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Beltrán-Rivera A, García-Arrarás JE. Cellular dedifferentiation. Revisiting Betty Hay's legacy. Dev Biol 2025; 523:1-8. [PMID: 40164323 DOI: 10.1016/j.ydbio.2025.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2024] [Revised: 03/25/2025] [Accepted: 03/28/2025] [Indexed: 04/02/2025]
Abstract
The concept of mature specialized cells and the stability of the differentiated state was fundamentally challenged by Elizabeth Hay's groundbreaking observations on amphibian limb regeneration, published in 1959. Building on previous work by C.S. Thornton, she discovered that muscle cells could dedifferentiate and transform into progenitor cells within the regeneration blastema reshaping our understanding of cell differentiation. This pivotal finding reshaped our understanding of cell differentiation, opening new avenues of research. Though controversial, her findings significantly advanced the fields of cell plasticity and regenerative biology.
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Otsuki L, Plattner SA, Taniguchi-Sugiura Y, Falcon F, Tanaka EM. Molecular basis of positional memory in limb regeneration. Nature 2025:10.1038/s41586-025-09036-5. [PMID: 40399677 DOI: 10.1038/s41586-025-09036-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 04/16/2025] [Indexed: 05/23/2025]
Abstract
The amputation of a salamander limb triggers anterior and posterior connective tissue cells to form distinct signalling centres that together fuel regeneration1. Anterior and posterior identities are established during development and are thought to persist for the whole life in the form of positional memory2. However, the molecular basis of positional memory and whether positional memory can be altered remain unknown. Here, we identify a positive-feedback loop that is responsible for posterior identity in the limb of an axolotl (Ambystoma mexicanum). Posterior cells express residual Hand2 transcription factor from development, and this primes them to form a Shh signalling centre after limb amputation. During regeneration, Shh signalling is also upstream of Hand2 expression. After regeneration, Shh is shut down but Hand2 is sustained, safeguarding posterior memory. We used this regeneration circuitry to convert anterior cells to a posterior-cell memory state. Transient exposure of anterior cells to Shh during regeneration kick-started an ectopic Hand2-Shh loop, leading to stable Hand2 expression and lasting competence to express Shh. Our results implicate positive-feedback in the stability of positional memory and reveal that positional memory is reprogrammed more easily in one direction (anterior to posterior) than in the other. Modifying positional memory in regenerative cells changes their signalling outputs, which has implications for tissue engineering.
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Affiliation(s)
- L Otsuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
| | - S A Plattner
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Y Taniguchi-Sugiura
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - F Falcon
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - E M Tanaka
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
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3
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Gamble DJ, Lopez S, Yazdi M, Castro-Torres T, Lozito TP. Probe Sequencing Analysis of Regenerating Lizard Tails Indicates Crosstalk Among Osteoclasts, Epidermal Cells, and Fibroblasts. J Dev Biol 2025; 13:15. [PMID: 40407684 PMCID: PMC12101308 DOI: 10.3390/jdb13020015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Revised: 04/14/2025] [Accepted: 04/24/2025] [Indexed: 05/26/2025] Open
Abstract
Lizards are distinguished as the only amniotes, and closest relatives of mammals, capable of multilineage epimorphic regeneration. Tail blastemas of green anole lizards (Anolis carolinensis) consist of col3a1+ fibroblastic connective tissue cells enclosed in krt5+ wound epidermis (WE), both of which are required for regeneration. Blastema and WE formation are known to be closely associated with phagocytic cell populations, including macrophages and osteoclasts. However, it remains unclear what specific phagocytic cell types are required to stimulate regeneration. Here, we explicitly assess the roles of osteoclast activity during blastema and WE formation in regenerating lizard tails. First, probe sequencing was performed at regenerative timepoints on fibroblasts isolated based on col3a1 expression toward establishing pathways involved in stimulating blastema formation and subsequent tail regrowth. Next, treatments with osteoclast inhibitor zoledronic acid (ZA) were used to assess the roles of osteoclast activity in lizard tail regeneration and fibroblast signaling. ZA treatment stunted lizard tail regrowth, suggesting osteoclast activity was required for blastema formation and regeneration. Transcriptomic profiling of fibroblasts isolated from ZA-treated and control lizards linked inhibition of osteoclast activity with limitations in fibroblasts to form pro-regenerative extracellular matrix and support WE formation. These results suggest that crosstalk between osteoclasts and fibroblasts regulates blastema and WE formation during lizard tail regeneration.
