifespan investigations in C. elegans.
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Affiliation(s)
- Mizanur Rahman
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, 79409, USA
| | - Hunter Edwards
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, 79409, USA
| | - Nikolajs Birze
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, 79409, USA
| | - Rebecca Gabrilska
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, 79409, USA
| | - Kendra P Rumbaugh
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, 79409, USA
| | - Jerzy Blawzdziewicz
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX, 79430, USA
| | - Nathaniel J Szewczyk
- Ohio Musculoskeletal and Neurological Institute and Department of Biomedical Sciences, Ohio University, Athens, OH, 45701, USA
| | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08854, USA
| | - Siva A Vanapalli
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, 79409, USA.
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9
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Pittman WE, Sinha DB, Kinser HE, Patil NS, Terry ES, Plutzer IB, Hong J, Pincus Z. A Simple Apparatus for Individual C. elegans Culture. Methods Mol Biol 2020; 2144:29-45. [PMID: 32410022 DOI: 10.1007/978-1-0716-0592-9_3] [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: 06/11/2023]
Abstract
We miniaturized standard, solid-phase C. elegans culture conditions to produce a system in which many isolated, individual C. elegans can be housed throughout their lives. This system, the "worm corral," is compatible with high-resolution brightfield and fluorescent microscopy, allowing imaging of fluorescent transgenes and morphological phenotypes from hatch until death. These culture devices can be constructed on the benchtop with commercially available reagents and standard laboratory equipment, making this an attainable solution for most labs.
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Affiliation(s)
- William E Pittman
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Drew B Sinha
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Holly E Kinser
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Nisha S Patil
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Eric S Terry
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Isaac B Plutzer
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Julia Hong
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Zachary Pincus
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA.
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10
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Atakan HB, Hof KS, Cornaglia M, Auwerx J, Gijs MAM. The Detection of Early Epigenetic Inheritance of Mitochondrial Stress in C. Elegans with a Microfluidic Phenotyping Platform. Sci Rep 2019; 9:19315. [PMID: 31848454 PMCID: PMC6917781 DOI: 10.1038/s41598-019-55979-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/05/2019] [Indexed: 02/05/2023] Open
Abstract
Fluctuations and deterioration in environmental conditions potentially have a phenotypic impact that extends over generations. Transgenerational epigenetics is the defined term for such intergenerational transient inheritance without an alteration in the DNA sequence. The model organism Caenorhabditis elegans is exceptionally valuable to address transgenerational epigenetics due to its short lifespan, well-mapped genome and hermaphrodite behavior. While the majority of the transgenerational epigenetics on the nematodes focuses on generations-wide heritage, short-term and in-depth analysis of this phenomenon in a well-controlled manner has been lacking. Here, we present a novel microfluidic platform to observe mother-to-progeny heritable transmission in C. elegans at high imaging resolution, under significant automation, and enabling parallelized studies. After approximately 24 hours of culture of L4 larvae under various concentrations and application periods of doxycycline, we investigated if mitochondrial stress was transferred from the mother nematodes to the early progenies. Automated and custom phenotyping algorithms revealed that a minimum doxycycline concentration of 30 µg/mL and a drug exposure time of 15 hours applied to the mothers could induce mitochondrial stress in first embryo progenies indeed, while this inheritance was not clearly observed later in L1 progenies. We believe that our new device could find further usage in transgenerational epigenetic studies modeled on C. elegans.
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Affiliation(s)
- H B Atakan
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - K S Hof
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - M Cornaglia
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - J Auwerx
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - M A M Gijs
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
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11
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Automated Platform for Long-Term Culture and High-Content Phenotyping of Single C. elegans Worms. Sci Rep 2019; 9:14340. [PMID: 31586133 PMCID: PMC6778082 DOI: 10.1038/s41598-019-50920-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/19/2019] [Indexed: 01/01/2023] Open
Abstract
The nematode Caenorhabditis elegans is a suitable model organism in drug screening. Traditionally worms are grown on agar plates, posing many challenges for long-term culture and phenotyping of animals under identical conditions. Microfluidics allows for 'personalized' phenotyping, as microfluidic chips permit collecting individual responses over worms' full life. Here, we present a multiplexed, high-throughput, high-resolution microfluidic approach to culture C. elegans from embryo to the adult stage at single animal resolution. We allocated single embryos to growth chambers, for observing the main embryonic and post-embryonic development stages and phenotypes, while exposing worms to up to 8 different well-controlled chemical conditions. Our approach allowed eliminating bacteria aggregation and biofilm formation-related clogging issues, which enabled us performing up to 80 hours of automated single worm culture studies. Our microfluidic platform is linked with an automated phenotyping code that registers organism-associated phenotypes at high-throughput. We validated our platform with a dose-response study of the anthelmintic drug tetramisole by studying its influence through the life cycle of the nematodes. In parallel, we could observe development effects and variations in single embryo and worm viability due to the bleaching procedure that is standardly used for harvesting the embryos from a worm culture agar plate.
