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Zhu L, Yang S, Zhang K, Wang H, Fang X, Wang J. Uncovering underlying physical principles and driving forces of cell differentiation and reprogramming from single-cell transcriptomics. Proc Natl Acad Sci U S A 2024; 121:e2401540121. [PMID: 39150785 DOI: 10.1073/pnas.2401540121] [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: 01/25/2024] [Accepted: 06/28/2024] [Indexed: 08/18/2024] Open
Abstract
Recent advances in single-cell sequencing technology have revolutionized our ability to acquire whole transcriptome data. However, uncovering the underlying transcriptional drivers and nonequilibrium driving forces of cell function directly from these data remains challenging. We address this by learning cell state vector fields from discrete single-cell RNA velocity to quantify the single-cell global nonequilibrium driving forces as landscape and flux. From single-cell data, we quantified the Waddington landscape, showing that optimal paths for differentiation and reprogramming deviate from the naively expected landscape gradient paths and may not pass through landscape saddles at finite fluctuations, challenging conventional transition state estimation of kinetic rate for cell fate decisions due to the presence of the flux. A key insight from our study is that stem/progenitor cells necessitate greater energy dissipation for rapid cell cycles and self-renewal, maintaining pluripotency. We predict optimal developmental pathways and elucidate the nucleation mechanism of cell fate decisions, with transition states as nucleation sites and pioneer genes as nucleation seeds. The concept of loop flux quantifies the contributions of each cycle flux to cell state transitions, facilitating the understanding of cell dynamics and thermodynamic cost, and providing insights into optimizing biological functions. We also infer cell-cell interactions and cell-type-specific gene regulatory networks, encompassing feedback mechanisms and interaction intensities, predicting genetic perturbation effects on cell fate decisions from single-cell omics data. Essentially, our methodology validates the landscape and flux theory, along with its associated quantifications, offering a framework for exploring the physical principles underlying cellular differentiation and reprogramming and broader biological processes through high-throughput single-cell sequencing experiments.
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Affiliation(s)
- Ligang Zhu
- College of Physics, Jilin University, Changchun 130021, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Songlin Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Kun Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Hong Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Xiaona Fang
- College of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Jin Wang
- Center for Theoretical Interdisciplinary Sciences, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
- Department of Chemistry, Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794
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2
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González-Llera L, Arana ÁJ, Sánchez L, Alvarez-Lorenzo C, Barreiro-Iglesias A. Isothermal calorimetry reveals that successful regeneration after a spinal cord injury in larval zebrafish is associated with an increase in energy expenditure. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149498. [PMID: 39074572 DOI: 10.1016/j.bbabio.2024.149498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 07/31/2024]
Affiliation(s)
- Laura González-Llera
- Department of Functional Biology, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; Aquatic One Health Research Center (ARCUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Álvaro J Arana
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary Science, Universidade de Santiago de Compostela, Lugo, Spain; Preclinical Animal Models Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Laura Sánchez
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary Science, Universidade de Santiago de Compostela, Lugo, Spain; Preclinical Animal Models Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Carmen Alvarez-Lorenzo
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma (GI-1645), Facultad de Farmacia, Instituto de Materiales (iMATUS) and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Antón Barreiro-Iglesias
- Department of Functional Biology, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; Aquatic One Health Research Center (ARCUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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3
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Poe AR, Zhu L, Tang SH, Valencia E, Kayser MS. Energetic demands regulate sleep-wake rhythm circuit development. eLife 2024; 13:RP97256. [PMID: 39037919 PMCID: PMC11262794 DOI: 10.7554/elife.97256] [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] [Indexed: 07/24/2024] Open
Abstract
Sleep and feeding patterns lack strong daily rhythms during early life. As diurnal animals mature, feeding is consolidated to the day and sleep to the night. In Drosophila, circadian sleep patterns are initiated with formation of a circuit connecting the central clock to arousal output neurons; emergence of circadian sleep also enables long-term memory (LTM). However, the cues that trigger the development of this clock-arousal circuit are unknown. Here, we identify a role for nutritional status in driving sleep-wake rhythm development in Drosophila larvae. We find that in the 2nd instar larval period (L2), sleep and feeding are spread across the day; these behaviors become organized into daily patterns by the 3rd instar larval stage (L3). Forcing mature (L3) animals to adopt immature (L2) feeding strategies disrupts sleep-wake rhythms and the ability to exhibit LTM. In addition, the development of the clock (DN1a)-arousal (Dh44) circuit itself is influenced by the larval nutritional environment. Finally, we demonstrate that larval arousal Dh44 neurons act through glucose metabolic genes to drive onset of daily sleep-wake rhythms. Together, our data suggest that changes to energetic demands in developing organisms trigger the formation of sleep-circadian circuits and behaviors.
