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Li Q, Jiang S, Lei K, Han H, Chen Y, Lin W, Xiong Q, Qi X, Gan X, Sheng R, Wang Y, Zhang Y, Ma J, Li T, Lin S, Zhou C, Chen D, Yuan Q. Metabolic rewiring during bone development underlies tRNA m7G-associated primordial dwarfism. J Clin Invest 2024; 134:e177220. [PMID: 39255038 PMCID: PMC11473147 DOI: 10.1172/jci177220] [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: 11/06/2023] [Accepted: 08/26/2024] [Indexed: 09/12/2024] Open
Abstract
Translation of mRNA to protein is tightly regulated by transfer RNAs (tRNAs), which are subject to various chemical modifications that maintain structure, stability, and function. Deficiency of tRNA N7-methylguanosine (m7G) modification in patients causes a type of primordial dwarfism, but the underlying mechanism remains unknown. Here we report that the loss of m7G rewires cellular metabolism, leading to the pathogenesis of primordial dwarfism. Conditional deletion of the catalytic enzyme Mettl1 or missense mutation of the scaffold protein Wdr4 severely impaired endochondral bone formation and bone mass accrual. Mechanistically, Mettl1 knockout decreased abundance of m7G-modified tRNAs and inhibited translation of mRNAs relating to cytoskeleton and Rho GTPase signaling. Meanwhile, Mettl1 knockout enhanced cellular energy metabolism despite incompetent proliferation and osteogenic commitment. Further exploration revealed that impairment of Rho GTPase signaling upregulated the level of branched-chain amino acid transaminase 1 (BCAT1) that rewired cell metabolism and restricted intracellular α-ketoglutarate (αKG). Supplementation of αKG ameliorated the skeletal defect of Mettl1-deficient mice. In addition to the selective translation of metabolism-related mRNAs, we further revealed that Mettl1 knockout globally regulated translation via integrated stress response (ISR) and mammalian target of rapamycin complex 1 (mTORC1) signaling. Restoring translation by targeting either ISR or mTORC1 aggravated bone defects of Mettl1-deficient mice. Overall, our study unveils a critical role of m7G tRNA modification in bone development by regulation of cellular metabolism and indicates suspension of translation initiation as a quality control mechanism in response to tRNA dysregulation.
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Affiliation(s)
- Qiwen Li
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shuang Jiang
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Kexin Lei
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Hui Han
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yaqian Chen
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Weimin Lin
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qiuchan Xiong
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xingying Qi
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xinyan Gan
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Rui Sheng
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuan Wang
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yarong Zhang
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jieyi Ma
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Tao Li
- West China–Washington Mitochondria and Metabolism Center and Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chenchen Zhou
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Demeng Chen
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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2
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Driscoll S, Merkuri F, Chain FJJ, Fish JL. Splicing is dynamically regulated during limb development. Sci Rep 2024; 14:19944. [PMID: 39198579 PMCID: PMC11358489 DOI: 10.1038/s41598-024-68608-z] [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: 03/18/2024] [Accepted: 07/25/2024] [Indexed: 09/01/2024] Open
Abstract
Modifications to highly conserved developmental gene regulatory networks are thought to underlie morphological diversification in evolution and contribute to human congenital malformations. Relationships between gene expression and morphology have been extensively investigated in the limb, where most of the evidence for alterations to gene regulation in development consists of pre-transcriptional mechanisms that affect expression levels, such as epigenetic alterations to regulatory sequences and changes to cis-regulatory elements. Here we report evidence that alternative splicing (AS), a post-transcriptional process that modifies and diversifies mRNA transcripts, is dynamic during limb development in two mammalian species. We evaluated AS patterns in mouse (Mus musculus) and opossum (Monodelphis domestica) across the three key limb developmental stages: the ridge, bud, and paddle. Our data show that splicing patterns are dynamic over developmental time and suggest differences between the two mammalian taxa. Additionally, multiple key limb development genes, including Fgf8, are differentially spliced across the three stages in both species, with expression levels of the conserved splice variants, Fgf8a and Fgf8b, changing across developmental time. Our data demonstrates that AS is a critical mediator of mRNA diversity in limb development and provides an additional mechanism for evolutionary tweaking of gene dosage.
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Affiliation(s)
- Sean Driscoll
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - Fjodor Merkuri
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA.
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA.
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3
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Yan Y, Zhu S, Jia M, Chen X, Qi W, Gu F, Valencak TG, Liu JX, Sun HZ. Advances in single-cell transcriptomics in animal research. J Anim Sci Biotechnol 2024; 15:102. [PMID: 39090689 PMCID: PMC11295521 DOI: 10.1186/s40104-024-01063-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 06/12/2024] [Indexed: 08/04/2024] Open
Abstract
Understanding biological mechanisms is fundamental for improving animal production and health to meet the growing demand for high-quality protein. As an emerging biotechnology, single-cell transcriptomics has been gradually applied in diverse aspects of animal research, offering an effective method to study the gene expression of high-throughput single cells of different tissues/organs in animals. In an unprecedented manner, researchers have identified cell types/subtypes and their marker genes, inferred cellular fate trajectories, and revealed cell‒cell interactions in animals using single-cell transcriptomics. In this paper, we introduce the development of single-cell technology and review the processes, advancements, and applications of single-cell transcriptomics in animal research. We summarize recent efforts using single-cell transcriptomics to obtain a more profound understanding of animal nutrition and health, reproductive performance, genetics, and disease models in different livestock species. Moreover, the practical experience accumulated based on a large number of cases is highlighted to provide a reference for determining key factors (e.g., sample size, cell clustering, and cell type annotation) in single-cell transcriptomics analysis. We also discuss the limitations and outlook of single-cell transcriptomics in the current stage. This paper describes the comprehensive progress of single-cell transcriptomics in animal research, offering novel insights and sustainable advancements in agricultural productivity and animal health.
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Affiliation(s)
- Yunan Yan
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Senlin Zhu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Minghui Jia
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xinyi Chen
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenlingli Qi
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fengfei Gu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Teresa G Valencak
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Agency for Health and Food Safety Austria, 1220, Vienna, Austria
| | - Jian-Xin Liu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Zeng Sun
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
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4
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Yuan G, Lin X, Liu Y, Greenblatt MB, Xu R. Skeletal stem cells in bone development, homeostasis, and disease. Protein Cell 2024; 15:559-574. [PMID: 38442300 PMCID: PMC11259547 DOI: 10.1093/procel/pwae008] [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: 12/18/2023] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
Tissue-resident stem cells are essential for development and repair, and in the skeleton, this function is fulfilled by recently identified skeletal stem cells (SSCs). However, recent work has identified that SSCs are not monolithic, with long bones, craniofacial sites, and the spine being formed by distinct stem cells. Recent studies have utilized techniques such as fluorescence-activated cell sorting, lineage tracing, and single-cell sequencing to investigate the involvement of SSCs in bone development, homeostasis, and disease. These investigations have allowed researchers to map the lineage commitment trajectory of SSCs in different parts of the body and at different time points. Furthermore, recent studies have shed light on the characteristics of SSCs in both physiological and pathological conditions. This review focuses on discussing the spatiotemporal distribution of SSCs and enhancing our understanding of the diversity and plasticity of SSCs by summarizing recent discoveries.
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Affiliation(s)
- Guixin Yuan
- The First Affiliated Hospital of Xiamen University-ICMRS Collaborating Center for Skeletal Stem Cell, State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, China
- Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Xixi Lin
- The First Affiliated Hospital of Xiamen University-ICMRS Collaborating Center for Skeletal Stem Cell, State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, China
- Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Ying Liu
- The First Affiliated Hospital of Xiamen University-ICMRS Collaborating Center for Skeletal Stem Cell, State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, China
- Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA
- Research Division, Hospital for Special Surgery, New York, NY 10065, USA
| | - Ren Xu
- The First Affiliated Hospital of Xiamen University-ICMRS Collaborating Center for Skeletal Stem Cell, State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, China
- Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute, School of Medicine, Xiamen University, Xiamen 361102, China
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5
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Zhang B, Zhang H. The human limb cell atlas: Charting uncharted territories and setting sail on the new voyage of limb development research. Sci Bull (Beijing) 2024:S2095-9273(24)00517-6. [PMID: 39084927 DOI: 10.1016/j.scib.2024.07.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Affiliation(s)
- Bao Zhang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Medical College of Jiaying University, Meizhou 514015, China
| | - Hongbo Zhang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; The SYSU-Perfect Diary Joint Skin Science Research Laboratory, Sun Yat-sen University, Guangzhou 510080, China.
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6
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Boutillon A, Banavar SP, Campàs O. Conserved physical mechanisms of cell and tissue elongation. Development 2024; 151:dev202687. [PMID: 38767601 PMCID: PMC11190436 DOI: 10.1242/dev.202687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Living organisms have the ability to self-shape into complex structures appropriate for their function. The genetic and molecular mechanisms that enable cells to do this have been extensively studied in several model and non-model organisms. In contrast, the physical mechanisms that shape cells and tissues have only recently started to emerge, in part thanks to new quantitative in vivo measurements of the physical quantities guiding morphogenesis. These data, combined with indirect inferences of physical characteristics, are starting to reveal similarities in the physical mechanisms underlying morphogenesis across different organisms. Here, we review how physics contributes to shape cells and tissues in a simple, yet ubiquitous, morphogenetic transformation: elongation. Drawing from observed similarities across species, we propose the existence of conserved physical mechanisms of morphogenesis.
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Affiliation(s)
- Arthur Boutillon
- Cluster of Excellence Physics of Life, TU Dresden, 01062 Dresden, Germany
| | - Samhita P. Banavar
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA
| | - Otger Campàs
- Cluster of Excellence Physics of Life, TU Dresden, 01062 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
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7
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Kwon HJ. Knockdown of vitamin D receptor affects early stages of pectoral fin development in zebrafish. Anat Histol Embryol 2024; 53:e13044. [PMID: 38695121 DOI: 10.1111/ahe.13044] [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: 01/25/2024] [Revised: 03/30/2024] [Accepted: 04/18/2024] [Indexed: 05/29/2024]
Abstract
The vitamin D receptor (VDR) signalling has been implicated in vertebrate limb or fin formation. However, the involvement of VDR signalling in the early stages of limb/fin development remains to be elucidated. In this study, the role of VDR signalling in pectoral fin development was investigated in zebrafish embryos. Knockdown of vdr induced the severe impairment of pectoral fin development. The zebrafish larvae lacking vdr exhibited reduced pectoral fins with no skeletal elements. In situ hybridization revealed depletion of vdr downregulated fibroblast growth factor 24 (fgf24), a marker of early pectoral fin bud mesenchyme, in the presumptive fin field even before fin buds were visible. Moreover, a perturbed expression pattern of bone morphogenetic protein 4 (bmp4), a marker of the pectoral fin fold, was observed in the developing fin buds of zebrafish embryos that lost the vdr function. These findings suggest that VDR signalling is crucial in the early stages of fin development, potentially influencing the process by regulating other signalling molecules such as Fgf24 and Bmp4.