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12
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Patel DS, Xu N, Lu H. Digging deeper: methodologies for high-content phenotyping in Caenorhabditis elegans. Lab Anim (NY) 2019; 48:207-216. [PMID: 31217565 DOI: 10.1038/s41684-019-0326-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 05/17/2019] [Indexed: 11/09/2022]
Abstract
Deep phenotyping is an emerging conceptual paradigm and experimental approach aimed at measuring and linking many aspects of a phenotype to understand its underlying biology. To date, deep phenotyping has been applied mostly in cultured cells and used less in multicellular organisms. However, in the past decade, it has increasingly been recognized that deep phenotyping could lead to a better understanding of how genetics, environment and stochasticity affect the development, physiology and behavior of an organism. The nematode Caenorhabditis elegans is an invaluable model system for studying how genes affect a phenotypic trait, and new technologies have taken advantage of the worm's physical attributes to increase the throughput and informational content of experiments. Coupling of these technical advancements with computational and analytical tools has enabled a boom in deep-phenotyping studies of C. elegans. In this Review, we highlight how these new technologies and tools are digging into the biological origins of complex, multidimensional phenotypes.
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Affiliation(s)
- Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Nan Xu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.,The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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Churgin MA, Szuperak M, Davis KC, Raizen DM, Fang-Yen C, Kayser MS. Quantitative imaging of sleep behavior in Caenorhabditis elegans and larval Drosophila melanogaster. Nat Protoc 2019; 14:1455-1488. [PMID: 30953041 DOI: 10.1038/s41596-019-0146-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 01/29/2019] [Indexed: 01/04/2023]
Abstract
Sleep is nearly universal among animals, yet remains poorly understood. Recent work has leveraged simple model organisms, such as Caenorhabditis elegans and Drosophila melanogaster larvae, to investigate the genetic and neural bases of sleep. However, manual methods of recording sleep behavior in these systems are labor intensive and low in throughput. To address these limitations, we developed methods for quantitative imaging of individual animals cultivated in custom microfabricated multiwell substrates, and used them to elucidate molecular mechanisms underlying sleep. Here, we describe the steps necessary to design, produce, and image these plates, as well as analyze the resulting behavioral data. We also describe approaches for experimentally manipulating sleep. Following these procedures, after ~2 h of experimental preparation, we are able to simultaneously image 24 C. elegans from the second larval stage to adult stages or 20 Drosophila larvae during the second instar life stage at a spatial resolution of 10 or 27 µm, respectively. Although this system has been optimized to measure activity and quiescence in Caenorhabditis larvae and adults and in Drosophila larvae, it can also be used to assess other behaviors over short or long periods. Moreover, with minor modifications, it can be adapted for the behavioral monitoring of a wide range of small animals.
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Affiliation(s)
- Matthew A Churgin
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Milan Szuperak
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristen C Davis
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Center for Excellence in Environmental Toxicology (CEET), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David M Raizen
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Chronobiology Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Center for Sleep and Circadian Neurobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher Fang-Yen
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.,Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew S Kayser
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Chronobiology Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Center for Sleep and Circadian Neurobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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14
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Breimann L, Preusser F, Preibisch S. Light-microscopy methods in C. elegans research. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2018.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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15
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Worms on a Chip. Bioanalysis 2019. [DOI: 10.1007/978-981-13-6229-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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16
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Atakan HB, Cornaglia M, Mouchiroud L, Auwerx J, Gijs MAM. Automated high-content phenotyping from the first larval stage till the onset of adulthood of the nematode Caenorhabditis elegans. LAB ON A CHIP 2018; 19:120-135. [PMID: 30484462 PMCID: PMC6309680 DOI: 10.1039/c8lc00863a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The nematode Caenorhabditis elegans is increasingly used as a model for human biology. However, in vivo culturing platforms for C. elegans allowing high-content phenotyping during their life cycle in an automated fashion are lacking so far. Here, a multiplexed microfluidic platform for the rapid high-content phenotyping of populations of C. elegans down to single animal resolution is presented. Nematodes are (i) reversibly and regularly confined during their life inside tapered channels for imaging fluorescence signal expression and to measure their growth parameters, and (ii) allowed to freely move in microfluidic chambers, during which the swimming behavior was video-recorded. The obtained data sets are analyzed in an automated way and 19 phenotypic parameters are extracted. Our platform is employed for studying the effect of bacteria dilution, a form of dietary restriction (DR) in nematodes, on a worm model of Huntington's disease and demonstrates the influence of DR on disease regression.
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Affiliation(s)
- Huseyin Baris Atakan
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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Abstract
Systems biology is an approach to collect high-dimensional data and analyze in an integrated manner. As aging is a complicated physiological functional decline in biological system, the methods in systems biology could be utilized in aging studies. Here we reviewed recent advances in systems biology in aging research and divide them into two major parts. One is the data resource, which includes omics data from DNA, RNA, proteins, epigenetic changes, metabolisms, and recently single-cell-level variations. The other is the data analysis methods consisting of network and modeling approaches. With all the data and the tools to analyze them, we could further promote our understanding of the systematic aging.
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