1
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El Azhar Y, Schulthess P, van Oostrom MJ, Weterings SDC, Meijer WHM, Tsuchida-Straeten N, Thomas WM, Bauer M, Sonnen KF. Unravelling differential Hes1 dynamics during axis elongation of mouse embryos through single-cell tracking. Development 2024; 151:dev202936. [PMID: 39315665 DOI: 10.1242/dev.202936] [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: 04/08/2024] [Accepted: 08/22/2024] [Indexed: 09/25/2024]
Abstract
The intricate dynamics of Hes expression across diverse cell types in the developing vertebrate embryonic tail have remained elusive. To address this, we have developed an endogenously tagged Hes1-Achilles mouse line, enabling precise quantification of dynamics at the single-cell resolution across various tissues. Our findings reveal striking disparities in Hes1 dynamics between presomitic mesoderm (PSM) and preneural tube (pre-NT) cells. While pre-NT cells display variable, low-amplitude oscillations, PSM cells exhibit synchronized, high-amplitude oscillations. Upon the induction of differentiation, the oscillation amplitude increases in pre-NT cells. Additionally, our study of Notch inhibition on Hes1 oscillations unveils distinct responses in PSM and pre-NT cells, corresponding to differential Notch ligand expression dynamics. These findings suggest the involvement of separate mechanisms driving Hes1 oscillations. Thus, Hes1 demonstrates dynamic behaviour across adjacent tissues of the embryonic tail, yet the varying oscillation parameters imply differences in the information that can be transmitted by these dynamics.
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Affiliation(s)
- Yasmine El Azhar
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, Utrecht 3584, The Netherlands
| | - Pascal Schulthess
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, Utrecht 3584, The Netherlands
| | - Marek J van Oostrom
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, Utrecht 3584, The Netherlands
| | - Sonja D C Weterings
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, Utrecht 3584, The Netherlands
| | - Wilke H M Meijer
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, Utrecht 3584, The Netherlands
| | | | - Wouter M Thomas
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, Utrecht 3584, The Netherlands
| | - Marianne Bauer
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, Utrecht 3584, The Netherlands
| | - Katharina F Sonnen
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, Utrecht 3584, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Technical University of Delft, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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2
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Li L, Chang J, Xu Z, Chu L, Zhang J, Xing Q, Bao Z. Functional allocation of Mitogen-activated protein kinases (MAPKs) unveils thermotolerance in scallop Argopecten irradians irradians. MARINE ENVIRONMENTAL RESEARCH 2024; 202:106750. [PMID: 39293275 DOI: 10.1016/j.marenvres.2024.106750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 09/09/2024] [Accepted: 09/12/2024] [Indexed: 09/20/2024]
Abstract
Global warming has significantly impacted agriculture, particularly in animal husbandry and aquaculture industry. Rising ocean temperatures due to global warming are severely affecting shellfish production, necessitating an understanding of how shellfish cope with thermal stress. The mitogen-activated protein kinases (MAPK) signaling pathway plays a crucial role in cell growth, differentiation, adaptation to environmental stress, inflammatory response, and managing high temperature stress. To investigate the function of MAPKs in bay scallops, a comparative genomics and bioinformatics approach identified three MAPK genes: AiERK, Aip38, and AiJNK. Structural and phylogenetic analyses of these proteins were conducted to determine their evolutionary relationships. Spatiotemporal expression patterns were examined at different developmental stages and in various tissues of healthy adult scallops. Additionally, the expression regulation of these genes was studied in selected tissues (hemocyte, gill, heart, mantle) following exposure to high temperatures (32 °C) for different durations (0 h, 6 h, 12 h, 24 h, 3 d, 6 d, 10 d). The spatiotemporal expressions of AiMAPKs were ubiquitous, with significant increases in AiERK expression observed at the umbo larval stage (3.09-fold), while Aip38 and AiJNK were identified as potential maternal effect genes. In adult scallops, different gene expression patterns of AiMAPKs were observed across eight tissues, with high expressions in the foot and gill, and lower expressions in the striated muscle. Following high temperature stress, AiMAPKs expressions in the gill and mantle were mainly up-regulated, while in the hemocyte, they were primarily down-regulated. These findings indicate time- and tissue-dependent expression patterns with functional allocation in response to different thermal durations. This study enhances our understanding of the function and evolution of AiMAPKs genes in shellfish and provides a theoretical basis for elucidating the energy regulation mechanism of bay scallops in response to high temperature stress.