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Affiliation(s)
- Hye-Joo Kwon
- University of Utah Asia Campus, Incheon, South Korea
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Jiang X, Zhao K, Sun Y, Song X, Yi C, Xiong T, Wang S, Yu Y, Chen X, Liu R, Yan X, Antos CL. The scale of zebrafish pectoral fin buds is determined by intercellular K+ levels and consequent Ca2+-mediated signaling via retinoic acid regulation of Rcan2 and Kcnk5b. PLoS Biol 2024; 22:e3002565. [PMID: 38527087 PMCID: PMC11018282 DOI: 10.1371/journal.pbio.3002565] [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: 07/21/2023] [Revised: 04/15/2024] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
K+ channels regulate morphogens to scale adult fins, but little is known about what regulates the channels and how they control morphogen expression. Using the zebrafish pectoral fin bud as a model for early vertebrate fin/limb development, we found that K+ channels also scale this anatomical structure, and we determined how one K+-leak channel, Kcnk5b, integrates into its developmental program. From FLIM measurements of a Förster Resonance Energy Transfer (FRET)-based K+ sensor, we observed coordinated decreases in intracellular K+ levels during bud growth, and overexpression of K+-leak channels in vivo coordinately increased bud proportions. Retinoic acid, which can enhance fin/limb bud growth, decreased K+ in bud tissues and up-regulated regulator of calcineurin (rcan2). rcan2 overexpression increased bud growth and decreased K+, while CRISPR-Cas9 targeting of rcan2 decreased growth and increased K+. We observed similar results in the adult caudal fins. Moreover, CRISPR targeting of Kcnk5b revealed that Rcan2-mediated growth was dependent on the Kcnk5b. We also found that Kcnk5b enhanced depolarization in fin bud cells via Na+ channels and that this enhanced depolarization was required for Kcnk5b-enhanced growth. Lastly, Kcnk5b-induced shha transcription and bud growth required IP3R-mediated Ca2+ release and CaMKK activity. Thus, we provide a mechanism for how retinoic acid via rcan2 can regulate K+-channel activity to scale a vertebrate appendage via intercellular Ca2+ signaling.
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Affiliation(s)
- Xiaowen Jiang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
| | - Kun Zhao
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
| | - Yi Sun
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
| | - Xinyue Song
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
| | - Chao Yi
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
| | - Tianlong Xiong
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
| | - Sen Wang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
| | - Yi Yu
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
- Center for Quantitative Biology, Peking University, Beijing, People’s Republic of China
| | - Xiduo Chen
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
| | - Run Liu
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
| | - Xin Yan
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
| | - Christopher L. Antos
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
- Institut für Pharmakologie und Toxikologie, Technische Universität Dresden, Dresden, Germany
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Ferguson CA, Firulli BA, Zoia M, Osterwalder M, Firulli AB. Identification and characterization of Hand2 upstream genomic enhancers active in developing stomach and limbs. Dev Dyn 2024; 253:215-232. [PMID: 37551791 PMCID: PMC11365009 DOI: 10.1002/dvdy.646] [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: 05/02/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND The bHLH transcription factor HAND2 plays important roles in the development of the embryonic heart, face, limbs, and sympathetic and enteric nervous systems. To define how and when HAND2 regulates these developmental systems, requires understanding the transcriptional regulation of Hand2. RESULTS Remarkably, Hand2 is flanked by an extensive upstream gene desert containing a potentially diverse enhancer landscape. Here, we screened the regulatory interval 200 kb proximal to Hand2 for putative enhancers using evolutionary conservation and histone marks in Hand2-expressing tissues. H3K27ac signatures across embryonic tissues pointed to only two putative enhancer regions showing deep sequence conservation. Assessment of the transcriptional enhancer potential of these elements using transgenic reporter lines uncovered distinct in vivo enhancer activities in embryonic stomach and limb mesenchyme, respectively. Activity of the identified stomach enhancer was restricted to the developing antrum and showed expression within the smooth muscle and enteric neurons. Surprisingly, the activity pattern of the limb enhancer did not overlap Hand2 mRNA but consistently yielded a defined subectodermal anterior expression pattern within multiple transgenic lines. CONCLUSIONS Together, these results start to uncover the diverse regulatory potential inherent to the Hand2 upstream regulatory interval.
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Affiliation(s)
- Chloe A. Ferguson
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN 46202-5225, USA
| | - Beth A. Firulli
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN 46202-5225, USA
| | - Matteo Zoia
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Marco Osterwalder
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Anthony B. Firulli
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN 46202-5225, USA
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Balachandran S, Prada-Medina CA, Mensah MA, Kakar N, Nagel I, Pozojevic J, Audain E, Hitz MP, Kircher M, Sreenivasan VKA, Spielmann M. STIGMA: Single-cell tissue-specific gene prioritization using machine learning. Am J Hum Genet 2024; 111:338-349. [PMID: 38228144 PMCID: PMC10870135 DOI: 10.1016/j.ajhg.2023.12.011] [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: 08/04/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 01/18/2024] Open
Abstract
Clinical exome and genome sequencing have revolutionized the understanding of human disease genetics. Yet many genes remain functionally uncharacterized, complicating the establishment of causal disease links for genetic variants. While several scoring methods have been devised to prioritize these candidate genes, these methods fall short of capturing the expression heterogeneity across cell subpopulations within tissues. Here, we introduce single-cell tissue-specific gene prioritization using machine learning (STIGMA), an approach that leverages single-cell RNA-seq (scRNA-seq) data to prioritize candidate genes associated with rare congenital diseases. STIGMA prioritizes genes by learning the temporal dynamics of gene expression across cell types during healthy organogenesis. To assess the efficacy of our framework, we applied STIGMA to mouse limb and human fetal heart scRNA-seq datasets. In a cohort of individuals with congenital limb malformation, STIGMA prioritized 469 variants in 345 genes, with UBA2 as a notable example. For congenital heart defects, we detected 34 genes harboring nonsynonymous de novo variants (nsDNVs) in two or more individuals from a set of 7,958 individuals, including the ortholog of Prdm1, which is associated with hypoplastic left ventricle and hypoplastic aortic arch. Overall, our findings demonstrate that STIGMA effectively prioritizes tissue-specific candidate genes by utilizing single-cell transcriptome data. The ability to capture the heterogeneity of gene expression across cell populations makes STIGMA a powerful tool for the discovery of disease-associated genes and facilitates the identification of causal variants underlying human genetic disorders.
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Affiliation(s)
- Saranya Balachandran
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Cesar A Prada-Medina
- Human Molecular Genetics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Martin A Mensah
- Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; BIH Charité Digital Clinician Scientist Program, BIH Biomedical Innovation Academy, Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Naseebullah Kakar
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany; Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Inga Nagel
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Jelena Pozojevic
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Enrique Audain
- Institute of Medical Genetics, Carl von Ossietzky University, 26129 Oldenburg, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck; Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, 24105 Kiel, Germany
| | - Marc-Phillip Hitz
- Institute of Medical Genetics, Carl von Ossietzky University, 26129 Oldenburg, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck; Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, 24105 Kiel, Germany
| | - Martin Kircher
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Varun K A Sreenivasan
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany.
| | - Malte Spielmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany; Human Molecular Genetics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck.
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11
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Nishizaka C, Fujiwara S, Mano H, Haga N. Difference between affected and unaffected sides of forearm bone length in children with congenital terminal transverse deficiencies at the level of carpal bone. J Pediatr Orthop B 2024; 33:76-82. [PMID: 36562436 PMCID: PMC10686272 DOI: 10.1097/bpb.0000000000001044] [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: 02/21/2022] [Accepted: 11/13/2022] [Indexed: 12/24/2022]
Abstract
The forearm of the affected sideis often shorter than that of the unaffected side in children with congenital terminal transverse deficiencies at the level of proximal or distal carpals. The aim of this study is to clarify the characteristics of forearm bone length in those children, especially to quantify the difference in forearm bone length between affected and unaffected sides. The subjects were children with carpal partial transverse deficiencies. The lengths of the radius and the ulna were measured in the radiographs. The lengths of affected and unaffected sides (A/U) were compared in order to quantify the discrepancy. The A/U ratio was defined as the length of the affected side divided by that of the unaffected side. The A/U ratios ranged from 77.1 to 99.0% in the radii and from 74.1 to 99.6% in the ulnae. In both the radius and ulna, the A/U ratios were significantly lower than the left/right ratios of normal adults. Additionally, the A/U ratios of the ulna were significantly lower than the A/U ratios of the radius. The forearm bones of affected side are significantly shorter than those of unaffected side. Although the cause remains unclear, it is possible that not only congenital factors but also acquired factors such as infrequent use of the affected upper limb are involved. A future longitudinal study is necessary to investigate whether length discrepancies can be reduced by using prostheses to increase the frequency of use on the affected limb.
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Affiliation(s)
- Chika Nishizaka
- Department of Rehabilitation Medicine, The University of Tokyo Hospital, Tokyo
| | - Sayaka Fujiwara
- Department of Rehabilitation Medicine, The University of Tokyo Hospital, Tokyo
| | - Hiroshi Mano
- Department of Rehabilitation Medicine, Shizuoka Children’s Hospital, Shizuoka
| | - Nobuhiko Haga
- Department of Rehabilitation Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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12
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Morishita Y, Lee SW, Suzuki T, Yokoyama H, Kamei Y, Tamura K, Kawasumi-Kita A. An archetype and scaling of developmental tissue dynamics across species. Nat Commun 2023; 14:8199. [PMID: 38081837 PMCID: PMC10713982 DOI: 10.1038/s41467-023-43902-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Morphometric studies have revealed the existence of simple geometric relationships among various animal shapes. However, we have little knowledge of the mathematical principles behind the morphogenetic dynamics that form the organ/body shapes of different species. Here, we address this issue by focusing on limb morphogenesis in Gallus gallus domesticus (chicken) and Xenopus laevis (African clawed frog). To compare the deformation dynamics between tissues with different sizes/shapes as well as their developmental rates, we introduce a species-specific rescaled spatial coordinate and a common clock necessary for cross-species synchronization of developmental times. We find that tissue dynamics are well conserved across species under this spacetime coordinate system, at least from the early stages of development through the phase when basic digit patterning is established. For this developmental period, we also reveal that the tissue dynamics of both species are mapped with each other through a time-variant linear transformation in real physical space, from which hypotheses on a species-independent archetype of tissue dynamics and morphogenetic scaling are proposed.
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Affiliation(s)
- Yoshihiro Morishita
- Laboratory for Developmental Morphogeometry, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan.
