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Lamandé SR, Ng ES, Cameron TL, Kung LHW, Sampurno L, Rowley L, Lilianty J, Patria YN, Stenta T, Hanssen E, Bell KM, Saxena R, Stok KS, Stanley EG, Elefanty AG, Bateman JF. Modeling human skeletal development using human pluripotent stem cells. Proc Natl Acad Sci U S A 2023; 120:e2211510120. [PMID: 37126720 PMCID: PMC10175848 DOI: 10.1073/pnas.2211510120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 04/04/2023] [Indexed: 05/03/2023] Open
Abstract
Chondrocytes and osteoblasts differentiated from induced pluripotent stem cells (iPSCs) will provide insights into skeletal development and genetic skeletal disorders and will generate cells for regenerative medicine applications. Here, we describe a method that directs iPSC-derived sclerotome to chondroprogenitors in 3D pellet culture then to articular chondrocytes or, alternatively, along the growth plate cartilage pathway to become hypertrophic chondrocytes that can transition to osteoblasts. Osteogenic organoids deposit and mineralize a collagen I extracellular matrix (ECM), mirroring in vivo endochondral bone formation. We have identified gene expression signatures at key developmental stages including chondrocyte maturation, hypertrophy, and transition to osteoblasts and show that this system can be used to model genetic cartilage and bone disorders.
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Affiliation(s)
- Shireen R. Lamandé
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Elizabeth S. Ng
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Trevor L. Cameron
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Louise H. W. Kung
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Lisa Sampurno
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Lynn Rowley
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Jinia Lilianty
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Yudha Nur Patria
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
- Department of Child Health, Universitas Gadjah Mada, Yogyakarta55281, Indonesia
| | - Tayla Stenta
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Eric Hanssen
- Ian Holmes Imaging Center and Department of Biochemistry and Pharmacology, Bio21 Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Katrina M. Bell
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Ritika Saxena
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Kathryn S. Stok
- Department of Biomedical Engineering, University of Melbourne, Parkville, VIC 3010, Australia
| | - Edouard G. Stanley
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Andrew G. Elefanty
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - John F. Bateman
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
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2
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Mack KL, Square TA, Zhao B, Miller CT, Fraser HB. Evolution of Spatial and Temporal cis-Regulatory Divergence in Sticklebacks. Mol Biol Evol 2023; 40:7048494. [PMID: 36805962 PMCID: PMC10015619 DOI: 10.1093/molbev/msad034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Cis-regulatory changes are thought to play a major role in adaptation. Threespine sticklebacks have repeatedly colonized freshwater habitats in the Northern Hemisphere, where they have evolved a suite of phenotypes that distinguish them from marine populations, including changes in physiology, behavior, and morphology. To understand the role of gene regulatory evolution in adaptive divergence, here we investigate cis-regulatory changes in gene expression between marine and freshwater ecotypes through allele-specific expression (ASE) in F1 hybrids. Surveying seven ecologically relevant tissues, including three sampled across two developmental stages, we identified cis-regulatory divergence affecting a third of genes, nearly half of which were tissue-specific. Next, we compared allele-specific expression in dental tissues at two timepoints to characterize cis-regulatory changes during development between marine and freshwater fish. Applying a genome-wide test for selection on cis-regulatory changes, we find evidence for lineage-specific selection on several processes between ecotypes, including the Wnt signaling pathway in dental tissues. Finally, we show that genes with ASE, particularly those that are tissue-specific, are strongly enriched in genomic regions of repeated marine-freshwater divergence, supporting an important role for these cis-regulatory differences in parallel adaptive evolution of sticklebacks to freshwater habitats. Altogether, our results provide insight into the cis-regulatory landscape of divergence between stickleback ecotypes across tissues and during development, and support a fundamental role for tissue-specific cis-regulatory changes in rapid adaptation to new environments.