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Affiliation(s)
- Linshu Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Jiaxi Chang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Zhaosong Xu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Longfei Chu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Junhao Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
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3
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Cipriano A, Colantoni A, Calicchio A, Fiorentino J, Gomes D, Moqri M, Parker A, Rasouli S, Caldwell M, Briganti F, Roncarolo MG, Baldini A, Weinacht KG, Tartaglia GG, Sebastiano V. Transcriptional and epigenetic characterization of a new in vitro platform to model the formation of human pharyngeal endoderm. Genome Biol 2024; 25:211. [PMID: 39118163 PMCID: PMC11312149 DOI: 10.1186/s13059-024-03354-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND The Pharyngeal Endoderm (PE) is an extremely relevant developmental tissue, serving as the progenitor for the esophagus, parathyroids, thyroids, lungs, and thymus. While several studies have highlighted the importance of PE cells, a detailed transcriptional and epigenetic characterization of this important developmental stage is still missing, especially in humans, due to technical and ethical constraints pertaining to its early formation. RESULTS Here we fill this knowledge gap by developing an in vitro protocol for the derivation of PE-like cells from human Embryonic Stem Cells (hESCs) and by providing an integrated multi-omics characterization. Our PE-like cells robustly express PE markers and are transcriptionally homogenous and similar to in vivo mouse PE cells. In addition, we define their epigenetic landscape and dynamic changes in response to Retinoic Acid by combining ATAC-Seq and ChIP-Seq of histone modifications. The integration of multiple high-throughput datasets leads to the identification of new putative regulatory regions and to the inference of a Retinoic Acid-centered transcription factor network orchestrating the development of PE-like cells. CONCLUSIONS By combining hESCs differentiation with computational genomics, our work reveals the epigenetic dynamics that occur during human PE differentiation, providing a solid resource and foundation for research focused on the development of PE derivatives and the modeling of their developmental defects in genetic syndromes.
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Affiliation(s)
- Andrea Cipriano
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Alessio Colantoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano Di Tecnologia (IIT), 00161, Rome, Italy
| | - Alessandro Calicchio
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Jonathan Fiorentino
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano Di Tecnologia (IIT), 00161, Rome, Italy
| | - Danielle Gomes
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Mahdi Moqri
- Biomedical Informatics Program, Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Alexander Parker
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Sajede Rasouli
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Matthew Caldwell
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Francesca Briganti
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, 94305, USA
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Maria Grazia Roncarolo
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
- Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, 94305, USA
- Center for Definitive and Curative Medicine (CDCM), Stanford School of Medicine, Stanford, CA, USA
| | - Antonio Baldini
- Department of Molecular Medicine and Medical Biotech., University Federico II, 80131, Naples, Italy
| | - Katja G Weinacht
- Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Gian Gaetano Tartaglia
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano Di Tecnologia (IIT), 00161, Rome, Italy.
- Center for Human Technology, Fondazione Istituto Italiano Di Tecnologia (IIT), 16152, Genoa, Italy.
| | - Vittorio Sebastiano
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA.
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA.
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Su J, Song Y, Zhu Z, Huang X, Fan J, Qiao J, Mao F. Cell-cell communication: new insights and clinical implications. Signal Transduct Target Ther 2024; 9:196. [PMID: 39107318 PMCID: PMC11382761 DOI: 10.1038/s41392-024-01888-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/09/2024] [Accepted: 06/02/2024] [Indexed: 09/11/2024] Open
Abstract
Multicellular organisms are composed of diverse cell types that must coordinate their behaviors through communication. Cell-cell communication (CCC) is essential for growth, development, differentiation, tissue and organ formation, maintenance, and physiological regulation. Cells communicate through direct contact or at a distance using ligand-receptor interactions. So cellular communication encompasses two essential processes: cell signal conduction for generation and intercellular transmission of signals, and cell signal transduction for reception and procession of signals. Deciphering intercellular communication networks is critical for understanding cell differentiation, development, and metabolism. First, we comprehensively review the historical milestones in CCC studies, followed by a detailed description of the mechanisms of signal molecule transmission and the importance of the main signaling pathways they mediate in maintaining biological functions. Then we systematically introduce a series of human diseases caused by abnormalities in cell communication and their progress in clinical applications. Finally, we summarize various methods for monitoring cell interactions, including cell imaging, proximity-based chemical labeling, mechanical force analysis, downstream analysis strategies, and single-cell technologies. These methods aim to illustrate how biological functions depend on these interactions and the complexity of their regulatory signaling pathways to regulate crucial physiological processes, including tissue homeostasis, cell development, and immune responses in diseases. In addition, this review enhances our understanding of the biological processes that occur after cell-cell binding, highlighting its application in discovering new therapeutic targets and biomarkers related to precision medicine. This collective understanding provides a foundation for developing new targeted drugs and personalized treatments.