- Precursory Research for Embryonic Science and Technology (PRESTO) Program, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Sang-Woo Lee
- Laboratory for Developmental Morphogeometry, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
| | - Takayuki Suzuki
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, 558-8585, Japan
| | - Hitoshi Yokoyama
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, 036-8561, Japan
| | - Yasuhiro Kamei
- Optics and Bioimaging Facility, Trans-Scale Biology Center, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Koji Tamura
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Aiko Kawasumi-Kita
- Laboratory for Developmental Morphogeometry, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
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13
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Kohlsdorf T. Reversibility of digit loss revisited: Limb diversification in Bachia lizards (gymnophthalmidae). JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:496-508. [PMID: 33544406 DOI: 10.1002/jez.b.23024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 01/07/2023]
Abstract
Strict interpretations of the Dollo's Law lead to postulation that trait loss is irreversible and organisms never recover ancestral phenotypes. Dollo, however, admitted the possibility of reversals in trait loss when predicted differences between reversed (derived) and ancestral forms. Phenotypic signatures from reversals are expected, as the historical context of a reversal in trait loss differs from the initial setting where the trait originally evolved. This article combines morphological and molecular information for Bachia scolecoides to discuss phenotypic and genetic patterns established during processes that reversed digit loss in Gymnophthalmidae (also termed microteiid lizards). Results suggest that pathways leading to the derived tetradactyl state of B. scolecoides comprise particularities in their origin and associated processes. Autopodial bones of B. scolecoides lack digit identity, and muscle anatomy is very similar between manus and pes. Gymnophthalmidae sequence patterns in the limb-specific sonic hedgehog enhancer (ZRS) suggest that regulation of shh expression did not degenerate in Bachia, given the prediction of similar motifs despite mutations specific to Bachia. Persistence of developmental mechanisms might explain intermittent character expression leading to reversals of digit loss, as ZRS signaling pathways remain active during the development of at least one pair of appendices in Bachia, especially if some precursors persisted at early stages. Patterns of ZRS sequences suggest that irreversibility of trait loss might be lineage-specific (restricted to Gymnophthalmini) and contingent to the type of signature established. These results provide insights regarding possible mechanisms that may allow reactivation of developmental programs in specific regions of the embryo.
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Affiliation(s)
- Tiana Kohlsdorf
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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14
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Witzmann F, Fröbisch N. Morphology and ontogeny of carpus and tarsus in stereospondylomorph temnospondyls. PeerJ 2023; 11:e16182. [PMID: 37904842 PMCID: PMC10613440 DOI: 10.7717/peerj.16182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/05/2023] [Indexed: 11/01/2023] Open
Abstract
Skeletal development is well known in temnospondyls, the most diverse group of Paleozoic and Mesozoic amphibians. However, the elements of carpus and tarsus (i.e., the mesopodium) were always the last bones to ossify relative to the other limb bones and with regard to the rest of the skeleton, and are preserved only in rare cases. Thus, in contrast to the other parts of the limb skeleton, little is known about the ontogeny and sequence of ossification of the temnospondyl carpus and tarsus. We intended to close this gap by studying the ontogenies of a number of Permo/Carboniferous stereospondylomorphs, the only temnospondyls with preserved growth series in which the successive ossification of carpals and tarsals can be traced. Studying the degree of mesopodial ossification within the same species show that it is not necessarily correlated with body size. This indicates that individual age rather than size determined the degree of mesopodial ossification in stereospondylomorphs and that the largest individuals are not necessarily the oldest ones. In the stereospondylomorph tarsus, the distal tarsals show preaxial development in accordance with most early tetrapods and salamanders. However, the more proximal mesopodials exhibit postaxial dominance, i.e., the preaxial column (tibiale, centrale 1) consistently started to ossify after the central column (centralia 2-4, intermedium) and the postaxial column (fibulare). Likewise, we observed preaxial development of the distal carpals in the stereospondylomorph carpus, as in most early tetrapods for which a statement can be made. However, in contrast to the tarsus, the more proximal carpals were formed by preaxial development, i.e., the preaxial column (radiale, centrale 1) ossified after the central column (centralia 2-4, intermedium) and before the postaxial column (ulnare). This pattern is unique among known early tetrapods and occurs only in certain extant salamanders. Furthermore, ossification proceeded from distal to proximal in the central column of the stereospondylomorph carpus, whereas the ossification advanced from proximal to distal in the central column of the tarsus. Despite these differences, a general ossification pattern that started from proximolateral (intermedium or centrale 4) to mediodistal (distal tarsal and carpal 1) roughly in a diagonal line is common to all stereospondylomorph mesopodials investigated. This pattern might basically reflect the alignment of stress within the mesopodium during locomotion. Our observations might point to a greater variability in the development of the mesopodium in stereospondylomorphs and probably other early tetrapods than in most extant tetrapods, possibly mirroring a similar variation as seen in the early phases of skeletogenesis in salamander carpus and tarsus.
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Affiliation(s)
- Florian Witzmann
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Nadia Fröbisch
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- Department of Biology, Humboldt Universität Berlin, Berlin, Germany
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15
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Chen Y, Zhou T, Liao Z, Gao W, Wu J, Zhang S, Li Y, Liu H, Zhou H, Xu C, Su P. Hnrnpk is essential for embryonic limb bud development as a transcription activator and a collaborator of insulator protein Ctcf. Cell Death Differ 2023; 30:2293-2308. [PMID: 37608075 PMCID: PMC10589297 DOI: 10.1038/s41418-023-01207-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
Proper development of the limb bud relies on the concordance of various signals, but its molecular mechanisms have not yet been fully illustrated. Here we report that heterogeneous nuclear ribonucleoprotein K (hnRNPK) is essential for limb bud development. Its ablation in the limb bud results in limbless forelimbs and severe deformities of the hindlimbs. In terms of mechanism, hnRNPK functions as a transcription activator for the vital genes involved in the three regulatory axes of limb bud development. Simultaneously, for the first time we elucidate that hnRNPK binds to and coordinates with the insulator protein CCCTC binding factor (CTCF) to maintain a three-dimensional chromatin architecture. Ablation of hnRNPK weakens the binding strength of CTCF to topologically associating domain (TAD) boundaries, then leading to the loose TADs, and decreased interactions between promoters and enhancers, and further decreased transcription of developmental genes. Our study establishes a fundamental and novel role of hnRNPK in regulating limb bud development.
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Affiliation(s)
- Yuyu Chen
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Taifeng Zhou
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Zhiheng Liao
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Wenjie Gao
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
| | - Jinna Wu
- Department of Breast Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Shun Zhang
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Yongyong Li
- Precision Medicine Institute, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Hengyu Liu
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Hang Zhou
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
| | - Caixia Xu
- Research Center for Translational Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
| | - Peiqiang Su
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
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16
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Li J, Zuo J, Lv X, Ma J, Li X, Fu S, Sun J. Hedgehog signaling is essential in the regulation of limb regeneration in the Chinese mitten crab, Eriocheir sinensis. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108981. [PMID: 37543149 DOI: 10.1016/j.fsi.2023.108981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/04/2023] [Accepted: 07/31/2023] [Indexed: 08/07/2023]
Abstract
Tissue autotomy is a unique adaptive response to environmental stress, followed by regeneration process compensating for the loss of body parts. The crustaceans present remarkable activity of appendage autotomy and regeneration, however, the molecular mechanism is still unclear. In this study, the Eriocheir sinensis Hedgehog (EsHH) and Smoothened (EsSMO) were identified in the regenerative limbs, and the function of Hedgehog signaling pathway on limb regeneration was evaluated. At the blastema growth stage of limb regeneration, the expression of EsHH and EsSMO was up-regulated in response to limb autotomy stress, and down-regulated at blastema differentiation stage. To clarify the effect of Hedgehog pathway during limb regeneration, the regenerative efficiency was evaluated with Smoothened inhibitor cyclopamine or RNAi (ds-HH) injection. We observed that the regenerative efficiency was significantly repressed with blockage of Hedgehog pathway at both the basal growth stage and the proecdysial growth stage, which was indicated by the delay of wound healing and blastema growth, as well as a decrease in the size of newly formed limbs. In addition, gene expression and BrdU incorporation assay showed that the proliferation and myogenic differentiation of blastema cells were suppressed with either cyclopamine or ds-HH injection. Thus, these results suggest that Hedgehog signaling pathway is essential for the establishment of limb regeneration in E. sinensis through promoting the proliferation and myogenic differentiation of blastema cells.
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Affiliation(s)
- Ju Li
- College of Life Science, Tianjin Normal University, Tianjin, 300387, China; Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, PR China.
| | - Jinmei Zuo
- College of Life Science, Tianjin Normal University, Tianjin, 300387, China
| | - Xiaoyan Lv
- College of Life Science, Tianjin Normal University, Tianjin, 300387, China
| | - Jiahe Ma
- College of Life Science, Tianjin Normal University, Tianjin, 300387, China
| | - Xiaohong Li
- College of Life Science, Tianjin Normal University, Tianjin, 300387, China
| | - Simiao Fu
- College of Life Science, Tianjin Normal University, Tianjin, 300387, China
| | - Jinsheng Sun
- College of Life Science, Tianjin Normal University, Tianjin, 300387, China; Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, PR China.
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17
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Young JJ. In preprints: of genitalia and six-legged mice. Development 2023; 150:dev202264. [PMID: 37647032 DOI: 10.1242/dev.202264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Affiliation(s)
- John J Young
- Simmons University, 300 The Fenway, Boston, MA 02115, USA
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18
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Loder S, Patel N, Morgani S, Sambon M, Leucht P, Levi B. Genetic models for lineage tracing in musculoskeletal development, injury, and healing. Bone 2023; 173:116777. [PMID: 37156345 PMCID: PMC10860167 DOI: 10.1016/j.bone.2023.116777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/07/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023]
Abstract
Musculoskeletal development and later post-natal homeostasis are highly dynamic processes, marked by rapid structural and functional changes across very short periods of time. Adult anatomy and physiology are derived from pre-existing cellular and biochemical states. Consequently, these early developmental states guide and predict the future of the system as a whole. Tools have been developed to mark, trace, and follow specific cells and their progeny either from one developmental state to the next or between circumstances of health and disease. There are now many such technologies alongside a library of molecular markers which may be utilized in conjunction to allow for precise development of unique cell 'lineages'. In this review, we first describe the development of the musculoskeletal system beginning as an embryonic germ layer and at each of the key developmental stages that follow. We then discuss these structures in the context of adult tissues during homeostasis, injury, and repair. Special focus is given in each of these sections to the key genes involved which may serve as markers of lineage or later in post-natal tissues. We then finish with a technical assessment of lineage tracing and the techniques and technologies currently used to mark cells, tissues, and structures within the musculoskeletal system.
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Affiliation(s)
- Shawn Loder
- Department of Plastic Surgery, University of Pittsburgh, Scaife Hall, Suite 6B, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Nicole Patel
- Center for Organogenesis and Trauma, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | | | | | - Benjamin Levi
- Center for Organogenesis and Trauma, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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19
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Armendariz DA, Sundarrajan A, Hon GC. Breaking enhancers to gain insights into developmental defects. eLife 2023; 12:e88187. [PMID: 37497775 PMCID: PMC10374278 DOI: 10.7554/elife.88187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Despite ground-breaking genetic studies that have identified thousands of risk variants for developmental diseases, how these variants lead to molecular and cellular phenotypes remains a gap in knowledge. Many of these variants are non-coding and occur at enhancers, which orchestrate key regulatory programs during development. The prevailing paradigm is that non-coding variants alter the activity of enhancers, impacting gene expression programs, and ultimately contributing to disease risk. A key obstacle to progress is the systematic functional characterization of non-coding variants at scale, especially since enhancer activity is highly specific to cell type and developmental stage. Here, we review the foundational studies of enhancers in developmental disease and current genomic approaches to functionally characterize developmental enhancers and their variants at scale. In the coming decade, we anticipate systematic enhancer perturbation studies to link non-coding variants to molecular mechanisms, changes in cell state, and disease phenotypes.
