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Breimann L, Bahry E, Zouinkhi M, Kolyvanov K, Street LA, Preibisch S, Ercan S. Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594414. [PMID: 38798598 PMCID: PMC11118362 DOI: 10.1101/2024.05.15.594414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Regulation of transcription during embryogenesis is key to development and differentiation. To study transcript expression throughout Caenorhabditis elegans embryogenesis at single-molecule resolution, we developed a high-throughput single-molecule fluorescence in situ hybridization (smFISH) method that relies on computational methods to developmentally stage embryos and quantify individual mRNA molecules in single embryos. We applied our system to sdc-2, a zygotically transcribed gene essential for hermaphrodite development and dosage compensation. We found that sdc-2 is rapidly activated during early embryogenesis by increasing both the number of mRNAs produced per transcription site and the frequency of sites engaged in transcription. Knockdown of sdc-2 and dpy-27, a subunit of the dosage compensation complex (DCC), increased the number of active transcription sites for the X chromosomal gene dpy-23 but not the autosomal gene mdh-1, suggesting that the DCC reduces the frequency of dpy-23 transcription. The temporal resolution from in silico staging of embryos showed that the deletion of a single DCC recruitment element near the dpy-23 gene causes higher dpy-23 mRNA expression after the start of dosage compensation, which could not be resolved using mRNAseq from mixed-stage embryos. In summary, we have established a computational approach to quantify temporal regulation of transcription throughout C. elegans embryogenesis and demonstrated its potential to provide new insights into developmental gene regulation.
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Affiliation(s)
- Laura Breimann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ella Bahry
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Helmholtz Imaging, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Marwan Zouinkhi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Klim Kolyvanov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Lena Annika Street
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Stephan Preibisch
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
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2
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Chou HT, Valencia F, Alexander JC, Bell AD, Deb D, Pollard DA, Paaby AB. Diversification of small RNA pathways underlies germline RNA interference incompetence in wild Caenorhabditis elegans strains. Genetics 2024; 226:iyad191. [PMID: 37865119 PMCID: PMC10763538 DOI: 10.1093/genetics/iyad191] [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: 07/09/2023] [Revised: 07/09/2023] [Accepted: 08/12/2023] [Indexed: 10/23/2023] Open
Abstract
The discovery that experimental delivery of dsRNA can induce gene silencing at target genes revolutionized genetics research, by both uncovering essential biological processes and creating new tools for developmental geneticists. However, the efficacy of exogenous RNA interference (RNAi) varies dramatically within the Caenorhabditis elegans natural population, raising questions about our understanding of RNAi in the lab relative to its activity and significance in nature. Here, we investigate why some wild strains fail to mount a robust RNAi response to germline targets. We observe diversity in mechanism: in some strains, the response is stochastic, either on or off among individuals, while in others, the response is consistent but delayed. Increased activity of the Argonaute PPW-1, which is required for germline RNAi in the laboratory strain N2, rescues the response in some strains but dampens it further in others. Among wild strains, genes known to mediate RNAi exhibited very high expression variation relative to other genes in the genome as well as allelic divergence and strain-specific instances of pseudogenization at the sequence level. Our results demonstrate functional diversification in the small RNA pathways in C. elegans and suggest that RNAi processes are evolving rapidly and dynamically in nature.