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Affiliation(s)
- Darian J. Gamble
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, 1425 San Pablo St., Los Angeles, CA 90033, USA;
| | - Samantha Lopez
- Department of Orthopedic Surgery, Keck School of Medicine, University of Southern California, 1540 Alcazar St., Los Angeles, CA 90089, USA; (S.L.); (M.Y.); (T.C.-T.)
| | - Melody Yazdi
- Department of Orthopedic Surgery, Keck School of Medicine, University of Southern California, 1540 Alcazar St., Los Angeles, CA 90089, USA; (S.L.); (M.Y.); (T.C.-T.)
| | - Toni Castro-Torres
- Department of Orthopedic Surgery, Keck School of Medicine, University of Southern California, 1540 Alcazar St., Los Angeles, CA 90089, USA; (S.L.); (M.Y.); (T.C.-T.)
| | - Thomas P. Lozito
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, 1425 San Pablo St., Los Angeles, CA 90033, USA;
- Department of Orthopedic Surgery, Keck School of Medicine, University of Southern California, 1540 Alcazar St., Los Angeles, CA 90089, USA; (S.L.); (M.Y.); (T.C.-T.)
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4
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E W, Fei L, Wang J, Wang X, Wang R, Wang X, Zhang P, Chen J, Wu J, Jiang M, Huang D, Jia D, Guo G, Han X. Dynamics of Cell Fate Decisions during Chemically Induced Multi-Lineage Trans-Differentiation at Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2409642. [PMID: 40051350 PMCID: PMC12061290 DOI: 10.1002/advs.202409642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 02/08/2025] [Indexed: 05/10/2025]
Abstract
Cell trans-differentiation offers a powerful means to manipulate cell identities. By exposing cells to a combination of small molecules (SMs), cell trans-differentiation can be induced in a simple and cost-effective manner. However, a comprehensive atlas detailing chemical-induced cell trans-differentiation across multiple cell fates has yet to be established. In this study, the underlying mechanisms of trans-differentiation is investigated and constructed an in-depth single-cell atlas of this process. The time-course trajectory is demonstrated for trans-differentiation of mouse embryonic fibroblasts (MEFs) into multiple cell lineages including epithelial, neural, extraembryonic endoderm like (XEN-like) cells, and endothelial cells, when induced by SMs cocktail 6TCF (E616452, tranylcypromine, CHIR99021, and forskolin). These trans-differentiated cells closely resemble various somatic cell types in the fetus. It is found that trans-differentiation is marked by dynamic shifts in entropy and the cell cycle during cell fate transitions. A common intermediate feature is revealed characterized by high ribosomal gene expression. This study combines high-resolution landscape with comparative analyses of trans-differentiation dynamics, providing new insights into the complex mechanisms driving cell fate determination in vitro. Future study shall explore the applicability of the model in human cell trans-differentiation.
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Affiliation(s)
- Weigao E
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Lijiang Fei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Jingjing Wang
- Liangzhu LaboratoryZhejiang University1369 West Wenyi RoadHangzhou311121China
| | - Xinru Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Renying Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Xueyi Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Peijing Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Jianhui Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Junqing Wu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Mengmeng Jiang
- Liangzhu LaboratoryZhejiang University1369 West Wenyi RoadHangzhou311121China
| | | | - Danmei Jia
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang University1369 West Wenyi RoadHangzhou311121China
| | - Xiaoping Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Zhejiang Key Laboratory of Multi‐omics Precision Diagnosis and Treatment of Liver DiseasesHangzhouZhejiang310000China
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5
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Wang J, Ye F, Chai H, Jiang Y, Wang T, Ran X, Xia Q, Xu Z, Fu Y, Zhang G, Wu H, Guo G, Guo H, Ruan Y, Wang Y, Xing D, Xu X, Zhang Z. Advances and applications in single-cell and spatial genomics. SCIENCE CHINA. LIFE SCIENCES 2025; 68:1226-1282. [PMID: 39792333 DOI: 10.1007/s11427-024-2770-x] [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: 08/20/2024] [Accepted: 10/10/2024] [Indexed: 01/12/2025]
Abstract
The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems. These advancements offer unprecedented resolution in the examination of the functional genomics of individual cells and their spatial context within tissues. In this review, we have comprehensively discussed the historical development and recent progress in the field of single-cell and spatial genomics. We have reviewed the breakthroughs in single-cell multi-omics technologies, spatial genomics methods, and the computational strategies employed toward the analyses of single-cell atlas data. Furthermore, we have highlighted the advances made in constructing cellular atlases and their clinical applications, particularly in the context of disease. Finally, we have discussed the emerging trends, challenges, and opportunities in this rapidly evolving field.
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Affiliation(s)
- Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Haoxi Chai
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, 310058, China
| | - Yujia Jiang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
| | - Teng Wang
- Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing, 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Xia Ran
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310000, China
| | - Qimin Xia
- Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ziye Xu
- Department of Laboratory Medicine of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yuting Fu
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Guodong Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hanyu Wu
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China.
- Institute of Hematology, Zhejiang University, Hangzhou, 310000, China.
| | - Hongshan Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Institute of Hematology, Zhejiang University, Hangzhou, 310000, China.
| | - Yijun Ruan
- Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, 310058, China.
| | - Yongcheng Wang
- Department of Laboratory Medicine of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Dong Xing
- Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing, 100871, China.