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Affiliation(s)
- Daniel A Armendariz
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States
| | - Anjana Sundarrajan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
- Lyda Hill Department of Bioinformatics, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States
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20
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Marín-Llera JC, García-García D, Garay-Pacheco E, Adrian Cortes-Morales V, Montesinos-Montesinos JJ, Chimal-Monroy J. Commitment of human mesenchymal stromal cells to skeletal lineages is independent of their morphogenetic capacity. World J Stem Cells 2023; 15:701-712. [PMID: 37545756 PMCID: PMC10401422 DOI: 10.4252/wjsc.v15.i7.701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/18/2023] [Accepted: 06/25/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Mesenchymal stromal cells (MSCs) are multipotent cell populations obtained from fetal and adult tissues. They share some characteristics with limb bud mesodermal cells such as differentiation potential into osteogenic, chondrogenic, and tenogenic lineages and an embryonic mesodermal origin. Although MSCs differentiate into skeletal-related lineages in vitro, they have not been shown to self-organize into complex skeletal structures or connective tissues, as in the limb. In this work, we demonstrate that the expression of molecular markers to commit MSCs to skeletal lineages is not sufficient to generate skeletal elements in vivo.
AIM To evaluate the potential of MSCs to differentiate into skeletal lineages and generate complex skeletal structures using the recombinant limb (RL) system.
METHODS We used the experimental system of RLs from dissociated-reaggregated human placenta (PL) and umbilical cord blood (UCB) MSCs. After being harvested and reaggregated in a pellet, cultured cells were introduced into an ectodermal cover obtained from an early chicken limb bud. Next, this filled ectoderm was grafted into the back of a donor chick embryo. Under these conditions, the cells received and responded to the ectoderm’s embryonic signals in a spatiotemporal manner to differentiate and pattern into skeletal elements. Their response to differentiation and morphogenetic signals was evaluated by quantitative polymerase chain reaction, histology, immunofluorescence, scanning electron microscopy, and in situ hybridization.
RESULTS We found that human PL-MSCs and UCB-MSCs constituting the RLs expressed chondrogenic, osteogenic, and tenogenic molecular markers while differentially committing into limb lineages but could not generate complex structures in vivo. MSCs-RL from PL or UCB were committed early to chondrogenic lineage. Nevertheless, the UCB-RL osteogenic commitment was favored, although preferentially to a tenogenic cell fate. These findings suggest that the commitment of MSCs to differentiate into skeletal lineages differs according to the source and is independent of their capacity to generate skeletal elements or connective tissue in vivo. Our results suggest that the failure to form skeletal structures may be due to the intrinsic characteristics of MSCs. Thus, it is necessary to thoroughly evaluate the biological aspects of MSCs and how they respond to morphogenetic signals in an in vivo context.
CONCLUSION PL-MSCs and UCB-MSCs express molecular markers of differentiation into skeletal lineages, but they are not sufficient to generate complex skeletal structures in vivo.
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Affiliation(s)
- Jessica Cristina Marín-Llera
- Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Coyoacan 04510, Mexico
| | - Damián García-García
- Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Coyoacan 04510, Mexico
| | - Estefania Garay-Pacheco
- Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Coyoacan 04510, Mexico
| | - Victor Adrian Cortes-Morales
- Laboratorio de Células Troncales Mesenquimales, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico
| | - Juan Jose Montesinos-Montesinos
- Laboratorio de Células Troncales Mesenquimales, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico
| | - Jesus Chimal-Monroy
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Coyoacan 04510, Mexico
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21
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Luxey M, Stieger G, Berki B, Tschopp P. Distinct patterning responses of wing and leg neuromuscular systems to different preaxial polydactylies. Front Cell Dev Biol 2023; 11:1154205. [PMID: 37215090 PMCID: PMC10192688 DOI: 10.3389/fcell.2023.1154205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
The tetrapod limb has long served as a paradigm to study vertebrate pattern formation and evolutionary diversification. The distal part of the limb, the so-called autopod, is of particular interest in this regard, given the numerous modifications in both its morphology and behavioral motor output. While the underlying alterations in skeletal form have received considerable attention, much less is known about the accompanying changes in the neuromuscular system. However, modifications in the skeleton need to be properly integrated with both muscle and nerve patterns, to result in a fully functional limb. This task is further complicated by the distinct embryonic origins of the three main tissue types involved-skeleton, muscles and nerves-and, accordingly, how they are patterned and connected with one another during development. To evaluate the degree of regulative crosstalk in this complex limb patterning process, here we analyze the developing limb neuromuscular system of Silkie breed chicken. These animals display a preaxial polydactyly, due to a polymorphism in the limb regulatory region of the Sonic Hedgehog gene. Using lightsheet microscopy and 3D-reconstructions, we investigate the neuromuscular patterns of extra digits in Silkie wings and legs, and compare our results to Retinoic Acid-induced polydactylies. Contrary to previous findings, Silkie autopod muscle patterns do not adjust to alterations in the underlying skeletal topology, while nerves show partial responsiveness. We discuss the implications of tissue-specific sensitivities to global limb patterning cues for our understanding of the evolution of novel forms and functions in the distal tetrapod limb.
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Affiliation(s)
- Maëva Luxey
- *Correspondence: Maëva Luxey, ; Patrick Tschopp,
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22
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Feigin CY, Moreno JA, Ramos R, Mereby SA, Alivisatos A, Wang W, van Amerongen R, Camacho J, Rasweiler JJ, Behringer RR, Ostrow B, Plikus MV, Mallarino R. Convergent deployment of ancestral functions during the evolution of mammalian flight membranes. SCIENCE ADVANCES 2023; 9:eade7511. [PMID: 36961889 PMCID: PMC10038344 DOI: 10.1126/sciadv.ade7511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/21/2023] [Indexed: 05/20/2023]
Abstract
Lateral flight membranes, or patagia, have evolved repeatedly in diverse mammalian lineages. While little is known about patagium development, its recurrent evolution may suggest a shared molecular basis. By combining transcriptomics, developmental experiments, and mouse transgenics, we demonstrate that lateral Wnt5a expression in the marsupial sugar glider (Petaurus breviceps) promotes the differentiation of its patagium primordium. We further show that this function of Wnt5a reprises ancestral roles in skin morphogenesis predating mammalian flight and has been convergently used during patagium evolution in eutherian bats. Moreover, we find that many genes involved in limb development have been redeployed during patagium outgrowth in both the sugar glider and bat. Together, our findings reveal that deeply conserved genetic toolkits contribute to the evolutionary transition to flight in mammals.
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Affiliation(s)
- Charles Y. Feigin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jorge A. Moreno
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Raul Ramos
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA
| | - Sarah A. Mereby
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ares Alivisatos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Wei Wang
- Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, USA
| | - Renée van Amerongen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Jasmin Camacho
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - John J. Rasweiler
- Department of Obstetrics and Gynecology, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Richard R. Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bruce Ostrow
- Department of Biology, Grand Valley State University, Allendale, MI 49401, USA
| | - Maksim V. Plikus
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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23
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Markman S, Zada M, David E, Giladi A, Amit I, Zelzer E. A single-cell census of mouse limb development identifies complex spatiotemporal dynamics of skeleton formation. Dev Cell 2023; 58:565-581.e4. [PMID: 36931270 DOI: 10.1016/j.devcel.2023.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 10/20/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023]
Abstract
Limb development has long served as a model system for coordinated spatial patterning of progenitor cells. Here, we identify a population of naive limb progenitors and show that they differentiate progressively to form the skeleton in a complex, non-consecutive, three-dimensional pattern. Single-cell RNA sequencing of the developing mouse forelimb identified three progenitor states: naive, proximal, and autopodial, as well as Msx1 as a marker for the naive progenitors. In vivo lineage tracing confirmed this role and localized the naive progenitors to the outer margin of the limb, along the anterior-posterior axis. Sequential pulse-chase experiments showed that the progressive transition of Msx1+ naive progenitors into proximal and autopodial progenitors coincides with their differentiation to Sox9+ chondroprogenitors, which occurs along all the forming skeletal segments. Indeed, tracking the spatiotemporal sequence of differentiation showed that the skeleton forms progressively in a complex pattern. These findings suggest an alternative model for limb skeleton development.
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Affiliation(s)
- Svetlana Markman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mor Zada
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Elazar Zelzer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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24
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Anand GM, Megale HC, Murphy SH, Weis T, Lin Z, He Y, Wang X, Liu J, Ramanathan S. Controlling organoid symmetry breaking uncovers an excitable system underlying human axial elongation. Cell 2023; 186:497-512.e23. [PMID: 36657443 PMCID: PMC10122509 DOI: 10.1016/j.cell.2022.12.043] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/28/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023]
Abstract
The human embryo breaks symmetry to form the anterior-posterior axis of the body. As the embryo elongates along this axis, progenitors in the tail bud give rise to tissues that generate spinal cord, skeleton, and musculature. This raises the question of how the embryo achieves axial elongation and patterning. While ethics necessitate in vitro studies, the variability of organoid systems has hindered mechanistic insights. Here, we developed a bioengineering and machine learning framework that optimizes organoid symmetry breaking by tuning their spatial coupling. This framework enabled reproducible generation of axially elongating organoids, each possessing a tail bud and neural tube. We discovered that an excitable system composed of WNT/FGF signaling drives elongation by inducing a neuromesodermal progenitor-like signaling center. We discovered that instabilities in the excitable system are suppressed by secreted WNT inhibitors. Absence of these inhibitors led to ectopic tail buds and branches. Our results identify mechanisms governing stable human axial elongation.
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Affiliation(s)
- Giridhar M Anand
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Heitor C Megale
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sean H Murphy
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Theresa Weis
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Zuwan Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Yichun He
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Xiao Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Jia Liu
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Sharad Ramanathan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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25
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Murphy P, Rolfe RA. Building a Co-ordinated Musculoskeletal System: The Plasticity of the Developing Skeleton in Response to Muscle Contractions. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2023; 236:81-110. [PMID: 37955772 DOI: 10.1007/978-3-031-38215-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The skeletal musculature and the cartilage, bone and other connective tissues of the skeleton are intimately co-ordinated. The shape, size and structure of each bone in the body is sculpted through dynamic physical stimuli generated by muscle contraction, from early development, with onset of the first embryo movements, and through repair and remodelling in later life. The importance of muscle movement during development is shown by congenital abnormalities where infants that experience reduced movement in the uterus present a sequence of skeletal issues including temporary brittle bones and joint dysplasia. A variety of animal models, utilising different immobilisation scenarios, have demonstrated the precise timing and events that are dependent on mechanical stimulation from movement. This chapter lays out the evidence for skeletal system dependence on muscle movement, gleaned largely from mouse and chick immobilised embryos, showing the many aspects of skeletal development affected. Effects are seen in joint development, ossification, the size and shape of skeletal rudiments and tendons, including compromised mechanical function. The enormous plasticity of the skeletal system in response to muscle contraction is a key factor in building a responsive, functional system. Insights from this work have implications for our understanding of morphological evolution, particularly the challenging concept of emergence of new structures. It is also providing insight for the potential of physical therapy for infants suffering the effects of reduced uterine movement and is enhancing our understanding of the cellular and molecular mechanisms involved in skeletal tissue differentiation, with potential for informing regenerative therapies.