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Affiliation(s)
- Jimeng Su
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ying Song
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
| | - Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
| | - Xinyue Huang
- Biomedical Research Institute, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jibiao Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
- Cancer Center, Peking University Third Hospital, Beijing, China.
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5
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Ming H, Zhang M, Rajput S, Logsdon D, Zhu L, Schoolcraft WB, Krisher RL, Jiang Z, Yuan Y. In vitro culture alters cell lineage composition and cellular metabolism of bovine blastocyst†. Biol Reprod 2024; 111:11-27. [PMID: 38408205 PMCID: PMC11247278 DOI: 10.1093/biolre/ioae031] [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: 06/19/2023] [Revised: 11/05/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Profiling bovine blastocyst transcriptome at the single-cell level has enabled us to reveal the first cell lineage segregation, during which the inner cell mass (ICM), trophectoderm (TE), and an undefined population of transitional cells were identified. By comparing the transcriptome of blastocysts derived in vivo (IVV), in vitro from a conventional culture medium (IVC), and in vitro from an optimized reduced nutrient culture medium (IVR), we found a delay of the cell fate commitment to ICM in the IVC and IVR embryos. Developmental potential differences between IVV, IVC, and IVR embryos were mainly contributed by ICM and transitional cells. Pathway analysis of these non-TE cells between groups revealed highly active metabolic and biosynthetic processes, reduced cellular signaling, and reduced transmembrane transport activities in IVC embryos that may lead to reduced developmental potential. IVR embryos had lower activities in metabolic and biosynthetic processes but increased cellular signaling and transmembrane transport, suggesting these cellular mechanisms may contribute to improved blastocyst development compared to IVC embryos. However, the IVR embryos had compromised development compared to IVV embryos with notably over-active transmembrane transport activities that impaired ion homeostasis.
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Affiliation(s)
- Hao Ming
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Mingxiang Zhang
- Colorado Center for Reproductive Medicine, Lone Tree, CO, USA
| | - Sandeep Rajput
- Colorado Center for Reproductive Medicine, Lone Tree, CO, USA
- Genus plc, DeForest, WI, USA
| | - Deirdre Logsdon
- Colorado Center for Reproductive Medicine, Lone Tree, CO, USA
| | - Linkai Zhu
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL, USA
| | | | - Rebecca L Krisher
- Colorado Center for Reproductive Medicine, Lone Tree, CO, USA
- Genus plc, DeForest, WI, USA
| | - Zongliang Jiang
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Ye Yuan
- Colorado Center for Reproductive Medicine, Lone Tree, CO, USA
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6
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Zhang Y, Yang Y, Ren L, Zhan M, Sun T, Zou Q, Zhang Y. Predicting intercellular communication based on metabolite-related ligand-receptor interactions with MRCLinkdb. BMC Biol 2024; 22:152. [PMID: 38978014 PMCID: PMC11232326 DOI: 10.1186/s12915-024-01950-w] [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: 03/16/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Metabolite-associated cell communications play critical roles in maintaining human biological function. However, most existing tools and resources focus only on ligand-receptor interaction pairs where both partners are proteinaceous, neglecting other non-protein molecules. To address this gap, we introduce the MRCLinkdb database and algorithm, which aggregates and organizes data related to non-protein L-R interactions in cell-cell communication, providing a valuable resource for predicting intercellular communication based on metabolite-related ligand-receptor interactions. RESULTS Here, we manually curated the metabolite-ligand-receptor (ML-R) interactions from the literature and known databases, ultimately collecting over 790 human and 670 mouse ML-R interactions. Additionally, we compiled information on over 1900 enzymes and 260 transporter entries associated with these metabolites. We developed Metabolite-Receptor based Cell Link Database (MRCLinkdb) to store these ML-R interactions data. Meanwhile, the platform also offers extensive information for presenting ML-R interactions, including fundamental metabolite information and the overall expression landscape of metabolite-associated gene sets (such as receptor, enzymes, and transporter proteins) based on single-cell transcriptomics sequencing (covering 35 human and 26 mouse tissues, 52 human and 44 mouse cell types) and bulk RNA-seq/microarray data (encompassing 62 human and 39 mouse tissues). Furthermore, MRCLinkdb introduces a web server dedicated to the analysis of intercellular communication based on ML-R interactions. MRCLinkdb is freely available at https://www.cellknowledge.com.cn/mrclinkdb/ . CONCLUSIONS In addition to supplementing ligand-receptor databases, MRCLinkdb may provide new perspectives for decoding the intercellular communication and advancing related prediction tools based on ML-R interactions.