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China.
| | - Xun Xu
- BGI Research, Shenzhen, 518083, China.
- BGI Research, Hangzhou, 310030, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China.
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing, 100871, China.
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6
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Song L, Wang L, He Z, Cui X, Peng C, Xu J, Yong Z, Liu Y, Fei JF. Improving Spatial Transcriptomics with Membrane-Based Boundary Definition and Enhanced Single-Cell Resolution. SMALL METHODS 2025; 9:e2401056. [PMID: 39871658 DOI: 10.1002/smtd.202401056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 01/03/2025] [Indexed: 01/29/2025]
Abstract
Accurately defining cell boundaries for spatial transcriptomics is technically challenging. The current major approaches are nuclear staining or mathematical inference, which either exclude the cytoplasm or determine a hypothetical boundary. Here, a new method is introduced for defining cell boundaries: labeling cell membranes using genetically coded fluorescent proteins, which allows precise indexing of sequencing spots and transcripts within cells on sections. Use of this membrane-based method greatly increases the number of genes captured in cells compared to the number captured using nucleus-based methods; the numbers of genes are increased by 67% and 119% in mouse and axolotl livers, respectively. The obtained expression profiles are more consistent with single-cell RNA-seq data, demonstrating more rational clustering and apparent cell type-specific markers. Furthermore, improved single-cell resolution is achieved to better identify rare cell types and elaborate spatial domains in the axolotl brain and intestine. In addition to regular cells, accurate recognition of multinucleated cells and cells lacking nuclei in the mouse liver is achieved, demonstrating its ability to analyze complex tissues and organs, which is not achievable using previous methods. This study provides a powerful tool for improving spatial transcriptomics that has broad potential for its applications in the biological and medical sciences.
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Affiliation(s)
- Li Song
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, China
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Liqun Wang
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, 510631, China
| | - Zitian He
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, China
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Xiao Cui
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, China
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Cheng Peng
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, 510631, China
| | - Jie Xu
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Zhouying Yong
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, 510631, China
| | - Yanmei Liu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, 510631, China
| | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, 510006, China
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
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7
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Raz AA, Yamashita YM. Rewinding the clock: mechanisms of dedifferentiation. Curr Opin Genet Dev 2025; 93:102353. [PMID: 40311173 DOI: 10.1016/j.gde.2025.102353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Revised: 04/04/2025] [Accepted: 04/14/2025] [Indexed: 05/03/2025]
Abstract
Adult stem cells maintain tissue homeostasis through the production of differentiating cells. Considerable recent work has identified that stem cells themselves are replaceable through the process of dedifferentiation. The capacity and mechanisms of dedifferentiation vary widely among species and organ contexts. However, some core features are commonly present. In this review, we summarize 'hallmarks' of dedifferentiation, including mechanisms for maintenance of potency, sensation of loss, and migration, and review the current understanding of dedifferentiation as a true replacement mechanism.
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Affiliation(s)
- Amelie A Raz
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA; Massachusetts Institute of Technology, Cambridge, MA, USA.
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8
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Raymond MJ, Cherubino MA, Vieira WA, Manon S, McCusker CD. Neural regulation of H3K27me3 during the induction of patterning competency in regenerating Axolotl limb cells. Commun Biol 2025; 8:659. [PMID: 40275079 PMCID: PMC12022170 DOI: 10.1038/s42003-025-08084-x] [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: 11/27/2023] [Accepted: 04/14/2025] [Indexed: 04/26/2025] Open
Abstract
Limb regeneration in the Mexican axolotl relies on the dedifferentiation of mature limb cells into blastema cells, which gain the ability to respond to patterning signals that guide tissue regeneration. While limb nerves are essential to make the blastema cells competent to pattern, the mechanisms remain unclear due to the complex and overlapping signals in amputated limbs. To overcome this challenge, we developed the Competency Accessory Limb Model (CALM), a simplified limb regeneration assay to study the induction and maintenance of patterning competency. Using CALM, here we show specific temporal windows during which cells acquire competency and associate this state with distinct H3K27me3 chromatin signatures. Furthermore, a combination of FGF and BMP signaling is sufficient to induce patterning competency in limb wound cells, and the ErBB signaling pathway is a downstream epigenetic target of these signals. These findings offer new insights into the molecular regulation of regenerative patterning.
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Affiliation(s)
- Michael J Raymond
- College of Science and Mathematics, Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA
| | - Matthew A Cherubino
- College of Science and Mathematics, Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA
| | - Warren A Vieira
- College of Science and Mathematics, Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA
| | - Sheyla Manon
- College of Science and Mathematics, Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA
| | - Catherine D McCusker
- College of Science and Mathematics, Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA.