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Affiliation(s)
- Paula Murphy
- School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
| | - Rebecca A Rolfe
- School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
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26
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DiFrisco J, Love AC, Wagner GP. The hierarchical basis of serial homology and evolutionary novelty. J Morphol 2023; 284:e21531. [PMID: 36317664 DOI: 10.1002/jmor.21531] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/26/2022] [Accepted: 10/29/2022] [Indexed: 11/05/2022]
Abstract
Given the pervasiveness of gene sharing in evolution and the extent of homology across the tree of life, why is everything not homologous with everything else? The continuity and overlapping genetic contributions to diverse traits across lineages seem to imply that no discrete determination of homology is possible. Although some argue that the widespread overlap in parts and processes should be acknowledged as "partial" homology, this threatens a broad base of presumed comparative morphological knowledge accepted by most biologists. Following a long scientific tradition, we advocate a strategy of "theoretical articulation" that introduces further distinctions to existing concepts to produce increased contrastive resolution among the labels used to represent biological phenomena. We pursue this strategy by drawing on successful patterns of reasoning from serial homology at the level of gene sequences to generate an enriched characterization of serial homology as a hierarchical, phylogenetic concept. Specifically, we propose that the concept of serial homology should be applied primarily to repeated but developmentally individualized body parts, such as cell types, differentiated body segments, or epidermal appendages. For these characters, a phylogenetic history can be reconstructed, similar to families of paralogous genes, endowing the notion of serial homology with a hierarchical, phylogenetic interpretation. On this basis, we propose a five-fold theoretical classification that permits a more fine-grained mapping of diverse trait-types. This facilitates answering the question of why everything is not homologous with everything else, as well as how novelty is possible given that any new character possesses evolutionary precursors. We illustrate the fecundity of our account by reference to debates over insect wing serial homologs and vertebrate paired appendages.
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Affiliation(s)
| | - Alan C Love
- Department of Philosophy, University of Minnesota, Minneapolis, Minnesota, USA.,Minnesota Center for Philosophy of Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,Yale Systems Biology Institute, Yale University, New Haven, Connecticut, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Medical School, New Haven, Connecticut, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA
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27
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Kaucka M, Joven Araus A, Tesarova M, Currie JD, Boström J, Kavkova M, Petersen J, Yao Z, Bouchnita A, Hellander A, Zikmund T, Elewa A, Newton PT, Fei JF, Chagin AS, Fried K, Tanaka EM, Kaiser J, Simon A, Adameyko I. Altered developmental programs and oriented cell divisions lead to bulky bones during salamander limb regeneration. Nat Commun 2022; 13:6949. [PMID: 36376278 PMCID: PMC9663504 DOI: 10.1038/s41467-022-34266-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
There are major differences in duration and scale at which limb development and regeneration proceed, raising the question to what extent regeneration is a recapitulation of development. We address this by analyzing skeletal elements using a combination of micro-CT imaging, molecular profiling and clonal cell tracing. We find that, in contrast to development, regenerative skeletal growth is accomplished based entirely on cartilage expansion prior to ossification, not limiting the transversal cartilage expansion and resulting in bulkier skeletal parts. The oriented extension of salamander cartilage and bone appear similar to the development of basicranial synchondroses in mammals, as we found no evidence for cartilage stem cell niches or growth plate-like structures during neither development nor regeneration. Both regenerative and developmental ossification in salamanders start from the cortical bone and proceeds inwards, showing the diversity of schemes for the synchrony of cortical and endochondral ossification among vertebrates.
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Affiliation(s)
- Marketa Kaucka
- Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
| | - Alberto Joven Araus
- Department of Cell and Molecular Biology, Biomedicum, Karolinska Institute, Stockholm, 17165, Sweden
| | - Marketa Tesarova
- Central European Institute of Technology, Brno University of Technology, Brno, 61200, Czech Republic
| | - Joshua D Currie
- Department of Biology, Wake Forest University, Winston-Salem, NC, USA
| | - Johan Boström
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, 1090, Austria
| | - Michaela Kavkova
- Central European Institute of Technology, Brno University of Technology, Brno, 61200, Czech Republic
| | - Julian Petersen
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, 1090, Austria
- Department of Orthodontics, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Zeyu Yao
- Department of Cell and Molecular Biology, Biomedicum, Karolinska Institute, Stockholm, 17165, Sweden
| | - Anass Bouchnita
- Department of Information Technology, Uppsala University, Uppsala, Sweden
- Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX, 79902, USA
| | - Andreas Hellander
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Tomas Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, 61200, Czech Republic
| | - Ahmed Elewa
- Department of Cell and Molecular Biology, Biomedicum, Karolinska Institute, Stockholm, 17165, Sweden
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Phillip T Newton
- Department of Women's and Children's Health, Karolinska Institute, Solna, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Solna, Sweden
| | - Ji-Feng Fei
- The Research Institute of Molecular Pathology (IMP), Vienna, 1030, Austria
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Andrei S Chagin
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, 17165, Sweden
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Göteborg, 41346, Sweden
| | - Kaj Fried
- Department of Neuroscience, Biomedicum, Karolinska Institute, Stockholm, 17165, Sweden
| | - Elly M Tanaka
- The Research Institute of Molecular Pathology (IMP), Vienna, 1030, Austria
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, 61200, Czech Republic
| | - András Simon
- Department of Cell and Molecular Biology, Biomedicum, Karolinska Institute, Stockholm, 17165, Sweden.
| | - Igor Adameyko
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, 1090, Austria.
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, 17165, Sweden.
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28
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Abstract
The tissue-resident skeletal stem cells (SSCs), which are self-renewal and multipotent, continuously provide cells (including chondrocytes, bone cells, marrow adipocytes, and stromal cells) for the development and homeostasis of the skeletal system. In recent decade, utilizing fluorescence-activated cell sorting, lineage tracing, and single-cell sequencing, studies have identified various types of SSCs, plotted the lineage commitment trajectory, and partially revealed their properties under physiological and pathological conditions. In this review, we retrospect to SSCs identification and functional studies. We discuss the principles and approaches to identify bona fide SSCs, highlighting pioneering findings that plot the lineage atlas of SSCs. The roles of SSCs and progenitors in long bone, craniofacial tissues, and periosteum are systematically discussed. We further focus on disputes and challenges in SSC research.
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29
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Duan R, Hijazi H, Gulec EY, Eker HK, Costa SR, Sahin Y, Ocak Z, Isikay S, Ozalp O, Bozdogan S, Aslan H, Elcioglu N, Bertola DR, Gezdirici A, Du H, Fatih JM, Grochowski CM, Akay G, Jhangiani SN, Karaca E, Gu S, Coban-Akdemir Z, Posey JE, Bayram Y, Sutton VR, Carvalho CM, Pehlivan D, Gibbs RA, Lupski JR. Developmental genomics of limb malformations: Allelic series in association with gene dosage effects contribute to the clinical variability. HGG ADVANCES 2022; 3:100132. [PMID: 36035248 PMCID: PMC9403727 DOI: 10.1016/j.xhgg.2022.100132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022] Open
Abstract
Genetic heterogeneity, reduced penetrance, and variable expressivity, the latter including asymmetric body axis plane presentations, have all been described in families with congenital limb malformations (CLMs). Interfamilial and intrafamilial heterogeneity highlight the complexity of the underlying genetic pathogenesis of these developmental anomalies. Family-based genomics by exome sequencing (ES) and rare variant analyses combined with whole-genome array-based comparative genomic hybridization were implemented to investigate 18 families with limb birth defects. Eleven of 18 (61%) families revealed explanatory variants, including 7 single-nucleotide variant alleles and 3 copy number variants (CNVs), at previously reported "disease trait associated loci": BHLHA9, GLI3, HOXD cluster, HOXD13, NPR2, and WNT10B. Breakpoint junction analyses for all three CNV alleles revealed mutational signatures consistent with microhomology-mediated break-induced replication, a mechanism facilitated by Alu/Alu-mediated rearrangement. Homozygous duplication of BHLHA9 was observed in one Turkish kindred and represents a novel contributory genetic mechanism to Gollop-Wolfgang Complex (MIM: 228250), where triplication of the locus has been reported in one family from Japan (i.e., 4n = 2n + 2n versus 4n = 3n + 1n allelic configurations). Genes acting on limb patterning are sensitive to a gene dosage effect and are often associated with an allelic series. We extend an allele-specific gene dosage model to potentially assist, in an adjuvant way, interpretations of interconnections among an allelic series, clinical severity, and reduced penetrance of the BHLHA9-related CLM spectrum.
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Affiliation(s)
- Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, School of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
| | | | - Silvia R. Costa
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
| | - Yavuz Sahin
- Medical Genetics, Genoks Genetics Center, Ankara, Turkey
| | - Zeynep Ocak
- Department of Medical Genetics, Faculty of Medicine, Istinye University, Istanbul, Turkey
| | - Sedat Isikay
- Department of Pediatric Neurology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Ozge Ozalp
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
| | - Sevcan Bozdogan
- Department of Medical Genetics, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Huseyin Aslan
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
| | - Nursel Elcioglu
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul, Turkey
- Eastern Mediterranean University Medical School, Magosa, 10 Mersin, Turkey
| | - Débora R. Bertola
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
- Genetics Unit, Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Baylor-Hopkins Center for Mendelian Genomics
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Medical Genetics, School of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
- Department of Medical Genetics, Konya City Hospital, Konya, Turkey
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
- Medical Genetics, Genoks Genetics Center, Ankara, Turkey
- Department of Medical Genetics, Faculty of Medicine, Istinye University, Istanbul, Turkey
- Department of Pediatric Neurology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
- Department of Medical Genetics, Faculty of Medicine, Cukurova University, Adana, Turkey
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul, Turkey
- Eastern Mediterranean University Medical School, Magosa, 10 Mersin, Turkey
- Genetics Unit, Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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30
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Chao G, Wannier TM, Gutierrez C, Borders NC, Appleton E, Chadha A, Lebar T, Church GM. helixCAM: A platform for programmable cellular assembly in bacteria and human cells. Cell 2022; 185:3551-3567.e39. [PMID: 36055250 PMCID: PMC9481732 DOI: 10.1016/j.cell.2022.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/09/2022] [Accepted: 08/11/2022] [Indexed: 01/26/2023]
Abstract
Interactions between cells are indispensable for signaling and creating structure. The ability to direct precise cell-cell interactions would be powerful for engineering tissues, understanding signaling pathways, and directing immune cell targeting. In humans, intercellular interactions are mediated by cell adhesion molecules (CAMs). However, endogenous CAMs are natively expressed by many cells and tend to have cross-reactivity, making them unsuitable for programming specific interactions. Here, we showcase "helixCAM," a platform for engineering synthetic CAMs by presenting coiled-coil peptides on the cell surface. helixCAMs were able to create specific cell-cell interactions and direct patterned aggregate formation in bacteria and human cells. Based on coiled-coil interaction principles, we built a set of rationally designed helixCAM libraries, which led to the discovery of additional high-performance helixCAM pairs. We applied this helixCAM toolkit for various multicellular engineering applications, such as spherical layering, adherent cell targeting, and surface patterning.