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Affiliation(s)
- Yuncong Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China
| | - Yu Yang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Meixiao Zhan
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China
| | - Taoping Sun
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
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7
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Martin RA, Tate AT. Pleiotropy alleviates the fitness costs associated with resource allocation trade-offs in immune signalling networks. Proc Biol Sci 2024; 291:20240446. [PMID: 38835275 DOI: 10.1098/rspb.2024.0446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/03/2024] [Indexed: 06/06/2024] Open
Abstract
Many genes and signalling pathways within plant and animal taxa drive the expression of multiple organismal traits. This form of genetic pleiotropy instigates trade-offs among life-history traits if a mutation in the pleiotropic gene improves the fitness contribution of one trait at the expense of another. Whether or not pleiotropy gives rise to conflict among traits, however, likely depends on the resource costs and timing of trait deployment during organismal development. To investigate factors that could influence the evolutionary maintenance of pleiotropy in gene networks, we developed an agent-based model of co-evolution between parasites and hosts. Hosts comprise signalling networks that must faithfully complete a developmental programme while also defending against parasites, and trait signalling networks could be independent or share a pleiotropic component as they evolved to improve host fitness. We found that hosts with independent developmental and immune networks were significantly more fit than hosts with pleiotropic networks when traits were deployed asynchronously during development. When host genotypes directly competed against each other, however, pleiotropic hosts were victorious regardless of trait synchrony because the pleiotropic networks were more robust to parasite manipulation, potentially explaining the abundance of pleiotropy in immune systems despite its contribution to life history trade-offs.
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Affiliation(s)
- Reese A Martin
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Ann T Tate
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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8
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Henriques MC, Carvalho I, Santos C, Herdeiro MT, Fardilha M, Pavlaki MD, Loureiro S. Unveiling the molecular mechanisms and developmental consequences of mercury (Hg) toxicity in zebrafish embryo-larvae: A comprehensive approach. Neurotoxicol Teratol 2023; 100:107302. [PMID: 37739188 DOI: 10.1016/j.ntt.2023.107302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Mercury (Hg) is a global contaminant affecting aquatic ecosystems' health. Chronic exposure to Hg has shown that the normal development of zebrafish embryo-larvae is affected. However, the molecular mechanisms behind the toxicity of Hg on fish embryonic development are still poorly understood. This work aimed to investigate the effects of Hg exposure on zebrafish embryo-larvae using a combined approach at individual (mortality, embryo development and locomotor behavior) and biochemical (neurotoxicity and oxidative stress enzymatic activities and protein phosphatase expression) levels. The Fish Embryo Toxicity assay followed the Organization for Economic Cooperation and Development Guideline 236 and used a concentration range between 13 and 401 μg Hg/L. Lethal and developmental endpoints were examined at 24, 48, 72 and 96 hpf. Biochemical markers, including Acetylcholinesterase (AChE), Catalase (CAT), Glutathione Reductase (GR), and Glutathione-S-Transferase (GST) activities and, for the first time, the expression of the protein phosphatase 1 gamma (PP1γ) was assessed after 24, 48, 72 and 96 h of exposure to 10 and 100 μg Hg/L. The behavioral effects of a sublethal range of Hg (from 0.8 to 13 μg Hg/L) were assessed using an automated video tracking system at 120 hpf. Several developmental abnormalities on zebrafish embryos and larvae, including pericardial edema, spin and tail deformities and reduced rate of consumption of the yolk sac, were found after exposure to Hg (LC50 at 96 hpf of 139 μg Hg/L) with EC50 values for total malformations ranging from 22 to 264 μg Hg/L. After 96 hpf, no significant effects were observed in the CAT and GR activities. However, an increase in the GST activity in a concentration and time-dependent manner was found, denoting possible stress-related adaptation of zebrafish embryos to deleterious effects of Hg exposure. The AchE activity showed a response pattern in line with the behavioral responses. At the lowest concentration tested, no significant effects were found for the AChE activity, whereas a decrease in AChE activity was observed at 100 μg Hg/L, suggesting that exposure to Hg induced neurotoxic effects in zebrafish embryos which in turn may explain the lack of equilibrium found in this study (EC50 at 96 hpf of 83 μg Hg/L). Moreover, a decrease in the PP1γ expression was found after 96 h of exposure to 10 and 100 μg Hg/L. Thus, we suggest that Hg may be an inhibitor of PP1γ in zebrafish embryos-larvae and thus, along with the alterations in the enzymatic activity of GST, explain some of the developmental malformations observed, as well as the lack of equilibrium. Hence, in this study, we propose the use of PP1 expression, in combination with apical and biochemical endpoints, as a precursor for assessing Hg's toxic mechanism on embryonic development.
