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To K, Fei L, Pett JP, Roberts K, Blain R, Polański K, Li T, Yayon N, He P, Xu C, Cranley J, Moy M, Li R, Kanemaru K, Huang N, Megas S, Richardson L, Kapuge R, Perera S, Tuck E, Wilbrey-Clark A, Mulas I, Memi F, Cakir B, Predeus AV, Horsfall D, Murray S, Prete M, Mazin P, He X, Meyer KB, Haniffa M, Barker RA, Bayraktar O, Chédotal A, Buckley CD, Teichmann SA. A multi-omic atlas of human embryonic skeletal development. Nature 2024; 635:657-667. [PMID: 39567793 PMCID: PMC11578895 DOI: 10.1038/s41586-024-08189-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/09/2024] [Indexed: 11/22/2024]
Abstract
Human embryonic bone and joint formation is determined by coordinated differentiation of progenitors in the nascent skeleton. The cell states, epigenetic processes and key regulatory factors that underlie lineage commitment of these cells remain elusive. Here we applied paired transcriptional and epigenetic profiling of approximately 336,000 nucleus droplets and spatial transcriptomics to establish a multi-omic atlas of human embryonic joint and cranium development between 5 and 11 weeks after conception. Using combined modelling of transcriptional and epigenetic data, we characterized regionally distinct limb and cranial osteoprogenitor trajectories across the embryonic skeleton and further described regulatory networks that govern intramembranous and endochondral ossification. Spatial localization of cell clusters in our in situ sequencing data using a new tool, ISS-Patcher, revealed mechanisms of progenitor zonation during bone and joint formation. Through trajectory analysis, we predicted potential non-canonical cellular origins for human chondrocytes from Schwann cells. We also introduce SNP2Cell, a tool to link cell-type-specific regulatory networks to polygenic traits such as osteoarthritis. Using osteolineage trajectories characterized here, we simulated in silico perturbations of genes that cause monogenic craniosynostosis and implicate potential cell states and disease mechanisms. This work forms a detailed and dynamic regulatory atlas of bone and cartilage maturation and advances our fundamental understanding of cell-fate determination in human skeletal development.
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Affiliation(s)
- Ken To
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Lijiang Fei
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - J Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Raphael Blain
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Tong Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nadav Yayon
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - James Cranley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Madelyn Moy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ruoyan Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Stathis Megas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Cambridge Centre for AI in Medicine, Department of Applied Mathematics and Theoretical Physics, Cambridge, UK
| | | | - Rakesh Kapuge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Ilaria Mulas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fani Memi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Batuhan Cakir
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - David Horsfall
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Simon Murray
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Pavel Mazin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Xiaoling He
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Newcastle University, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Omer Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Alain Chédotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Institut de Pathologie, Groupe Hospitalier Est, Hospices Civils de Lyon, Lyon, France
- University Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, Lyon, France
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Centre for AI in Medicine, Department of Applied Mathematics and Theoretical Physics, Cambridge, UK.
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.
- CIFAR Macmillan Multi-scale Human Programme, CIFAR, Toronto, Canada.
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Pazzaglia UE, Reguzzoni M, Manconi R, Zecca PA, Zarattini G, Campagnolo M, Raspanti M. The combined cartilage growth - calcification patterns in the wing-fins of Rajidae (Chondrichthyes): A divergent model from endochondral ossification of tetrapods. Microsc Res Tech 2022; 85:3642-3652. [PMID: 36250446 DOI: 10.1002/jemt.24217] [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: 05/03/2022] [Revised: 07/08/2022] [Accepted: 07/21/2022] [Indexed: 01/07/2023]
Abstract
The relationship between cartilage growth - mineralization patterns were studied in adult Rajidae with X-ray morphology/morphometry, undecalcified resin-embedded, heat-deproteinated histology and scanning electron microscopy. Morphometry of the wing-fins, nine central rays of the youngest and oldest specimens documented a significant decrement of radials mean length between inner, middle and outer zones, but without a regular progression along the ray. This suggests that single radial length growth is regulated in such a way to align inter-radial joints parallel to the wing metapterygia curvature. Trans-illumination and heat-deproteination techniques showed polygonal and cylindrical morphotypes of tesserae, whose aligned pattern ranged from mono-columnar, bi-columnar, and multi-columnar up to the crustal-like layout. Histology of tessellated cartilage allowed to identify of zones of the incoming mineral deposition characterized by enhanced duplication rate of chondrocytes with the formation of isogenic groups, whose morphology and topography suggested a relationship with the impending formation of the radials calcified column. The morphotype and layout of radial tesserae were related to mechanical demands (stiffening) and the size/mass of the radial cartilage body. The cartilage calcification pattern of the batoids model shares several morphological features with tetrapods' endochondral ossification, that is, (chondrocytes' high duplication rate, alignment in rows, increased volume of chondrocyte lacunae), but without the typical geometry of the metaphyseal growth plates. RESEARCH HIGHLIGHTS: 1. The wing-fins system consists of stiff radials, mobile inter-radial joints and a flat inter-radial membrane adapted to the mechanical demand of wing wave movement. 2. Growth occurs by forming a mixed calcified-uncalcified cartilage texture, developing intrinsic tensional stresses documented by morphoanatomical data.