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Affiliation(s)
- Amy R Poe
- Department of Psychiatry, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Lucy Zhu
- Department of Psychiatry, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Si Hao Tang
- Department of Psychiatry, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Ella Valencia
- Department of Psychiatry, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Matthew S Kayser
- Department of Psychiatry, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Department of Neuroscience, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
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4
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Poe AR, Zhu L, Tang SH, Valencia E, Kayser MS. Energetic Demands Regulate Sleep-Wake Rhythm Circuit Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.19.558472. [PMID: 37786713 PMCID: PMC10541615 DOI: 10.1101/2023.09.19.558472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Sleep and feeding patterns lack strong daily rhythms during early life. As diurnal animals mature, feeding is consolidated to the day and sleep to the night. In Drosophila, circadian sleep patterns are initiated with formation of a circuit connecting the central clock to arousal output neurons; emergence of circadian sleep also enables long-term memory (LTM). However, the cues that trigger the development of this clock-arousal circuit are unknown. Here, we identify a role for nutritional status in driving sleep-wake rhythm development in Drosophila larvae. We find that in the 2nd instar larval period (L2), sleep and feeding are spread across the day; these behaviors become organized into daily patterns by the 3rd instar larval stage (L3). Forcing mature (L3) animals to adopt immature (L2) feeding strategies disrupts sleep-wake rhythms and the ability to exhibit LTM. In addition, the development of the clock (DN1a)-arousal (Dh44) circuit itself is influenced by the larval nutritional environment. Finally, we demonstrate that larval arousal Dh44 neurons act through glucose metabolic genes to drive onset of daily sleep-wake rhythms. Together, our data suggest that changes to energetic demands in developing organisms trigger the formation of sleep-circadian circuits and behaviors.
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Affiliation(s)
- Amy R. Poe
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lucy Zhu
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Si Hao Tang
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ella Valencia
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew S. Kayser
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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5
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Libby A, Rayon T. In preprints: puzzling together roles for glucose metabolism during gastrulation. Development 2024; 151:dev202774. [PMID: 38381701 DOI: 10.1242/dev.202774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Affiliation(s)
- Ashley Libby
- Developmental Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Teresa Rayon
- Epigenetics & Signalling Programmes, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
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Agarwal P, Cadart C, Fort L, Gahan J, Greenspan L, Juan T, Kameneva P, Miao Y. Pathway to Independence: the future of developmental biology. Development 2023; 150:dev202360. [PMID: 37812057 DOI: 10.1242/dev.202360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
In 2022, Development launched its Pathway to Independence (PI) Programme, aimed at supporting postdocs as they transition to their first independent position. We selected eight talented researchers as the first cohort of PI Fellows. In this article, each of our Fellows provides their perspective on the future of their field. Together, they paint an exciting picture of the current state of and open questions in developmental biology.
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Affiliation(s)
- Priti Agarwal
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Clotilde Cadart
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Loic Fort
- Vanderbilt University School of Medicine, 465 21st Avenue South, U 3200 MRB III, Nashville, TN 37240-7935, USA
| | - James Gahan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Leah Greenspan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Thomas Juan
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - Polina Kameneva
- The Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Yuchuan Miao
- Department of Genetics, Harvard Medical School and Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
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Wang M, Xue J, Li C, Qi L, Nie L, Xue Z. Glucose promoting the early embryonic development by increasing the lipid synthesis at 2-cell stage. Front Cell Dev Biol 2023; 11:1208501. [PMID: 37534102 PMCID: PMC10392834 DOI: 10.3389/fcell.2023.1208501] [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: 04/27/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
The optimization of culture conditions is one of the main strategies to improve the embryo development competence in in vitro fertilization (IVF). Glucose is an important carbon source while also exists in the oviductal fluid in vivo, the effect of glucose in embryo development microenvironment is still unclear. Here we employed the LC-MS to detect and analyze the metabolites in the culture medium of different cleavage stages including 2-Cell, 4-Cell and 8-Cell mouse embryos, respectively. The effects of the external glucose were estimated by measuring the development rate at different glucose concentrations from 0 to 5 mmol/L, and the gene expression changes were detected to explore the potential mechanism after the addition of glucose in the media. Our results indicated the 2-Cell and 8-Cell stages had defined characteristic metabolites, while 4-Cell stage was the transition state. Global and contiguous metabolic characteristics showed the glycometabolism play a critical role at each early cleavage stages during the embryo development. The 8-Cell rates demonstrated the addition of glucose in culture media significantly improve the embryo competence, the highest rate was 87.33% using 3 mmol/L glucose in media, in contrast only 9.95% using the media without glucose. Meanwhile, the blocked embryos were mainly enriched at 2-Cell stage. Further transcriptome study found 3 mmol/L glucose in media remarkably upregulated the gene expression of lipid biosynthesis at 2-Cell stage, the increased lipid was confirmed by nile red staining. These data indicated the glucose may promote the development competence through increasing the lipid biosynthesis to overcoming the 2-Cell block. Our findings were helpful for the further optimization of IVF culture media, as well as the estimation of embryo quality using metabolites in the culture media.