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Affiliation(s)
- Magda Carvalho Henriques
- Institute of Biomedicine (iBiMED) & Department of Medical Sciences, University of Aveiro, Aveiro, Portugal; CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Inês Carvalho
- Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Cátia Santos
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Maria Teresa Herdeiro
- Institute of Biomedicine (iBiMED) & Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Margarida Fardilha
- Institute of Biomedicine (iBiMED) & Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Maria Dimitriou Pavlaki
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Aveiro, Portugal.
| | - Susana Loureiro
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Aveiro, Portugal
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Martin R, Tate AT. Pleiotropy alleviates the fitness costs associated with resource allocation trade-offs in immune signaling networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561276. [PMID: 37873469 PMCID: PMC10592669 DOI: 10.1101/2023.10.06.561276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Many genes and signaling pathways within plant and animal taxa drive the expression of multiple organismal traits. This form of genetic pleiotropy instigates trade-offs among life-history traits if a mutation in the pleiotropic gene improves the fitness contribution of one trait at the expense of another. Whether or not pleiotropy gives rise to conflict among traits, however, likely depends on the resource costs and timing of trait deployment during organismal development. To investigate factors that could influence the evolutionary maintenance of pleiotropy in gene networks, we developed an agent-based model of co-evolution between parasites and hosts. Hosts comprise signaling networks that must faithfully complete a developmental program while also defending against parasites, and trait signaling networks could be independent or share a pleiotropic component as they evolved to improve host fitness. We found that hosts with independent developmental and immune networks were significantly more fit than hosts with pleiotropic networks when traits were deployed asynchronously during development. When host genotypes directly competed against each other, however, pleiotropic hosts were victorious regardless of trait synchrony because the pleiotropic networks were more robust to parasite manipulation, potentially explaining the abundance of pleiotropy in immune systems despite its contribution to life history trade-offs.
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Affiliation(s)
- Reese Martin
- Department of Biological Sciences, Vanderbilt University, Nashville TN, 37235
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Ann T Tate
- Department of Biological Sciences, Vanderbilt University, Nashville TN, 37235
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
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10
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Brown W, Wesalo J, Samanta S, Luo J, Caldwell SE, Tsang M, Deiters A. Genetically Encoded Aminocoumarin Lysine for Optical Control of Protein-Nucleotide Interactions in Zebrafish Embryos. ACS Chem Biol 2023; 18:1305-1314. [PMID: 37272594 PMCID: PMC10278064 DOI: 10.1021/acschembio.3c00028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/17/2023] [Indexed: 06/06/2023]
Abstract
The strategic placement of unnatural amino acids into the active site of kinases and phosphatases has allowed for the generation of photocaged signaling proteins that offer spatiotemporal control over activation of these pathways through precise light exposure. However, deploying this technology to study cell signaling in the context of embryo development has been limited. The promise of optical control is especially useful in the early stages of an embryo where development is driven by tightly orchestrated signaling events. Here, we demonstrate light-induced activation of Protein Kinase A and a RASopathy mutant of NRAS in the zebrafish embryo using a new light-activated amino acid. We applied this approach to gain insight into the roles of these proteins in gastrulation and heart development and forge a path for further investigation of RASopathy mutant proteins in animals.