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Affiliation(s)
- Ugo E Pazzaglia
- DSMC, University of Brescia, Brescia, Italy.,DMC, University of Insubria, Varese, Italy
| | | | - Renata Manconi
- DVM (Zoology Lab), University of Sassari, Sassari, Italy
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Lu Y, Xu H, Jiang Y, Hu Z, Du R, Zhao X, Tian Y, Zhu Q, Zhang Y, Liu Y, Wang Y. Comprehensive analysis of differently expression mRNA and non-coding RNAs, and their regulatory mechanisms on relationship in thiram-induced tibial dyschondroplasia in chicken. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113924. [PMID: 35908532 DOI: 10.1016/j.ecoenv.2022.113924] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/10/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Thiram pollution is one of the main causes of tibial dyschondroplasia (TD) induced by feed sources. Several studies have speculated that miRNA, circRNA and lncRNA may have significant impact on the development of TD, however, the specific mRNAs and noncoding RNAs and their respective regulatory mechanisms and functions in the development of TD have not been explored. Therefore, in this present study, we screened the differentially expressed mRNA, miRNA, circRNA and lncRNA by whole-transcriptome sequencing (RNA-seq) and differentially expressed genes (DEGs) enrichment, as well as constructed the interaction network among the mRNA-miRNA, mRNA-lncRNA and mRNA-miRNA-circRNA. The sequencing results were verified by fluorescence real-time quantitative PCR (RT-qPCR). The results obtained in this study, revealed that the cells were atrophied and disordered in the TD group, and the expression of BMP6, TGF-β and VEGF were significantly reduced. A total of 141 mRNAs, 10 miRNAs, 23 lncRNAs and 35 circRNAs of DEGs were obtained (p<0.05) Theses DEGs were enriched in the adhere junction and insulin signaling pathways. In addition, the mRNA-miRNA-circRNA network suggested that several pivotal ceRNA showed a regulatory relationship between the transcripts with miRNA, circRNA or lncRNA. Taken together, the results in the present study, represent an insight for further functional research on the ceRNA regulatory mechanism of TD in broilers.
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Affiliation(s)
- Yuxiang Lu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Hengyong Xu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Yuru Jiang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Zhi Hu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Ranran Du
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Xiaoling Zhao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Yaofu Tian
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Qing Zhu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Yao Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Yiping Liu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Yan Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
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Jiang X, Li A, Wang Y, Iqbal M, Waqas M, Yang H, Li Z, Mehmood K, Qamar H, Li J. Ameliorative effect of naringin against thiram-induced tibial dyschondroplasia in broiler chicken. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:11337-11348. [PMID: 31960246 DOI: 10.1007/s11356-020-07732-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/12/2020] [Indexed: 06/10/2023]
Abstract
Tetramethyl thiuram disulfide (thiram) is widely used in agricultural production as an insecticide and fungicide, which can also lead to tibial dyschondroplasia (TD) in poultry. TD is characterized by leg disorders and growth performance retardation, and no targeted drugs have been found to treat TD until now. Therefore, the objective of the present study was to explore the ameliorative effect of traditional Chinese medicine naringin on thiram-induced TD chickens. A total of 180 one-day-old Arbor Acres (AA) broiler chickens were randomly divided into three equal groups (n = 60): control group (standard diet), thiram-induced group (thiram 50 mg/kg from day 3 to day 7), and naringin-treated group (naringin 30 mg/kg from day 8 to day 18). During the 18-day experiment, the growth performance, tibial bone parameters, antioxidant property of liver, serum biochemical changes and clinical symptoms were recorded to evaluate the protective effect of naringin in thiram-induced TD broiler chickens. Additionally, mRNA expressions and protein levels of Ihh and PTHrP genes were determined via quantitative real-time polymerase chain reaction and western blot. Administration of naringin showed significant results by alleviating lameness, increased growth performance, recuperated growth plate (GP) width, and improved functions and antioxidant enzyme level of liver in broilers affected by TD. Moreover, naringin treatment restored the development of damaged tibia bone via downregulating Ihh and upregulating PTHrP mRNA and protein expressions. In conclusion, our study determines naringin could be used as an effective medicine to treat TD.
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Affiliation(s)
- Xiong Jiang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Hubei Three Gorges Polytechnic, Yichang, 443000, Hubei province, People's Republic of China
| | - Aoyun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yaping Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Mudassar Iqbal
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- University College of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Muhammad Waqas
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Faculty of Veterinary & Animal Sciences, University of the Poonch, District Poonch, Rawalakot, Azad Jammu & Kashmir, 12350, Pakistan
| | - Hao Yang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Zhixing Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Khalid Mehmood
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- University College of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Hammad Qamar
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jiakui Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
- College of Animals Husbandry and Veterinary Medicine, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, Tibet, People's Republic of China.
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