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Affiliation(s)
- Han Ting Chou
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Francisco Valencia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jacqueline C Alexander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Avery Davis Bell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Diptodip Deb
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Janelia Research Campus, Ashburn, VA 20147, USA
| | - Daniel A Pollard
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - Annalise B Paaby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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3
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Aubry G, Lee HJ, Lu H. Advances in Microfluidics: Technical Innovations and Applications in Diagnostics and Therapeutics. Anal Chem 2023; 95:444-467. [PMID: 36625114 DOI: 10.1021/acs.analchem.2c04562] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Guillaume Aubry
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Hyun Jee Lee
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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4
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Zhu H, Shen W, Luo C, Liu F. An integrated microfluidic device for multiplexed imaging of spatial gene expression patterns of Drosophila embryos. LAB ON A CHIP 2022; 22:4081-4092. [PMID: 36165088 DOI: 10.1039/d2lc00514j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To reveal the underlying mechanism of the biological function of multicellular systems, it is important to obtain comprehensive spatial gene expression profiles. Among the emerging single-cell spatial-omics techniques, immunofluorescence (IF)-based iterative multiplexed imaging is a promising approach. However, the conventional method is usually costly, time-consuming, labor-intensive, and has low throughput. Moreover, it has yet to be demonstrated in intact multicellular organisms. Here, we developed an integrated microfluidic system to overcome these challenges for quantitatively measuring multiple protein profiles sequentially in situ in the same Drosophila embryo. We designed an array of hydrodynamic trapping sites to automatically capture over ten Drosophila embryos with orientation selectivity at more than 90% trapping rates. We also optimized the geometry of confinement and the on-chip IF protocol to achieve the same high signal-to-noise ratio as the off-chip traditional IF experiments. Moreover, we developed an efficient de-staining protocol by combining on-chip antibody stripping and fluorophore bleaching. Using the same secondary antibody to sequentially stain different genes, we confirmed that the de-stained genes have no detectable interference with the subsequently stained genes, and the gene expression profiles are preserved after multiple cycles of staining and de-staining processes. This preliminary test shows that our newly developed integrated microfluidic system can be a powerful tool for multiplexed imaging of Drosophila embryos. Our work opens a new avenue to design microfluidic chips for multicellular organisms and single-cell spatial-omics techniques.
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Affiliation(s)
- Hongcun Zhu
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China.
| | - Wenting Shen
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China.
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
| | - Feng Liu
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
- Key Laboratory of Hebei Province for Molecular Biophysics, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300130, China
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5
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Wu J, Gao Y, Xi J, You X, Zhang X, Zhang X, Cao Y, Liu P, Chen X, Luan Y. A high-throughput microplate toxicity screening platform based on Caenorhabditis elegans. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 245:114089. [PMID: 36126550 DOI: 10.1016/j.ecoenv.2022.114089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 06/15/2023]
Abstract
Caenorhabditis elegans (C. elegans), an established model organism, has been widely used in environmental toxicology research. However, most of the current toxicity testing methods based on worms are time-consuming. In this study we aimed to develop an automated and highly-integrated platform for high-throughput and in situ toxicity testing. Considering the superiority of C. elegans as a neurotoxicological model, this platform mainly evaluates general toxicology and neurotoxicology endpoints, which are usually induced by metals and pesticides, the major environmental contaminants. Microplates were used as a worm culturing system, which have good compatibility with any commercial microplate applicable instruments. We developed a microfluidic-based module for worm dispensing, and an image acquisition/analysis module for monitoring worms and detecting toxicity endpoints in bright filed. These were collectively incorporated with a commercial pipetting workstation for automated food/drug delivery and a high-content analysis system for fluorescence detection. The integrated platform achieved an efficient on-demand worm dispensing, long-term maintenance, regular monitoring and imaging, survival assay and behavioral analyses, and visualized gene reporter assay. Moreover, "Lab on Web" was achieved by connecting the platform to the web for remote operation, worm monitoring, and phenotype calculation. To demonstrate the ability of the platform for automated toxicity testing assays; worms were treated with cadmium and longevity, neurotoxicity, developmental toxicity and gst-4 expression were evaluated. We determined its feasibility and proposed the potential application in high-throughput toxicity screening for environmental risk assessment in the nearest future.
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Affiliation(s)
- Jiaying Wu
- School of Public Health, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yue Gao
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Xi
- School of Public Health, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xinyue You
- School of Public Health, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaohong Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Xinyu Zhang
- School of Public Health, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yiyi Cao
- School of Public Health, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Peichuan Liu
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiang Chen
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yang Luan
- School of Public Health, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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6
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Kaul S, Chou HT, Charles S, Aubry G, Lu H, Paaby AB. Single-molecule FISH in C. elegans embryos reveals early embryonic expression dynamics of par-2 , lgl-1 and chin-1 and possible differences between hyper-diverged strains. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000609. [PMID: 35903776 PMCID: PMC9315406 DOI: 10.17912/micropub.biology.000609] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/03/2022] [Accepted: 07/19/2022] [Indexed: 11/04/2022]
Abstract
Wild C. elegans strains harbor natural variation in developmental pathways, but investigating these differences requires precise and well-powered phenotyping methods. Here we employ a microfluidics platform for single-molecule FISH to simultaneously visualize the transcripts of three genes in embryos of two distinct strains. We capture transcripts at high resolution by developmental stage in over one hundred embryos of each strain and observe wide-scale conservation of expression, but subtle differences in par-2 and chin-1 abundance and rate of change. As both genes reside in a genomic interval of hyper-divergence, these results may reflect consequences of pathway evolution over long timescales.