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Affiliation(s)
- Wes Brown
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Joshua Wesalo
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Subhas Samanta
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ji Luo
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Steven E. Caldwell
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael Tsang
- Department
of Developmental Biology, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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11
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Ming H, Zhang M, Rajput S, Logsdon D, Zhu L, Schoolcraft WB, Krisher R, Jiang Z, Yuan Y. In Vitro Culture Alters Cell Lineage Composition and Cellular Metabolism of Bovine Blastocyst. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544379. [PMID: 37333292 PMCID: PMC10274902 DOI: 10.1101/2023.06.09.544379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Profiling transcriptome at single cell level of bovine blastocysts derived in vivo (IVV), in vitro from conventional culture medium (IVC), and reduced nutrient culture medium (IVR) has enabled us to reveal cell lineage segregation, during which forming inner cell mass (ICM), trophectoderm (TE), and an undefined population of transitional cells. Only IVV embryos had well-defined ICM, indicating in vitro culture may delay the first cell fate commitment to ICM. Differences between IVV, IVC and IVR embryos were mainly contributed by ICM and transitional cells. Pathway analysis by using the differentially expressed genes of these non-TE cells between groups pointed to highly active metabolic and biosynthetic processes, with reduced cellular signaling and membrane transport in IVC embryos, which may lead to reduced developmental potential. IVR embryos had lower activities in metabolic and biosynthetic processes, but increased cellular signaling and membrane transport, suggesting these cellular mechanisms may contribute to the improved blastocyst development compared to IVC embryos. However, the IVR embryos had compromised development when compared to IVV embryos with notably over-active membrane transport activities that led to impaired ion homeostasis.
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Affiliation(s)
- Hao Ming
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Mingxiang Zhang
- Colorado Center for Reproductive Medicine, Lone Tree, CO 80124, USA
| | - Sandeep Rajput
- Colorado Center for Reproductive Medicine, Lone Tree, CO 80124, USA
- Genus plc, 1525 River Rd, DeForest, WI 53532, USA
| | - Deirdre Logsdon
- Colorado Center for Reproductive Medicine, Lone Tree, CO 80124, USA
| | - Linkai Zhu
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | | | - Rebecca Krisher
- Colorado Center for Reproductive Medicine, Lone Tree, CO 80124, USA
- Genus plc, 1525 River Rd, DeForest, WI 53532, USA
| | - Zongliang Jiang
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Ye Yuan
- Colorado Center for Reproductive Medicine, Lone Tree, CO 80124, USA
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12
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Pereira F, Pereira A, Monteiro SM, Venâncio C, Félix L. Mitigation of nicotine-induced developmental effects by 24-epibrassinolide in zebrafish. Comp Biochem Physiol C Toxicol Pharmacol 2023; 266:109552. [PMID: 36682642 DOI: 10.1016/j.cbpc.2023.109552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/09/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023]
Abstract
Nicotine is a highly addictive substance that can cause teratogenic impacts in the embryo through redox-dependent pathways. As antioxidants, naturally occurring chemicals can protect cells from redox imbalance. The purpose of this study was to evaluate the effectiveness of 24-epibrassinolide (24-EPI), a natural brassinosteroid with well-known antioxidant properties, in protecting zebrafish embryos against nicotine's teratogenic effects. For 96 h, embryos (2 h post-fertilization - hpf) were exposed to 100 μM nicotine, co-exposed with 24-EPI (0.01, 0.1, and 1 μM), and 24-EPI alone (1 μM). Lethal and sublethal developmental characteristics were evaluated during exposure. Biochemical tests were performed at the conclusion of the exposure, and distinct behavioural paradigms were analysed 24 h later. Nicotine exposure resulted in a higher proportion of larvae with deformities, which were decreased following co-exposure to 24-EPI. Nicotine exposure also caused an increase in oxidative stress as observed by the increased activity of superoxide dismutase and catalase accompanied by an increase in the malondialdehyde levels. Besides, metabolic changes were noticed as observed by the increased lactate dehydrogenase activity that were hypothesised to be associated to nicotine-induced hypoxia which may be responsible for the increased oxidative damage. In addition, locomotor deficits were observed as well as a decrease in the acetylcholinesterase activity denoting nicotine-induced cognitive dysfunction. However, co-exposure to 24-EPI alleviated behavioural deficits and improved nicotine-induced emotional states. Overall, and although further studies are required to clarify these effects, 24-EPI showed promising ameliorative properties against the teratogenic effects induced by nicotine.
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Affiliation(s)
- Francisco Pereira
- Life Sciences and Environment School (ECVA), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Adriana Pereira
- Life Sciences and Environment School (ECVA), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Sandra M Monteiro
- Life Sciences and Environment School (ECVA), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), UTAD, Vila Real, Portugal; Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, Vila Real, Portugal
| | - Carlos Venâncio
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), UTAD, Vila Real, Portugal; Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, Vila Real, Portugal; Department of Animal Science, School of Agrarian and Veterinary Sciences (ECAV), UTAD, Vila Real, Portugal
| | - Luís Félix
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), UTAD, Vila Real, Portugal; Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, Vila Real, Portugal.