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Affiliation(s)
- George Chao
- Genetics Department, Harvard Medical School, Boston, MA 02115, USA.
| | | | - Clair Gutierrez
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Evan Appleton
- Genetics Department, Harvard Medical School, Boston, MA 02115, USA
| | - Anjali Chadha
- Department of Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tina Lebar
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - George M Church
- Genetics Department, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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31
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Guinard G. THE FORELIMBS OF ALVAREZSAUROIDEA (DINOSAURIA: THEROPODA): INSIGHT FROM EVOLUTIONARY TERATOLOGY. J Morphol 2022; 283:1257-1272. [PMID: 35915891 DOI: 10.1002/jmor.21500] [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: 12/28/2021] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 11/09/2022]
Abstract
Alvarezsauroidea (Tetanurae) are non-avian theropod dinosaurs whose forelimb evolution is characterised by overdevelopment of digit I, at the expense of the other two digits, complemented by a drastic forelimb shortening in derived species (Parvicursorinae). These variations are recognised as evolutionary developmental anomalies. Evolutionary teratology hence leads to a double diagnosis with 1) macrodactyly of digit I and microdactyly of digits II and III, plus 2) anterior micromelia. The teratological macrodactyly/microdactyly coupling evolved first. Developmental mechanisms disturbing limb proportion are thought to be convergent with those of other Tetanurae (Tyrannosauridae, Carcharodontosauridae). As for the manual anomalies, both are specific to Alvarezsauroidea (macrodactyly/microdactyly) and inherited (digit loss/reduction). While considering the frame-shift theory, posterior digits develop before the most anterior one. There would therefore be a decrease in the area devoted to digits II (condensation 3) and III (condensation 4), in connection with the Shh signalling pathway, interacting with other molecular players such as the GLI 3 protein and the Hox system. Developmental independence of digit I (condensation 2) would contribute to generate a particular morphology. Macrodactyly would be linked to a variation in Hoxd-13, impacting Gli3 activity, increasing cell proliferation. The loss/reduction of digital ray/phalanges (digits II and III), would be associated to Shh activity, a mechanism inherited from the theropodan ancestry. The macrodactyly/macrodactyly coupling, and then anterior micromelia, fundamentally changed the forelimb mechanical function, compared to the 'classical' grasping structure of basal representatives and other theropods. The distal ossification of the macrodactylian digit has been identified as physiological, implying the use of the structure. However, the debate of a particular 'adaptive' use is pointless since the ecology of an organism is interactively complex, being both at the scale of the individual and dependent on circumstances. Other anatomical features also allow for compensation and a different predation (cursorial hindlimbs). This article is protected by copyright. All rights reserved.
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Koyano-Nakagawa N, Gong W, Das S, Theisen JWM, Swanholm TB, Van Ly D, Dsouza N, Singh BN, Kawakami H, Young S, Chen KQ, Kawakami Y, Garry DJ. Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud. Nat Commun 2022; 13:4221. [PMID: 35864091 PMCID: PMC9304341 DOI: 10.1038/s41467-022-31848-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 07/05/2022] [Indexed: 12/02/2022] Open
Abstract
Sonic hedgehog (Shh) is essential for limb development, and the mechanisms that govern the propagation and maintenance of its expression has been well studied; however, the mechanisms that govern the initiation of Shh expression are incomplete. Here we report that ETV2 initiates Shh expression by changing the chromatin status of the developmental limb enhancer, ZRS. Etv2 expression precedes Shh in limb buds, and Etv2 inactivation prevents the opening of limb chromatin, including the ZRS, resulting in an absence of Shh expression. Etv2 overexpression in limb buds causes nucleosomal displacement at the ZRS, ectopic Shh expression, and polydactyly. Areas of nucleosome displacement coincide with ETS binding site clusters. ETV2 also functions as a transcriptional activator of ZRS and is antagonized by ETV4/5 repressors. Known human polydactyl mutations introduce novel ETV2 binding sites in the ZRS, suggesting that ETV2 dosage regulates ZRS activation. These studies identify ETV2 as a pioneer transcription factor (TF) regulating the onset of Shh expression, having both a chromatin regulatory role and a transcriptional activation role.
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Affiliation(s)
- Naoko Koyano-Nakagawa
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA
- Hamre, Schumann, Mueller & Larson, P.C., Minneapolis, MN, 55402, USA
- Mitchell Hamline School of Law, St. Paul, MN, 55105, USA
| | - Wuming Gong
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Satyabrata Das
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Joshua W M Theisen
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Tran B Swanholm
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Daniel Van Ly
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Nikita Dsouza
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Bhairab N Singh
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Hiroko Kawakami
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Samantha Young
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Katherine Q Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Yasuhiko Kawakami
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Daniel J Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
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Barzilai-Tutsch H, Morin V, Toulouse G, Chernyavskiy O, Firth S, Marcelle C, Serralbo O. Transgenic quails reveal dynamic TCF/β-catenin signaling during avian embryonic development. eLife 2022; 11:72098. [PMID: 35833630 PMCID: PMC9395189 DOI: 10.7554/elife.72098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 07/13/2022] [Indexed: 11/26/2022] Open
Abstract
The Wnt/β-catenin signaling pathway is highly conserved throughout evolution, playing crucial roles in several developmental and pathological processes. Wnt ligands can act at a considerable distance from their sources and it is therefore necessary to examine not only the Wnt-producing but also the Wnt-receiving cells and tissues to fully appreciate the many functions of this pathway. To monitor Wnt activity, multiple tools have been designed which consist of multimerized Wnt signaling response elements (TCF/LEF binding sites) driving the expression of fluorescent reporter proteins (e.g. GFP, RFP) or of LacZ. The high stability of those reporters leads to a considerable accumulation in cells activating the pathway, thereby making them easily detectable. However, this makes them unsuitable to follow temporal changes of the pathway’s activity during dynamic biological events. Even though fluorescent transcriptional reporters can be destabilized to shorten their half-lives, this dramatically reduces signal intensities, particularly when applied in vivo. To alleviate these issues, we developed two transgenic quail lines in which high copy number (12× or 16×) of the TCF/LEF binding sites drive the expression of destabilized GFP variants. Translational enhancer sequences derived from viral mRNAs were used to increase signal intensity and specificity. This resulted in transgenic lines efficient for the characterization of TCF/β-catenin transcriptional dynamic activities during embryogenesis, including using in vivo imaging. Our analyses demonstrate the use of this transcriptional reporter to unveil novel aspects of Wnt signaling, thus opening new routes of investigation into the role of this pathway during amniote embryonic development.
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Affiliation(s)
| | - Valerie Morin
- NeuroMyoGene Institute (INMG), Claude Bernard University Lyon 1, Lyon, France
| | - Gauthier Toulouse
- NeuroMyoGene Institute (INMG), Claude Bernard University Lyon 1, Lyon, France
| | | | | | - Christophe Marcelle
- NeuroMyoGene Institute (INMG), Claude Bernard University Lyon 1, LYON, France
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Tilley L, Papadopoulos SC, Pende M, Fei JF, Murawala P. The use of transgenics in the laboratory axolotl. Dev Dyn 2022; 251:942-956. [PMID: 33949035 PMCID: PMC8568732 DOI: 10.1002/dvdy.357] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/10/2021] [Accepted: 04/29/2021] [Indexed: 11/09/2022] Open
Abstract
The ability to generate transgenic animals sparked a wave of research committed to implementing such technology in a wide variety of model organisms. Building a solid base of ubiquitous and tissue-specific reporter lines has set the stage for later interrogations of individual cells or genetic elements. Compared to other widely used model organisms such as mice, zebrafish and fruit flies, there are only a few transgenic lines available in the laboratory axolotl (Ambystoma mexicanum), although their number is steadily expanding. In this review, we discuss a brief history of the transgenic methodologies in axolotl and their advantages and disadvantages. Next, we discuss available transgenic lines and insights we have been able to glean from them. Finally, we list challenges when developing transgenic axolotl, and where further work is needed in order to improve their standing as both a developmental and regenerative model.
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Affiliation(s)
- Lydia Tilley
- Mount Desert Island Biological Laboratory (MDIBL), Salisbury Cove, Maine
| | - Sofia-Christina Papadopoulos
- Mount Desert Island Biological Laboratory (MDIBL), Salisbury Cove, Maine
- Clinic for Kidney and Hypertension Diseases, Hannover Medical School, Hannover, Germany
| | - Marko Pende
- Mount Desert Island Biological Laboratory (MDIBL), Salisbury Cove, Maine
| | - Ji-Feng Fei
- Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Prayag Murawala
- Mount Desert Island Biological Laboratory (MDIBL), Salisbury Cove, Maine
- Clinic for Kidney and Hypertension Diseases, Hannover Medical School, Hannover, Germany
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35
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Investigating chromatin accessibility during development and differentiation by ATAC-sequencing to guide the identification of cis-regulatory elements. Biochem Soc Trans 2022; 50:1167-1177. [PMID: 35604124 PMCID: PMC9246326 DOI: 10.1042/bst20210834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/17/2022]
Abstract
Mapping accessible chromatin across time scales can give insights into its dynamic nature, for example during cellular differentiation and tissue or organism development. Analysis of such data can be utilised to identify functional cis-regulatory elements (CRE) and transcription factor binding sites and, when combined with transcriptomics, can reveal gene regulatory networks (GRNs) of expressed genes. Chromatin accessibility mapping is a powerful approach and can be performed using ATAC-sequencing (ATAC-seq), whereby Tn5 transposase inserts sequencing adaptors into genomic DNA to identify differentially accessible regions of chromatin in different cell populations. It requires low sample input and can be performed and analysed relatively quickly compared with other methods. The data generated from ATAC-seq, along with other genomic approaches, can help uncover chromatin packaging and potential cis-regulatory elements that may be responsible for gene expression. Here, we describe the ATAC-seq approach and give examples from mainly vertebrate embryonic development, where such datasets have identified the highly dynamic nature of chromatin, with differing landscapes between cellular precursors for different lineages.
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DiFrisco J, Wagner GP, Love AC. Reframing research on evolutionary novelty and co-option: Character identity mechanisms versus deep homology. Semin Cell Dev Biol 2022; 145:3-12. [PMID: 35400563 DOI: 10.1016/j.semcdb.2022.03.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 01/31/2022] [Accepted: 03/23/2022] [Indexed: 11/27/2022]
Abstract
A central topic in research at the intersection of development and evolution is the origin of novel traits. Despite progress on understanding how developmental mechanisms underlie patterns of diversity in the history of life, the problem of novelty continues to challenge researchers. Here we argue that research on evolutionary novelty and the closely associated phenomenon of co-option can be reframed fruitfully by: (1) specifying a conceptual model of mechanisms that underwrite character identity, (2) providing a richer and more empirically precise notion of co-option that goes beyond common appeals to "deep homology", and (3) attending to the nature of experimental interventions that can determine whether and how the co-option of identity mechanisms can help to explain novel character origins. This reframing has the potential to channel future investigation to make substantive progress on the problem of evolutionary novelty. To illustrate this potential, we apply our reframing to two case studies: treehopper helmets and beetle horns.
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Affiliation(s)
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Yale Systems Biology Institute, Yale University, New Haven, CT, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Medical School, New Haven, CT, USA; Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Alan C Love
- Department of Philosophy, University of Minnesota, Minneapolis, MN, USA; Minnesota Center for Philosophy of Sciences, University of Minnesota, Minneapolis, MN, USA.