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9
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Wang KT, Chen YC, Tsai FY, Judy CP, Adler CE. Pluripotent Stem Cell Plasticity is Sculpted by a Slit-Independent Robo Pathway in a Regenerative Animal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.14.648795. [PMID: 40376085 PMCID: PMC12080947 DOI: 10.1101/2025.04.14.648795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2025]
Abstract
Whole-body regeneration requires adult stem cells with high plasticity to differentiate into missing cell types. Planarians possess a unique configuration of organs embedded in a vast pool of pluripotent stem cells. How stem cells integrate positional information with discrete fates remains unknown. Here, we use the planarian pharynx to define the cell fates that depend on the pioneer transcription factor FoxA. We find that Roundabout receptor RoboA suppresses aberrant pharynx cell fates by altering foxA expression, independent of the canonical ligand Slit. An RNAi screen for extracellular proteins identifies Anosmin-1 as a potential partner of RoboA. Perturbing global patterning demonstrates that roboA / anosmin-1 functions locally in the brain. By contrast, altering pharynx fate with foxA knockdown induces head-specific neurons in the pharynx, indicating a latent plasticity of stem cells. Our data links critical extracellular cues with cell fate decisions of highly plastic stem cells, ensuring the fidelity of organ regeneration.
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10
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Tajer BJ, Kalu G, Jay S, Wynn E, Decaux A, Gilbert P, Singer HD, Kidd MD, Nelson JA, Harake N, Lopez NJ, Souchet NR, Luong AG, Savage AM, Min S, Karabacak A, Böhm S, Kim RT, Froitzheim T, Sousounis K, Courtemanche K, Han J, Payzin-Dogru D, Blair SJ, Roy S, Fei JF, Tanaka EM, Whited JL. Optimized toolkit for the manipulation of immortalized axolotl fibroblasts. Methods 2025; 240:21-34. [PMID: 40187387 DOI: 10.1016/j.ymeth.2025.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 02/27/2025] [Accepted: 03/27/2025] [Indexed: 04/07/2025] Open
Abstract
The axolotl salamander model has broad utility for regeneration studies, but this model is limited by a lack of efficient cell-culture-based tools. The Axolotl Limb-1 (AL-1) fibroblast line, the only available immortalized axolotl cell line, was first published over 20 years ago, but many established molecular biology techniques, such as lipofectamine transfection, CRISPR-Cas9 mutagenesis, and antibiotic selection, work poorly or remain untested in AL-1 cells. Innovating technologies to manipulate AL-1 cells in culture and study their behavior following transplantation into the axolotl will complement in-vivo studies, decrease the number of animals used, and enable the faster, more streamlined investigation of regenerative biology questions. Here, we establish transfection, mutagenesis, antibiotic selection, and in-vivo transplantation techniques in axolotl AL-1 cells. These techniques will enable efficient culture with AL-1 cells and guide future tool development for the culture and manipulation of other salamander cell lines.
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Affiliation(s)
- Benjamin J Tajer
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Glory Kalu
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Sarah Jay
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA; Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, 69342 Lyon Cedex 07, France
| | - Eric Wynn
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Antoine Decaux
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA; Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, 69342 Lyon Cedex 07, France
| | - Paul Gilbert
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Hani D Singer
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Maddeline D Kidd
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Jeffery A Nelson
- Bauer Core Facility, Harvard University, Northwest Building, Room B239, 52 Oxford St., Cambridge, MA 02138, USA
| | - Noora Harake
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Noah J Lopez
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Nathan R Souchet
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Anna G Luong
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Aaron M Savage
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Sangwon Min
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Alparslan Karabacak
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Sebastian Böhm
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Ryan T Kim
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Tim Froitzheim
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Konstantinos Sousounis
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Katherine Courtemanche
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Jihee Han
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Duygu Payzin-Dogru
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Steven J Blair
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA
| | - Stéphane Roy
- Department of Stomatology, Faculty of Dentistry, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, China
| | - Elly M Tanaka
- Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr.-Bohr-Gasse 3, 1030 Vienna, Austria
| | - Jessica L Whited
- Departmet of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02318, USA; Broad Institute, 415 Main St., Cambridge, MA 02142, USA; Department of Orthopedic Surgery, Brigham & Women's Hospital, Mass General Brigham, 75 Francis St., Boston, MA 02115, USA.