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Affiliation(s)
- Katya L Mack
- Department of Biology, Stanford University, Stanford, CA
| | - Tyler A Square
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Bin Zhao
- Department of Biology, Stanford University, Stanford, CA
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
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3
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Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis. FISHES 2022. [DOI: 10.3390/fishes7030115] [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
Early development, when many important developmental events occur, is a critical period for fish. However, research on the early development of clearhead icefish is very limited, especially in molecular research. In this study, we aimed to explore the dynamic changes in the biological functions of five key periods in clearhead icefish early development, namely the YL (embryonic), PM (first day after hatching), KK (fourth day after hatching), LC (seventh day after hatching), and SL (tenth day after hatching) stages, through transcriptome sequencing and different analysis strategies. A trend expression analysis and an enrichment analysis revealed that the expression ofgenes encoding G protein-coupled receptors and their ligands, i.e., prss1_2_3, pomc, npy, npb, sst, rln3, crh, gh, and prl that are associated with digestion and feeding regulation gradually increased during early development. In addition, a weighted gene co-expression network analysis (WGCNA) showed that eleven modules were significantly associated with early development, among which nine modules were significantly positively correlated. Through the enrichment analysis and hub gene identification results of these nine modules, it was found that the pathways related to eye, bone, and heart development were significantly enriched in the YL stage, and the ccnd2, seh1l, kdm6a, arf4, and ankrd28 genes that are associated with cell proliferation and differentiation played important roles in these developmental processes; the pak3, dlx3, dgat2, and tas1r1 genes that are associated with jaw and tooth development, TG (triacylglycerol) synthesis, and umami amino acid receptors were identified as hub genes for the PM stage; the pathways associated with aerobic metabolism and unsaturated fatty acid synthesis were significantly enriched in the KK stage, with the foxk, slc13a2_3_5, ndufa5, and lsc2 genes playing important roles; the pathways related to visual perception were significantly enriched in the LC stage; and the bile acid biosynthetic and serine-type peptidase activity pathways were significantly enriched in the SL stage. These results provide a more detailed understanding of the processes of early development of clearhead icefish.
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Li K, Fan L, Tian Y, Lou S, Li D, Ma L, Wang L, Pan Y. Application of zebrafish in the study of craniomaxillofacial developmental anomalies. Birth Defects Res 2022; 114:583-595. [PMID: 35437950 DOI: 10.1002/bdr2.2014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/18/2022] [Accepted: 04/03/2022] [Indexed: 12/13/2022]
Abstract
Craniomaxillofacial developmental anomalies are one of the most prevalent congenital defects worldwide and could result from any disruption of normal development processes, which is generally influenced by interactions between genes and the environment. Currently, with the advances in genetic screening strategies, an increasing number of novel variants and their roles in orofacial diseases have been explored. Zebrafish is recognized as a powerful animal model, and its homologous genes and similar oral structure and development process provide an ideal platform for studying the contributions of genetic and environmental factors to human craniofacial malformations. Here, we reviewed zebrafish models for the study of craniomaxillofacial developmental anomalies, such as human nonsyndromic cleft lip with or without an affected palate and jaw and tooth developmental anomalies. Due to its potential for gene expression and regulation research, zebrafish may provide new perspectives for understanding craniomaxillofacial diseaseand its treatment.
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Affiliation(s)
- Kang Li
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Liwen Fan
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yu Tian
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Shu Lou
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Dandan Li
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Lan Ma
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Lin Wang
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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Wang B, Chen T, Wang A, Fang J, Wang J, Yao W, Wu Y. Anisodamine affects the pigmentation, mineral density, craniofacial area, and eye development in zebrafish embryos. J Appl Toxicol 2021; 42:1067-1077. [PMID: 34967033 DOI: 10.1002/jat.4278] [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: 11/05/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 11/11/2022]
Abstract
Anisodamine is one of the major components of the tropine alkaloid family and is widely used in the treatment of pain, motion sickness, pupil dilatation, and detoxification of organophosphorus poisoning. As a muscarinic receptor antagonist, the low toxicity and moderate drug effect of anisodamine often result in high doses for clinical use, making it important to fully investigate its toxicity. In this study, zebrafish embryos were exposed to 1.3-, 2.6-, and 5.2-mM anisodamine for 7 days to study the toxic effects of drug exposure on pigmentation, mineral density, craniofacial area, and eye development. The results showed that exposure to anisodamine at 1.3 mM resulted in cranial malformations and abnormal pigmentation in zebrafish embryos; 2.6- and 5.2-mM anisodamine resulted in significant eye development defects and reduced bone density in zebrafish embryos. The associated toxicities were correlated with functional development of neural crest cells through gene expression (col1a2, ddb1, dicer1, mab21l1, mab21l2, sox10, tyrp1b, and mitfa) in the dose of 5.2-mM exposed group. In conclusion, this study provides new evidence of the developmental toxicity of high doses of anisodamine in aqueous solutions to organisms and provides a warning for the safe use of this drug.
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Affiliation(s)
- Binjie Wang
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China
| | - Tianyi Chen
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China
| | - Anli Wang
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China.,National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing; Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiakai Fang
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China.,Thermo Fisher Scientific China Co Ltd, Hangzhou, Zhejiang, People's Republic of China
| | - Jiye Wang
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China
| | - Weixuan Yao
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China
| | - Yuanzhao Wu
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China
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