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Affiliation(s)
- Samiksha Kaul
- School of Biological Sciences, Georgia Institute of Technology
| | - Han Ting Chou
- School of Biological Sciences, Georgia Institute of Technology
| | - Seleipiri Charles
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology
| | - Guillaume Aubry
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology
| | - Hang Lu
- Wallace H. Coulter Department of Biomedical Engineering and School of Chemical & Biomolecular Engineering, Georgia Institute of Technology
| | - Annalise B. Paaby
- School of Biological Sciences, Georgia Institute of Technology
,
Correspondence to: Annalise B. Paaby (
)
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7
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Frey N, Sönmez UM, Minden J, LeDuc P. Microfluidics for understanding model organisms. Nat Commun 2022; 13:3195. [PMID: 35680898 PMCID: PMC9184607 DOI: 10.1038/s41467-022-30814-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
New microfluidic systems for whole organism analysis and experimentation are catalyzing biological breakthroughs across many fields, from human health to fundamental biology principles. This perspective discusses recent microfluidic tools to study intact model organisms to demonstrate the tremendous potential for these integrated approaches now and into the future. We describe these microsystems' technical features and highlight the unique advantages for precise manipulation in areas including immobilization, automated alignment, sorting, sensory, mechanical and chemical stimulation, and genetic and thermal perturbation. Our aim is to familiarize technologically focused researchers with microfluidics applications in biology research, while providing biologists an entrée to advanced microengineering techniques for model organisms. Building small-scale tools for biology research eliminates the need for time-consuming methods and enables novel experimental paradigms. Here, the authors discuss microfluidics' potential for manipulating or stimulating model organisms and identify barriers to making these tools accessible.
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Affiliation(s)
- Nolan Frey
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Utku M Sönmez
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jonathan Minden
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Philip LeDuc
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Computation Biology, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
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8
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Fang C, Li Y, Hu S, Wang H, Chen X, Zhu X. Self-Assembled Growing DNA Tree Mediated by Exosomes for Amplified Imaging of Messenger RNA in Living Cells. Anal Chem 2021; 93:8414-8422. [PMID: 34114453 DOI: 10.1021/acs.analchem.1c00211] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Sensitive, accurate, and nondestructive probing of endogenous messenger RNA (mRNA) in living cells places extremely high demands on nanocarriers and probes and is still a challenge. In the present study, we describe a target-triggered self-assembled DNA tree for amplified analysis of mRNA in intact living cells. The probes assembled into a DNA tree are transported into cells by exosomes, which is beneficial for reducing cell damage and realizing nondestructive analysis. The probes are l-configured single-stranded DNAs (LDNAs) that can resist the degradation of exonuclease and endonuclease, thus laying the foundation for accurate analysis. Under the induction of the target mRNA, the probes in the cells assemble into a small plantlet and eventually grow into a tree after a few rounds of self-cycling, achieving the exponential amplification of fluorescence signals. Compared with the signal amplification based on one-dimensional DNA trunk self-assembly, the three-dimensional DNA tree shows an excellent sensitivity both ex situ and in situ. In this way, favorable sensitivity, accuracy, and nondestructive analysis are integrated into one system. This DNA tree expands the analysis platform for analyzing more biomarkers on a genetic level in an intracellular, nondestructive, and hypersensitive manner and holds great potential in clinical diagnostic and research applications.
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Affiliation(s)
- Cheng Fang
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai 200040, P. R. China
| | - Yuming Li
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai 200040, P. R. China
| | - Song Hu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Hao Wang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Xiaoxia Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.,School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China.,Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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