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Purushothaman S, Lopez Aviña BB, Seifert AW. Sonic hedgehog is Essential for Proximal-Distal Outgrowth of the Limb Bud in Salamanders. Front Cell Dev Biol 2022; 10:797352. [PMID: 35433673 PMCID: PMC9010949 DOI: 10.3389/fcell.2022.797352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/24/2022] [Indexed: 11/20/2022] Open
Abstract
The developing forelimb has been a foundational model to understand how specified progenitor cells integrate genetic information to produce the tetrapod limb bauplan. Although the reigning hypothesis is that all tetrapods develop limbs in a similar manner, recent work suggests that urodeles have evolved a derived mode of limb dvelopment. Here, we demonstrate through pharmacological and genetic inactivation of Sonic hedgehog (Shh) signaling in axolotls that Shh directs expansion and survival of limb progenitor cells in addition to patterning the limb across the proximodistal and antero-posterior axis. In contrast to inactivation of Shh in mouse or chick embryos where a humerus, radius, and single digit develop, Shh crispant axolotls completely lack forelimbs. In rescuing limb development by implanting SHH-N protein beads into the nascent limb field of Shh crispants, we show that the limb field is specified in the absence of Shh and that hedgehog pathway activation is required to initiate proximodistal outgrowth. When our results are examined alongside other derived aspects of salamander limb development and placed in a phylogenetic context, a new hypothesis emerges whereby the ability for cells at an amputation plane to activate morphogenesis and regenerate a limb may have evolved uniquely in urodeles.
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38
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An Fgf-Shh positive feedback loop drives growth in developing unpaired fins. Proc Natl Acad Sci U S A 2022; 119:e2120150119. [PMID: 35238632 PMCID: PMC8916008 DOI: 10.1073/pnas.2120150119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The origin and diversification of appendage types is a central question in vertebrate evolution. Understanding the genetic mechanisms that underlie fin and limb development can reveal relationships between different appendages. Here we demonstrate, using chemical genetics, a mutually agonistic interaction between Fgf and Shh genes in the developing dorsal fin of the channel catfish, Ictalurus punctatus. We also find that Fgf8 and Shh orthologs are expressed in the apical ectodermal ridge and zone of polarizing activity, respectively, in the median fins of representatives from other major vertebrate lineages. These findings demonstrate the importance of this feedback loop in median fins and offer developmental evidence for a median fin-first scenario for vertebrate paired appendage origins.
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39
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Liang N, Deme L, Kong Q, Sun L, Cao Y, Wu T, Huang X, Xu S, Yang G. Divergence of Tbx4 hindlimb enhancer HLEA underlies the hindlimb loss during cetacean evolution. Genomics 2022; 114:110292. [DOI: 10.1016/j.ygeno.2022.110292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/13/2022] [Accepted: 02/01/2022] [Indexed: 11/04/2022]
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He P, Ruan D, Huang Z, Wang C, Xu Y, Cai H, Liu H, Fei Y, Heng BC, Chen W, Shen W. Comparison of Tendon Development Versus Tendon Healing and Regeneration. Front Cell Dev Biol 2022; 10:821667. [PMID: 35141224 PMCID: PMC8819183 DOI: 10.3389/fcell.2022.821667] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/07/2022] [Indexed: 12/27/2022] Open
Abstract
Tendon is a vital connective tissue in human skeletal muscle system, and tendon injury is very common and intractable in clinic. Tendon development and repair are two closely related but still not fully understood processes. Tendon development involves multiple germ layer, as well as the regulation of diversity transcription factors (Scx et al.), proteins (Tnmd et al.) and signaling pathways (TGFβ et al.). The nature process of tendon repair is roughly divided in three stages, which are dominated by various cells and cell factors. This review will describe the whole process of tendon development and compare it with the process of tendon repair, focusing on the understanding and recent advances in the regulation of tendon development and repair. The study and comparison of tendon development and repair process can thus provide references and guidelines for treatment of tendon injuries.
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Affiliation(s)
- Peiwen He
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Institute of Sports Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, China
| | - Dengfeng Ruan
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Institute of Sports Medicine, Zhejiang University, Hangzhou, China
| | - Zizhan Huang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Institute of Sports Medicine, Zhejiang University, Hangzhou, China
| | - Canlong Wang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Institute of Sports Medicine, Zhejiang University, Hangzhou, China
| | - Yiwen Xu
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Institute of Sports Medicine, Zhejiang University, Hangzhou, China
| | - Honglu Cai
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Institute of Sports Medicine, Zhejiang University, Hangzhou, China
| | - Hengzhi Liu
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Institute of Sports Medicine, Zhejiang University, Hangzhou, China
| | - Yang Fei
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Institute of Sports Medicine, Zhejiang University, Hangzhou, China
| | - Boon Chin Heng
- Central Laboratory, Peking University School of Stomatology, Bejing, China
| | - Weishan Chen
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Institute of Sports Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Weishan Chen, ; Weiliang Shen,
| | - Weiliang Shen
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Institute of Sports Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, China
- Dr. Li Dak Sum and Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, China
- China Orthopaedic Regenerative Medicine (CORMed), Hangzhou, China
- *Correspondence: Weishan Chen, ; Weiliang Shen,
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41
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Roscito JG, Sameith K, Kirilenko BM, Hecker N, Winkler S, Dahl A, Rodrigues MT, Hiller M. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Rep 2022; 38:110280. [DOI: 10.1016/j.celrep.2021.110280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 01/02/2023] Open
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MILLAN CLARO LUISFELIPE, MÁRQUEZ FLÓREZ KALENIA, DUQUE-DAZA CARLOSA, GARZÓN-ALVARADO DIEGOA. THREE-DIMENSIONAL COMPUTATIONAL MODEL OF EARLY UPPER LIMB DEVELOPMENT. J MECH MED BIOL 2021. [DOI: 10.1142/s021951942250004x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Limb development begins during embryogenesis when a series of biochemical interactions are triggered between a particular region of the mesoderm and the ectoderm. These processes affect the morphogenesis and growth of bones, joints, and all the other constituent elements of limbs; nevertheless, how the biochemical regulation affects mesenchymal condensation is not entirely clear. In this study, a three-dimensional computational model is designed to predict the appearance and location of the mesenchymal condensation in the stylopod and zeugopod; the biochemical events were described with reaction–diffusion equations that were solved using the finite elements method. The result of the gene expression in our model was consistent with the one reported in literature; the obtained patterns of Fgf8, Fgf10, and Wnt3a can predict the shape of the mesenchymal condensation of early upper limb development; the simple diffusive patterns of molecules were suitable to explain the areas where sox9 is expressed. Furthermore, our results suggest that the expression of Tgf-[Formula: see text] in the upper limb could be due to the inhibition of retinoic acid. These results suggest the importance of building computational scenarios where pathologies may be comprehensively examined.
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Affiliation(s)
| | | | - CARLOS A. DUQUE-DAZA
- Numerical Methods and Modeling Research Group (GNUM), Universidad Nacional de Colombia, Bogotá, Colombia
| | - DIEGO A. GARZÓN-ALVARADO
- Numerical Methods and Modeling Research Group (GNUM), Biotechnology Institute (IBUN), Universidad Nacional de Colombia, Bogotá, Colombia
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Sato Y, Fujiwara M, Nishino H, Harada R, Kawasaki E, Morimoto R, Ohgo S, Wada N. Normal skeletal pattern formation in chick limb bud with a mesenchymal hole is mediated by adjustment of cellular properties along the anterior-posterior axis in the limb bud. Dev Biol 2021; 483:76-88. [PMID: 34973174 DOI: 10.1016/j.ydbio.2021.12.016] [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: 01/13/2021] [Revised: 12/12/2021] [Accepted: 12/26/2021] [Indexed: 11/18/2022]
Abstract
The chick limb bud has plasticity to reconstruct a normal skeletal pattern after a part of mesenchymal mass is excised to make a hole in its early stage of development. To understand the details of hole closure and re-establishment of normal limb axes to reconstruct a normal limb skeleton, we focused on cellular and molecular changes during hole repair and limb restoration. We excised a cube-shaped mass of mesenchymal cells from the medial region of chick hindlimb bud (stage 23) and observed the following morphogenesis. The hole had closed by 15 h after excision, followed by restoration of the limb bud morphology, and the cartilage pattern was largely restored by 48 h. Lineage analysis of the mesenchymal cells showed that cells at the anterior and posterior margins of the hole were adjoined at the hole closure site, whereas cells at the proximal and distal margins were not. To investigate cell polarity during hole repair, we analyzed intracellular positioning of the Golgi apparatus relative to the nuclei. We found that the Golgi apparatus tended to be directed toward the hole among cells at the anterior and posterior margins but not among cells at identical positions in normal limb buds or cells at the proximal and distal hole margins. In the manipulated limb buds, the frequency of cell proliferation was maintained compared with the control side. Tbx3 expression, which was usually restricted to anterior and posterior margins of the limb bud, was temporarily expanded medially and then reverted to a normal pattern as limb reconstruction proceeded, with Tbx3 negative cells reappearing in the medial regions of the limb buds. Thus, mesenchymal hole closure and limb reconstruction are mainly mediated by cells at the anterior and posterior hole margins. These results suggest that adjustment of cellular properties along the anteroposterior axis is crucial to restore limb damage and reconstruct normal skeletal patterns.
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Affiliation(s)
- Yuki Sato
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Momoko Fujiwara
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Haruka Nishino
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Rei Harada
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Eriko Kawasaki
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Ryo Morimoto
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Shiro Ohgo
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Naoyuki Wada
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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Diaz RE, Taylor-Diaz EA, Trainor PA, Diogo R, Molnar JL. Comparative development of limb musculature in phylogenetically and ecologically divergent lizards. Dev Dyn 2021; 251:1576-1612. [PMID: 34927301 DOI: 10.1002/dvdy.447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Squamate reptiles (lizards, snakes, and amphisbaenians) exhibit incredible diversity in their locomotion, behavior, morphology, and ecological breadth. Although they often are used as models of locomotor diversity, surprisingly little attention has been given to muscle development in squamate reptiles. In fact, the most detailed examination was conducted almost 80 years ago and solely focused on the proximal limb regions. Herein, we present forelimb and hindlimb muscle morphogenesis data for three lizard species with different locomotion and feeding strategies: the desert grassland whiptail lizard, the central bearded dragon, and the veiled chameleon. This study fills critical gaps in our understanding of muscle morphogenesis in squamate reptiles and presents a comparative and temporospatial analysis of muscle development. RESULTS Our results reveal a conserved pattern of early muscle development among lizards with different adult morphologies and ecologies. The variations that exist are concentrated in distal regions, particularly the specialized autopodia of chameleons, where differentiation of muscles associated with the digits is delayed. CONCLUSIONS The chameleon autopod provides an example of major evolutionary modifications to the skeleton with only minor disruption of the conserved order and pattern of limb muscle development. This robustness of muscle patterning facilitates the evolution of extreme yet functional phenotypes.