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11
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García-García D, Knapp D, Kim M, Jamwal K, Fuqua H, Seaman RP, Grindle RE, Nowoshilow S, Novatchkova M, Kolling FW, Graber JH, Murawala P. The essential role of connective-tissue cells during axolotl limb regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.30.645595. [PMID: 40236065 PMCID: PMC11996436 DOI: 10.1101/2025.03.30.645595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Axolotls ( Ambystoma mexicanum ) are known for their remarkable limb-regeneration abilities, which involve the formation of the blastema, a specialized structure consisting of progenitor cells contributed by all major tissues of the limb. Lateral plate mesoderm (LPM)-derived connective tissue (CT) cells dedifferentiate and play a critical role in blastema formation and subsequent limb regeneration. However, the complexity of the blastema's cellular composition and the extent of CT participation and necessity have not been rigorously explored. To address this gap, we conducted spatial transcriptomics using a select array of probes, revealing that CT cells constitute up to 75% of the blastema cells at their peak. Genetic ablation of CT cells significantly delays or truncates limb regeneration, underscoring their necessity during this process. Finally, we analyzed the molecular profile of CT cells throughout the stages of blastema formation and made it accessible through an interactive web platform. Our work reaffirms the central role of CT cells in axolotl limb regeneration and lays the foundation for identifying molecular mechanisms that govern blastema formation during the initial phases of limb regeneration.
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12
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Sasidharan Y, Suryavanshi V, Smit ME. A space for time. Exploring temporal regulation of plant development across spatial scales. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 122:e70130. [PMID: 40163327 PMCID: PMC11956849 DOI: 10.1111/tpj.70130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 03/15/2025] [Accepted: 03/19/2025] [Indexed: 04/02/2025]
Abstract
Plants continuously undergo change during their life cycle, experiencing dramatic phase transitions altering plant form, and regulating the assignment and progression of cell fates. The relative timing of developmental events is tightly controlled and involves integration of environmental, spatial, and relative age-related signals and actors. While plant phase transitions have been studied extensively and many of their regulators have been described, less is known about temporal regulation on a smaller, cell-level scale. Here, using examples from both plant and animal systems, we outline time-dependent changes. Looking at systemic scale changes, we discuss the timing of germination, juvenile-to-adult transition, flowering, and senescence, together with regeneration timing. Switching to temporal regulation on a cellular level, we discuss several instances from the animal field in which temporal control has been examined extensively at this scale. Then, we switch back to plants and summarize examples where plant cell-level changes are temporally regulated. As time cannot easily be separated from signaling derived from the environment and tissue context, we next discuss factors that have been implicated in controlling the timing of developmental events, reviewing temperature, photoperiod, nutrient availability, as well as tissue context and mechanical cues on the cellular scale. Afterwards, we provide an overview of mechanisms that have been shown or implicated in the temporal control of development, considering metabolism, division control, mobile signals, epigenetic regulation, and the action of transcription factors. Lastly, we look at remaining questions for the future study of developmental timing in plants and how recent technical advancement can enable these efforts.
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Affiliation(s)
- Yadhusankar Sasidharan
- Department of Developmental Genetics, Centre for Plant Molecular Biology (ZMBP)Eberhard Karls UniversityTuebingenD‐72076Germany
| | - Vijayalakshmi Suryavanshi
- Department of Developmental Genetics, Centre for Plant Molecular Biology (ZMBP)Eberhard Karls UniversityTuebingenD‐72076Germany
| | - Margot E. Smit
- Department of Developmental Genetics, Centre for Plant Molecular Biology (ZMBP)Eberhard Karls UniversityTuebingenD‐72076Germany
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13
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Xu QZ, Li YX, Shi WG, Dong Y, Li Z, Ip JCH, Galaska MP, Han C, Zhang Q, Sun YY, Zhao LL, Sun KM, Wang ZL, Qiu JW, Zhang XL. Chromosome-level genome assembly and single-cell analysis unveil molecular mechanisms of arm regeneration in the ophiuroid Ophiura sarsii vadicola. Genome Biol 2025; 26:82. [PMID: 40165295 PMCID: PMC11959729 DOI: 10.1186/s13059-025-03542-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 03/12/2025] [Indexed: 04/02/2025] Open
Abstract
BACKGROUND Ophiuroids, belonging to Ophiuroidea in Echinodermata, possess remarkable regenerative capacities in their arms, relying on cellular recruitment and de-differentiation. However, limited high-quality genomic resources have hindered the investigation of the underlying molecular mechanisms of ophiuroid regeneration. RESULTS Here, we report a chromosome-level genome of Ophiura sarsii vadicola, 259.28 Mbp in length with a scaffold N50 length of 66.91 Mbp. We then perform bulk and single-cell RNA sequencing analysis to investigate gene expression and cellular dynamics during arm regeneration. We identify five distinct cellular clusters involved in the arm regeneration and infer the dynamic transformations from sensory stimulation to injury response, wound healing, and tissue regeneration. We find that progenitor cells derived from connective tissue cells differentiate into muscle, cartilage, endothelial, and epithelial cells. Pseudotime analysis indicates that muscle differentiation occurs early in the regeneration process. CONCLUSIONS Our genomic resource and single-cell atlas shed light on the mechanisms of organ regeneration in ophiuroids.