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13
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Kuyyamudi C, Menon SN, Sinha S. Precision of morphogen-driven tissue patterning during development is enhanced through contact-mediated cellular interactions. Phys Rev E 2023; 107:024407. [PMID: 36932610 DOI: 10.1103/physreve.107.024407] [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: 11/16/2021] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Cells in developing embryos reliably differentiate to attain location-specific fates, despite fluctuations in morphogen concentrations that provide positional information and in molecular processes that interpret it. We show that local contact-mediated cell-cell interactions utilize inherent asymmetry in the response of patterning genes to the global morphogen signal yielding a bimodal response. This results in robust developmental outcomes with a consistent identity for the dominant gene at each cell, substantially reducing the uncertainty in the location of boundaries between distinct fates.
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Affiliation(s)
- Chandrashekar Kuyyamudi
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
| | - Shakti N Menon
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
| | - Sitabhra Sinha
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
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14
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Vicioso-Mantis M, Balbás MAM. Spatial genome organization, TGFβ, and biomolecular condensates: Do they talk during development? Bioessays 2022; 44:e2200145. [PMID: 36253122 DOI: 10.1002/bies.202200145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 11/08/2022]
Abstract
Cis-regulatory elements govern gene expression programs to determine cell identity during development. Recently, the possibility that multiple enhancers are orchestrated in clusters of enhancers has been suggested. How these elements are arranged in the 3D space to control the activation of a specific promoter remains unclear. Our recent work revealed that the TGFβ pathway drives the assembly of enhancer clusters and precise gene activation during neurogenesis. We discovered that the TGFβ pathway coactivator JMJD3 was essential in maintaining these structures in the 3D space. To do that, JMJD3 required an intrinsically disordered region involved in forming phase-separated biomolecular condensates found in the enhancer clusters. Our data support the existence of a relationship between 3D-conformation of the chromatin, biomolecular condensates, and TGFβ-driven response during mammalian neurogenesis. In this review, we discuss how signaling (TGFβ), epigenetics (JMJD3), and biochemical properties (biomolecular condensates nucleation) are coordinated to modulate the genome structure to guarantee proper neural development. Moreover, we comment on the potential underlying mechanisms and implications of the enhancer-mediated regulation. Finally, we point out the knowledge gaps that still need to be addressed.
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Affiliation(s)
- Marta Vicioso-Mantis
- Department of Molecular Genomics. Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Marian A Martínez Balbás
- Department of Molecular Genomics. Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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15
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Pladevall-Morera D, Zylicz JJ. Chromatin as a sensor of metabolic changes during early development. Front Cell Dev Biol 2022; 10:1014498. [PMID: 36299478 PMCID: PMC9588933 DOI: 10.3389/fcell.2022.1014498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Cellular metabolism is a complex network of biochemical reactions fueling development with energy and biomass; however, it can also shape the cellular epigenome. Indeed, some intermediates of metabolic reactions exert a non-canonical function by acting as co-factors, substrates or inhibitors of chromatin modifying enzymes. Therefore, fluctuating availability of such molecules has the potential to regulate the epigenetic landscape. Thanks to this functional coupling, chromatin can act as a sensor of metabolic changes and thus impact cell fate. Growing evidence suggest that both metabolic and epigenetic reprogramming are crucial for ensuring a successful embryo development from the zygote until gastrulation. In this review, we provide an overview of the complex relationship between metabolism and epigenetics in regulating the early stages of mammalian embryo development. We report on recent breakthroughs in uncovering the non-canonical functions of metabolism especially when re-localized to the nucleus. In addition, we identify the challenges and outline future perspectives to advance the novel field of epi-metabolomics especially in the context of early development.