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Affiliation(s)
- Raul E Diaz
- Department of Biological Sciences, California State University, Los Angeles, California, USA.,Department of Herpetology, Natural History Museum of Los Angeles County, Los Angeles, California, USA
| | - Elizabeth A Taylor-Diaz
- Department of Biological Sciences, California State University, Los Angeles, California, USA
| | - Paul A Trainor
- Investigator, Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Rui Diogo
- Department of Anatomy, Howard University College of Medicine, Washington, District of Columbia, USA
| | - Julia L Molnar
- Department of Anatomy, New York Institute of Technology, College of Osteopathic Medicine, Old Westbury, New York, USA
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45
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Pors J, Philipp T, Terry J. Placental Expression of the Forelimb Patterning Transcription Factor MEIS2 in Trisomy 15. Fetal Pediatr Pathol 2021; 40:597-604. [PMID: 32138576 DOI: 10.1080/15513815.2020.1732509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BackgroundObservations of first trimester human trisomy 15 (T15) embryos have identified meromelic changes in the upper limbs. These changes are similar to those observed in animal studies investigating the effects of overexpression of Meis2, a signaling transcription factor expressed during forelimb development. Although it would be exceedingly difficult to assess MEIS2 expression in the human embryonic arm, MEIS2 has been reported as consistently expressed in first trimester placental villus stroma. Methods: This study addresses whether gene dosage effect might underlie meromelia in T15 by comparing MEIS2 expression in placentas from T15 and euploid spontaneous abortions employing manual and automated assessment of MEIS2 immunohistochemical scoring. Results: Average MEIS2 expression is increased in T15 first trimester placental tissue compared to euploid controls but that the difference is marginal. Manual and automated scoring showed moderately strong correlation. Conclusion: Extrapolation of these results suggests MEIS2 overexpression may not be required for meromelia in T15.
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Affiliation(s)
- Jennifer Pors
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tom Philipp
- Department of Gynecology and Obstetrics, Danube Hospital, Vienna, Austria
| | - Jefferson Terry
- Pathology, BC Children's Hospital, Vancouver, British Columbia, Canada
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O'Reilly S. Gremlin: a complex molecule regulating wound healing and fibrosis. Cell Mol Life Sci 2021; 78:7917-7923. [PMID: 34731251 PMCID: PMC11071963 DOI: 10.1007/s00018-021-03964-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/27/2021] [Accepted: 09/29/2021] [Indexed: 12/19/2022]
Abstract
Gremlin-1 is part of the TGF-β superfamily and is a BMP antagonist that blocks BMP signalling to precisely control BMP gradients. Gremlin-1 is primarily involved in organogenesis and limb patterning however, has recently been described as being involved in fibrotic diseases. Initially described as a key factor involved in diabetic kidney fibrosis due to being induced by high glucose, it has now been described as being associated with lung, liver, eye, and skin fibrosis. This suggests that it is a key conserved molecule mediating fibrotic events irrespective of organ. It appears that Gremlin-1 may have effects mediated by BMP-dependent and independent pathways. The aim of this review is to evaluate the role of Gremlin-1 in fibrosis, its mechanisms and if this can be targeted therapeutically in fibrotic diseases, which currently have very limited treatment options and are highly prevalent.
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Rare phenotype: Hand preaxial polydactyly associated with LRP6-related tooth agenesis in humans. NPJ Genom Med 2021; 6:93. [PMID: 34759310 PMCID: PMC8581002 DOI: 10.1038/s41525-021-00262-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
Low-density lipoprotein receptor-related protein 6 (LRP6) is a pathogenic gene of selective tooth agenesis-7 (OMIM#616724). Although the malformation of the digits and fore- and hindlimbs has been reported in Lrp6-deficient mice, it has been rarely discovered in humans with LRP6 mutations. Here, we demonstrate an unreported autosomal dominant LRP6 heterozygous mutation (c.2840 T > C;p.Met947Thr) in a tooth agenesis family with hand polydactyly, and another unreported autosomal dominant LRP6 heterozygous mutation (c.1154 G > C;p.Arg385Pro) in a non-syndromic tooth agenesis family. Bioinformatic prediction demonstrated the deleterious effects of the mutations, and LRP6 structure changes suggested the corresponding functional impairments. Analysis on the pattern of LRP6-related tooth agenesis demonstrated the maxillary lateral incisor was the most affected. Our study report that LRP6 mutation might be associated with hand preaxial polydactyly in humans, which broaden the phenotypic spectrum of LRP6-related disorders, and provide valuable information on the characteristics of LRP6-related tooth agenesis.
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Socha M, Sowińska-Seidler A, Melo US, Kragesteen BK, Franke M, Heinrich V, Schöpflin R, Nagel I, Gruchy N, Mundlos S, Sreenivasan VK, López C, Vingron M, Bukowska-Olech E, Spielmann M, Jamsheer A. Position effects at the FGF8 locus are associated with femoral hypoplasia. Am J Hum Genet 2021; 108:1725-1734. [PMID: 34433009 DOI: 10.1016/j.ajhg.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022] Open
Abstract
Copy-number variations (CNVs) are a common cause of congenital limb malformations and are interpreted primarily on the basis of their effect on gene dosage. However, recent studies show that CNVs also influence the 3D genome chromatin organization. The functional interpretation of whether a phenotype is the result of gene dosage or a regulatory position effect remains challenging. Here, we report on two unrelated families with individuals affected by bilateral hypoplasia of the femoral bones, both harboring de novo duplications on chromosome 10q24.32. The ∼0.5 Mb duplications include FGF8, a key regulator of limb development and several limb enhancer elements. To functionally characterize these variants, we analyzed the local chromatin architecture in the affected individuals' cells and re-engineered the duplications in mice by using CRISPR-Cas9 genome editing. We found that the duplications were associated with ectopic chromatin contacts and increased FGF8 expression. Transgenic mice carrying the heterozygous tandem duplication including Fgf8 exhibited proximal shortening of the limbs, resembling the human phenotype. To evaluate whether the phenotype was a result of gene dosage, we generated another transgenic mice line, carrying the duplication on one allele and a concurrent Fgf8 deletion on the other allele, as a control. Surprisingly, the same malformations were observed. Capture Hi-C experiments revealed ectopic interaction with the duplicated region and Fgf8, indicating a position effect. In summary, we show that duplications at the FGF8 locus are associated with femoral hypoplasia and that the phenotype is most likely the result of position effects altering FGF8 expression rather than gene dosage effects.
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Pakvasa M, Tucker AB, Shen T, He TC, Reid RR. The Pleiotropic Intricacies of Hedgehog Signaling: From Craniofacial Patterning to Carcinogenesis. FACE (THOUSAND OAKS, CALIF.) 2021; 2:260-274. [PMID: 35812774 PMCID: PMC9268505 DOI: 10.1177/27325016211024326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Hedgehog signaling was discovered more than 40 years ago in experiments demonstrating that it is a fundamental mediator of limb development. Since that time, it has been shown to be important in development, homeostasis, and disease. The hedgehog pathway proceeds through a pathway highly conserved throughout animals beginning with the extracellular diffusion of hedgehog ligands, proceeding through an intracellular signaling cascade, and ending with the activation of specific target genes. A vast amount of research has been done elucidating hedgehog signaling mechanisms and regulation. This research has found a complex system of genetics and signaling that helps determine how organisms develop and function. This review provides an overview of what is known about hedgehog genetics and signaling, followed by an in-depth discussion of the role of hedgehog signaling in craniofacial development and carcinogenesis.
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Affiliation(s)
- Mikhail Pakvasa
- Pritzker School of Medicine, University of Chicago, Chicago, IL USA
- Molecular Oncology Lab, Department of Orthopedic Surgery & Rehabilitation Medicine,University of Chicago Medicine, Chicago, IL
| | - Andrew B. Tucker
- Pritzker School of Medicine, University of Chicago, Chicago, IL USA
- Molecular Oncology Lab, Department of Orthopedic Surgery & Rehabilitation Medicine,University of Chicago Medicine, Chicago, IL
| | - Timothy Shen
- Pritzker School of Medicine, University of Chicago, Chicago, IL USA
| | - Tong-Chuan He
- Molecular Oncology Lab, Department of Orthopedic Surgery & Rehabilitation Medicine,University of Chicago Medicine, Chicago, IL
| | - Russell R. Reid
- Molecular Oncology Lab, Department of Orthopedic Surgery & Rehabilitation Medicine,University of Chicago Medicine, Chicago, IL
- Section of Plastic and Reconstructive Surgery, University of Chicago Medicine, Chicago, IL
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50
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Smith‐Paredes D, Griffith O, Fabbri M, Yohe L, Blackburn DG, Siler CD, Bhullar BS, Wagner GP. Hidden limbs in the "limbless skink" Brachymeles lukbani: Developmental observations. J Anat 2021; 239:693-703. [PMID: 33870497 PMCID: PMC8349411 DOI: 10.1111/joa.13447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/21/2021] [Accepted: 03/31/2021] [Indexed: 12/15/2022] Open
Abstract
Reduced limbs and limblessness have evolved independently in many lizard clades. Scincidae exhibit a wide range of limb-reduced morphologies, but only some species have been used to study the embryology of limb reduction (e.g., digit reduction in Chalcides and limb reduction in Scelotes). The genus Brachymeles, a Southeast Asian clade of skinks, includes species with a range of limb morphologies, from pentadactyl to functionally and structurally limbless species. Adults of the small, snake-like species Brachymeles lukbani show no sign of external limbs in the adult except for small depressions where they might be expected to occur. Here, we show that embryos of B. lukbani in early stages of development, on the other hand, show a truncated but well-developed limb with a stylopod and a zeugopod, but no signs of an autopod. As development proceeds, the limb's small size persists even while the embryo elongates. These observations are made based on external morphology. We used florescent whole-mount immunofluorescence to visualize the morphology of skeletal elements and muscles within the embryonic limb of B. lukabni. Early stages have a humerus and separated ulna and radius cartilages; associated with these structures are dorsal and ventral muscle masses as those found in the embryos of other limbed species. While the limb remains small, the pectoral girdle grows in proportion to the rest of the body, with well-developed skeletal elements and their associated muscles. In later stages of development, we find the small limb is still present under the skin, but there are few indications of its presence, save for the morphology of the scale covering it. By use of CT scanning, we find that the adult morphology consists of a well-developed pectoral girdle, small humerus, extremely reduced ulna and radius, and well-developed limb musculature connected to the pectoral girdle. These muscles form in association with a developing limb during embryonic stages, a hint that "limbless" lizards that possess these muscles may have or have had at least transient developing limbs, as we find in B. lukbani. Overall, this newly observed pattern of ontogenetic reduction leads to an externally limbless adult in which a limb rudiment is hidden and covered under the trunk skin, a situation called cryptomelia. The results of this work add to our growing understanding of clade-specific patterns of limb reduction and the convergent evolution of limbless phenotypes through different developmental processes.
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Affiliation(s)
- Daniel Smith‐Paredes
- Department of Earth and Planetary Science and Peabody Museum of Natural HistoryYale UniversityNew HavenCTUSA
| | - Oliver Griffith
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Matteo Fabbri
- Department of Earth and Planetary Science and Peabody Museum of Natural HistoryYale UniversityNew HavenCTUSA
| | - Laurel Yohe
- Department of Earth and Planetary Science and Peabody Museum of Natural HistoryYale UniversityNew HavenCTUSA
| | - Daniel G. Blackburn
- Department of Biology, and Electron Microscopy CenterTrinity CollegeHartfordCTUSA
| | - Cameron D. Siler
- Department of Biology and Sam Noble Oklahoma Museum of Natural HistoryUniversity of OklahomaNormanOKUSA
| | - Bhart‐Anjan S. Bhullar
- Department of Earth and Planetary Science and Peabody Museum of Natural HistoryYale UniversityNew HavenCTUSA
| | - Günter P. Wagner
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
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