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Affiliation(s)
- Qin-Zeng Xu
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, PR China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, PR China.
| | - Yi-Xuan Li
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, PR China
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, PR China
| | - Wen-Ge Shi
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, PR China
| | - Yue Dong
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, PR China
| | - Zhong Li
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, PR China
| | - Jack Chi-Ho Ip
- Science Unit, Lingnan University, Hong Kong SAR, PR China
| | - Matthew P Galaska
- Pacific Marine Environmental Lab, National Oceanic and Atmospheric Administration, Seattle, WA, USA
- Anchor QEA, Seattle, WA, USA
| | - Chen Han
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, PR China
| | - Qian Zhang
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, PR China
| | - Yu-Yao Sun
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, PR China
| | - Lin-Lin Zhao
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, PR China
| | - Kai-Ming Sun
- Institute of Oceanographic Instrumentation, Qilu University of Technology (Shandong Academy of Sciences), Qingdao, PR China
| | - Zong-Ling Wang
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, PR China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, PR China
| | - Xue-Lei Zhang
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, PR China
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14
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Cheng L, Wang Y, Guan J, Deng H. Decoding human chemical reprogramming: mechanisms and principles. Trends Biochem Sci 2025:S0968-0004(25)00053-2. [PMID: 40169299 DOI: 10.1016/j.tibs.2025.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Revised: 02/27/2025] [Accepted: 03/06/2025] [Indexed: 04/03/2025]
Abstract
Pluripotent stem cells hold great promise as an unlimited resource for regenerative medicine due to their capacity to self-renew and differentiate into various cell types. Chemical reprogramming using small molecules precisely regulates cell signaling pathways and epigenetic states, providing a novel approach for generating human pluripotent stem cells. Since its successful establishment in 2022, human chemical reprogramming has rapidly achieved significant progress, demonstrating its significant potential in regenerative medicine. Mechanistic analyses have revealed distinct molecular pathways and regulatory mechanisms unique to chemical reprogramming, differing from traditional transcription-factor-driven methods. In this review we highlight recent advancements in our understanding of the mechanisms of human chemical reprogramming, with the goal of enhancing insights into the principles of cell fate control and advancing regenerative medicine.
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Affiliation(s)
- Lin Cheng
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yanglu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Jingyang Guan
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China.
| | - Hongkui Deng
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Changping Laboratory, Beijing, China.
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15
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Medina-Feliciano JG, Valentín-Tirado G, Luna-Martínez K, Beltran-Rivera A, Miranda-Negrón Y, Garcia-Arraras JE. Single-cell RNA sequencing of the holothurian regenerating intestine reveals the pluripotency of the coelomic epithelium. eLife 2025; 13:RP100796. [PMID: 40111904 PMCID: PMC11925454 DOI: 10.7554/elife.100796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2025] Open
Abstract
In holothurians, the regenerative process following evisceration involves the development of a 'rudiment' or 'anlage' at the injured end of the mesentery. This regenerating anlage plays a pivotal role in the formation of a new intestine. Despite its significance, our understanding of the molecular characteristics inherent to the constituent cells of this structure has remained limited. To address this gap, we employed state-of-the-art scRNA-seq and hybridization chain reaction fluorescent in situ hybridization analyses to discern the distinct cellular populations associated with the regeneration anlage. Through this approach, we successfully identified 13 distinct cell clusters. Among these, two clusters exhibit characteristics consistent with putative mesenchymal cells, while another four show features akin to coelomocyte cell populations. The remaining seven cell clusters collectively form a large group encompassing the coelomic epithelium of the regenerating anlage and mesentery. Within this large group of clusters, we recognized previously documented cell populations such as muscle precursors, neuroepithelial cells, and actively proliferating cells. Strikingly, our analysis provides data for identifying at least four other cellular populations that we define as the precursor cells of the growing anlage. Consequently, our findings strengthen the hypothesis that the coelomic epithelium of the anlage is a pluripotent tissue that gives rise to diverse cell types of the regenerating intestinal organ. Moreover, our results provide the initial view into the transcriptomic analysis of cell populations responsible for the amazing regenerative capabilities of echinoderms.