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Affiliation(s)
| | - Jan J. Zylicz
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
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16
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Baracaldo-Santamaría D, Corrales-Hernández MG, Ortiz-Vergara MC, Cormane-Alfaro V, Luque-Bernal RM, Calderon-Ospina CA, Cediel-Becerra JF. Connexins and Pannexins: Important Players in Neurodevelopment, Neurological Diseases, and Potential Therapeutics. Biomedicines 2022; 10:2237. [PMID: 36140338 PMCID: PMC9496069 DOI: 10.3390/biomedicines10092237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Cell-to-cell communication is essential for proper embryonic development and its dysfunction may lead to disease. Recent research has drawn attention to a new group of molecules called connexins (Cxs) and pannexins (Panxs). Cxs have been described for more than forty years as pivotal regulators of embryogenesis; however, the exact mechanism by which they provide this regulation has not been clearly elucidated. Consequently, Cxs and Panxs have been linked to congenital neurodegenerative diseases such as Charcot-Marie-Tooth disease and, more recently, chronic hemichannel opening has been associated with adult neurodegenerative diseases (e.g., Alzheimer's disease). Cell-to-cell communication via gap junctions formed by hexameric assemblies of Cxs, known as connexons, is believed to be a crucial component in developmental regulation. As for Panxs, despite being topologically similar to Cxs, they predominantly seem to form channels connecting the cytoplasm to the extracellular space and, despite recent research into Panx1 (Pannexin 1) expression in different regions of the brain during the embryonic phase, it has been studied to a lesser degree. When it comes to the nervous system, Cxs and Panxs play an important role in early stages of neuronal development with a wide span of action ranging from cellular migration during early stages to neuronal differentiation and system circuitry formation. In this review, we describe the most recent available evidence regarding the molecular and structural aspects of Cx and Panx channels, their role in neurodevelopment, congenital and adult neurological diseases, and finally propose how pharmacological modulation of these channels could modify the pathogenesis of some diseases.
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Affiliation(s)
- Daniela Baracaldo-Santamaría
- Pharmacology Unit, Department of Biomedical Sciences, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia
| | - María Gabriela Corrales-Hernández
- Pharmacology Unit, Department of Biomedical Sciences, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia
| | - Maria Camila Ortiz-Vergara
- Pharmacology Unit, Department of Biomedical Sciences, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia
| | - Valeria Cormane-Alfaro
- Pharmacology Unit, Department of Biomedical Sciences, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia
| | - Ricardo-Miguel Luque-Bernal
- Anatomy and Embriology Units, Department of Biomedical Sciences, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia
| | - Carlos-Alberto Calderon-Ospina
- Pharmacology Unit, Department of Biomedical Sciences, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia
- GENIUROS Research Group, Center for Research in Genetics and Genomics (CIGGUR), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia
| | - Juan-Fernando Cediel-Becerra
- Histology and Embryology Unit, Department of Biomedical Sciences, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia
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17
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Bilateral Feedback in Oscillator Model Is Required to Explain the Coupling Dynamics of Hes1 with the Cell Cycle. MATHEMATICS 2022. [DOI: 10.3390/math10132323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biological processes are governed by the expression of proteins, and for some proteins, their level of expression can fluctuate periodically over time (i.e., they oscillate). Many oscillatory proteins (e.g., cell cycle proteins and those from the HES family of transcription factors) are connected in complex ways, often within large networks. This complexity can be elucidated by developing intuitive mathematical models that describe the underlying critical aspects of the relationships between these processes. Here, we provide a mathematical explanation of a recently discovered biological phenomenon: the phasic position of the gene Hes1’s oscillatory expression at the beginning of the cell cycle of an individual human breast cancer stem cell can have a predictive value on how long that cell will take to complete a cell cycle. We use a two-component model of coupled oscillators to represent Hes1 and the cell cycle in the same cell with minimal assumptions. Inputting only the initial phase angles, we show that this model is capable of predicting the dynamic mitosis to mitosis behaviour of Hes1 and predicting cell cycle length patterns as found in real-world experimental data. Moreover, we discover that bidirectional coupling between Hes1 and the cell cycle is critical within the system for the data to be reproduced and that nonfixed asymmetry in the interactions between the oscillators is required. The phase dynamics we present here capture the complex interplay between Hes1 and the cell cycle, helping to explain nongenetic cell cycle variability, which has critical implications in cancer treatment contexts.
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18
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Abstract
Tight spatiotemporal control of cellular behavior and cell fate decisions is paramount to the formation of multicellular organisms during embryonic development. Intercellular communication via signaling pathways mediates this control. Interestingly, these signaling pathways are not static, but dynamic and change in activity over time. Signaling oscillations as a specific type of dynamics are found in various signaling pathways and model systems. Functions of oscillations include the regulation of periodic events or the transmission of information by encoding signals in the dynamic properties of a signaling pathway. For instance, signaling oscillations in neural or pancreatic progenitor cells modulate their proliferation and differentiation. Oscillations between neighboring cells can also be synchronized, leading to the emergence of waves traveling through the tissue. Such population-wide signaling oscillations regulate for example the consecutive segmentation of vertebrate embryos, a process called somitogenesis. Here, we outline our current understanding of signaling oscillations in embryonic development, how signaling oscillations are generated, how they are studied and how they contribute to the regulation of embryonic development.
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