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Affiliation(s)
- Mingwen Wang
- Reproductive Medical Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinfeng Xue
- Reproductive Medical Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chanyi Li
- Reproductive Medical Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lingbin Qi
- Reproductive Medical Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lan Nie
- Department of Infertility and Endocrine, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Zhigang Xue
- Reproductive Medical Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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Ohlendorf R, Tan NYH, Nakayama N. Engineering Themes in Plant Forms and Functions. ANNUAL REVIEW OF PLANT BIOLOGY 2023; 74:777-801. [PMID: 37216204 DOI: 10.1146/annurev-arplant-061422-094751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Living structures constantly interact with the biotic and abiotic environment by sensing and responding via specialized functional parts. In other words, biological bodies embody highly functional machines and actuators. What are the signatures of engineering mechanisms in biology? In this review, we connect the dots in the literature to seek engineering principles in plant structures. We identify three thematic motifs-bilayer actuator, slender-bodied functional surface, and self-similarity-and provide an overview of their structure-function relationships. Unlike human-engineered machines and actuators, biological counterparts may appear suboptimal in design, loosely complying with physical theories or engineering principles. We postulate what factors may influence the evolution of functional morphology and anatomy to dissect and comprehend better the why behind the biological forms.
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Affiliation(s)
- Rahel Ohlendorf
- Department of Bioengineering, Imperial College London, London, United Kingdom;
| | | | - Naomi Nakayama
- Department of Bioengineering, Imperial College London, London, United Kingdom;
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9
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Rideout EJ, Tennessen JM. Editorial. Semin Cell Dev Biol 2023; 138:81-82. [PMID: 35970667 DOI: 10.1016/j.semcdb.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Elizabeth J Rideout
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Jason M Tennessen
- Department of Biology, Indiana University, Bloomington, IN 47404, USA.
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An G, Hong T, Park H, Lim W, Song G. Oxamyl exerts developmental toxic effects in zebrafish by disrupting the mitochondrial electron transport chain and modulating PI3K/Akt and p38 Mapk signaling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160458. [PMID: 36435248 DOI: 10.1016/j.scitotenv.2022.160458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/15/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Oxamyl, a carbamate insecticide, is mainly used to control nematodes in the agricultural field. Although oxamyl is a widely used insecticide that is associated with ecological concerns, limited studies have examined the toxic effects of oxamyl on the developmental stage and the underlying mechanisms. In this study, the developmental toxicity of oxamyl was demonstrated using zebrafish, which is a representative model as it is associated with rapid embryogenesis and a toxic response similar to that of other vertebrates. The morphological alteration of zebrafish larvae was analyzed to confirm the sub-lethal toxicity of oxamyl. Analysis of transgenic zebrafish (olig2:dsRED and flk1:eGFP line) and mRNA levels of genes associated with individual organ development revealed that oxamyl exerted toxic effects on the development of neuron, notochord, and vascular system. Next, the adverse effect of oxamyl on the mitochondrial electron transport chain was examined. Treatment with oxamyl altered the PI3K/Akt signaling and p38 Mapk signaling pathways in zebrafish. Thus, this study elucidated the mechanisms underlying the developmental toxicity of oxamyl and provided information on the parameters to assess the developmental toxicity of other environmental contaminants.
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Affiliation(s)
- Garam An
- Institute of Animal Molecular Biotechnology and Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Taeyeon Hong
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hahyun Park
- Institute of Animal Molecular Biotechnology and Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Whasun Lim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| | - Gwonhwa Song
- Institute of Animal Molecular Biotechnology and Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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