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16
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Londono R, Pan Z, Hudnall ML, Lozito TP. Simulation of adult limb regeneration with lizard tail spinal cord implants reveals distinct roles of radial glia and microglia populations. RESEARCH SQUARE 2025:rs.3.rs-6010337. [PMID: 40092433 PMCID: PMC11908338 DOI: 10.21203/rs.3.rs-6010337/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
Lizards are the closest relatives of humans able to suppress fibrosis and regrow multiple tissue lineages following appendage regeneration. As amniotes capable of tail, but not limb regrowth, lizards are also distinguished as the only vertebrate group that include both regenerative and non-regenerative appendages in the same animal. Lizard tail stumps naturally form blastemas - heterogenous collections of fibroblasts, adult stem cells, and immune cells that suppress scar formation and potentiate new tissue growth. Conversely, amputated lizard limbs form scars similar to those observed in human patients. Lizard blastema formation is dependent upon tail spinal cord tissue, which contains distinct populations of radial glia and microglia. Using the parthenogenetic lizard Lepidodactylus lugubris as a platform for tail-to-limb spinal cord implantations, we developed an ectopic blastema model toward defining the roles of radial glial and microglia in appendage regeneration. Removal of either population inhibits fibroblast proliferation and blastema formation, but only microglia depletion leads to enhanced fibrosis. Similarly, effects of radial glia, but not microglia, depletion on fibroblast proliferation are reversed via Hedgehog agonism. Taken together, these results indicate that lizard limbs contain all the necessary cell types and biological responses necessary for blastema formation but lack the proliferative and anti-fibrotic signals provided by tail spinal cord radial glia and microglia, respectively. Radial glia contribute Hedgehog signals that cause fibroblast proliferation but do not affect fibrosis. Conversely, microglia enhance fibroblast sensitivity to Hedgehog signaling and inhibit differentiation into fibrocytes. In summary, this study demonstrates blastema stimulation in amputated limbs of adult amniotes with application of lizard spinal cord cells and holds promise as a blueprint for limiting painful scarring and supporting new tissue growth following amputation injuries in human patients.
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Affiliation(s)
- Ricardo Londono
- Center for Cellular and Molecular Engineering, Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zheyu Pan
- Department of Orthopaedic Surgery, Keck School of Medicine, University of Southern California, 1540 Alcazar St, Los Angeles, CA 90089, USA
| | - Megan L Hudnall
- Department of Orthopaedic Surgery, Keck School of Medicine, University of Southern California, 1540 Alcazar St, Los Angeles, CA 90089, USA
| | - Thomas P Lozito
- Department of Orthopaedic Surgery, Keck School of Medicine, University of Southern California, 1540 Alcazar St, Los Angeles, CA 90089, USA
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, 1425 San Pablo St, Los Angeles, CA 90033, US
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17
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Farhadi A, Xue L, Zhao Q, Tan K. An overview of recent progress in the molecular mechanisms and key biological macromolecules involved in limb regeneration of decapods. Int J Biol Macromol 2025; 292:139354. [PMID: 39743118 DOI: 10.1016/j.ijbiomac.2024.139354] [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: 09/19/2024] [Revised: 12/16/2024] [Accepted: 12/28/2024] [Indexed: 01/04/2025]
Abstract
Understanding the molecular mechanisms of limb regeneration in decapods can significantly enhance aquaculture production by improving survival and growth, as well as facilitating the development of lab-grown crustacean meat as a sustainable protein source. This review explores the molecular mechanisms of decapod limb regeneration, focusing on the key signaling pathways, genes, and proteins involved in this process. The initial stages of regeneration involve immune response and hemolymph coagulation, which are regulated via signaling pathways such as Toll, MAPK, IMD, and JAK/STAT. Subsequent stages, including blastema formation and limb growth, are regulated by signaling pathways such as Wnt, Hippo, Hedgehog, Ecdysteroid, TGF-β, Notch, Insulin-like, Fibroblast Growth Factor, Epidermal Growth Factor, and BMP. This review also discusses the interplay among environmental factors, nutrition, and hormonal signaling in regeneration and how these elements influence regenerative capability. Furthermore, this review highlights existing research gaps in decapod regeneration and suggests future research directions. This review aims to bridge existing gaps in decapod regeneration research and guide future studies toward potential breakthroughs in aquaculture practices.
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Affiliation(s)
- Ardavan Farhadi
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan 570228, China.
| | - Laizhong Xue
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan 570228, China
| | - Qun Zhao
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan 570228, China.
| | - Karsoon Tan
- College of Marine Science, Guangxi Key Laboratory of Beibu Gulf Biodiversity Conservation, Beibu Gulf Ocean Development Research Center, Beibu Gulf University, Qinzhou, Guangxi, China.
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18
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Marshall EJ, Ramarapu R, Leathers TA, Morrison-Welch N, Sandberg K, Kawashima M, Rogers CD. NSAID-mediated cyclooxygenase inhibition disrupts ectodermal derivative formation in axolotl embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.10.30.621122. [PMID: 39554061 PMCID: PMC11565853 DOI: 10.1101/2024.10.30.621122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Embryonic exposures to non-stseroidal anti-inflammatory drugs (NSAIDs) have been linked to preterm birth, neural tube closure defects, abnormal enteric innervation, and craniofacial malformations, potentially due to disrupted neural tube or neural crest (NC) cell development. Naproxen (NPX), a common non-steroidal anti-inflammatory drug (NSAID) used to relieve pain and inflammation, exerts its effects through non-selective cyclooxygenase (COX) inhibition. Our lab has identified that the cyclooxygenase (COX-1 and COX-2) isoenzymes are expressed during the early stages of vertebrate embryonic development, and that global inhibition of COX-1 and COX-2 function disrupts NC cell migration and differentiation in Ambystoma mexicanum (axolotl) embryos. NC cells differentiate into various adult tissues including craniofacial cartilage, bone, and neurons in the peripheral and enteric nervous systems. To investigate the specific phenotypic and molecular effects of NPX exposure on NC development and differentiation, and to identify molecular links between COX inhibition and NC derivative anomalies, we exposed late neurula and early tailbud stage axolotl embryos to various concentrations of NPX and performed immunohistochemistry (IHC) for markers of migratory and differentiating NC cells. Our results reveal that NPX exposure impairs the migration of SOX9+ NC cells, leading to abnormal development of craniofacial cartilage structures, including Meckel's cartilage in the jaw. NPX exposure also alters the expression of markers associated with peripheral and central nervous system (PNS and CNS) development, suggesting concurrent neurodevelopmental changes.
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Affiliation(s)
- Emma J Marshall
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, Davis, CA, USA
| | - Raneesh Ramarapu
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, Davis, CA, USA
| | - Tess A Leathers
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, Davis, CA, USA
| | | | - Kathryn Sandberg
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, Davis, CA, USA
| | - Maxim Kawashima
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, Davis, CA, USA
| | - Crystal D Rogers
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, Davis, CA, USA
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19
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Moreno-Blas D, Adell T, González-Estévez C. Autophagy in Tissue Repair and Regeneration. Cells 2025; 14:282. [PMID: 39996754 PMCID: PMC11853389 DOI: 10.3390/cells14040282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2024] [Revised: 02/01/2025] [Accepted: 02/13/2025] [Indexed: 02/26/2025] Open
Abstract
Autophagy is a cellular recycling system that, through the sequestration and degradation of intracellular components regulates multiple cellular functions to maintain cellular homeostasis and survival. Dysregulation of autophagy is closely associated with the development of physiological alterations and human diseases, including the loss of regenerative capacity. Tissue regeneration is a highly complex process that relies on the coordinated interplay of several cellular processes, such as injury sensing, defense responses, cell proliferation, differentiation, migration, and cellular senescence. These processes act synergistically to repair or replace damaged tissues and restore their morphology and function. In this review, we examine the evidence supporting the involvement of the autophagy pathway in the different cellular mechanisms comprising the processes of regeneration and repair across different regenerative contexts. Additionally, we explore how modulating autophagy can enhance or accelerate regeneration and repair, highlighting autophagy as a promising therapeutic target in regenerative medicine for the development of autophagy-based treatments for human diseases.
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Affiliation(s)
| | | | - Cristina González-Estévez
- Department of Genetics, Microbiology and Statistics, School of Biology and Institute of Biomedicine (IBUB), University of Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain; (D.M.-B.); (T.A.)
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20
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Rivadeneira EO, Allen R, Adam M, Seifert AW. Specific cell states underlie complex tissue regeneration in spiny mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.10.637521. [PMID: 39990382 PMCID: PMC11844359 DOI: 10.1101/2025.02.10.637521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
Cell proliferation is an elemental feature of epimorphic regeneration in vertebrate taxa. We previously reported that in contrast to fibrotic repair observed in laboratory mouse ( Mus ) strains, highly regenerative spiny mice ( Acomys spp.) exhibit cell cycle progression and cell proliferation to faithfully replace missing tissue. However, little is known about proliferation dynamics, and specific cell types and states that may contribute to complex tissue regeneration in mammals. Using temporal pulse-chase experiments, we show that stromal cells in Acomys dimidiatus rapidly re-enter the cell cycle in response to injury and maintain tight spatiotemporal control of cell cycle progression to restrict the proliferative population to a distal area relative to the injury. Conversely, Mus stromal cells incorporate thymidine analogs without cell division supporting an S-phase arrest after D10. Deploying immunostaining and scRNA-seq, we identify several key cell types (CRABP1+, αSMA+) differentially associated with regenerating versus scar tissue. Importantly, our single cell data revealed distinct gene expression profiles for cross-species stromal cell types, identifying cell states specific for regenerative or fibrotic healing. While CRABP1+ fibroblasts are enriched in Acomys ears before and after injury, similar fibroblasts enriched in young, postnatal Mus ears remain unable to promote regeneration. Our data underscore the finely regulated dynamics of proliferating cells during regeneration and emphasize that regeneration depends on multiple factors including the presence of specific cell types and the ability of cells to acquire specific states. Key Conclusions Differentiated cells in Acomys , Mus and Danio re-enter the cell cycle in response to injury, while homeostatic cycling cells contribute to blastema formation in Ambystoma Pulse-chase thymidine analog labeling shows tight spatiotemporal control of proliferating stromal cells during regeneration in Acomys . Following injury, CRABP1 and αSMA are expressed in distinct stromal cell populations in Acomys but are co-expressed in Mus stromal cell populations. Species-specific cell states underlie regenerative and fibrotic repair CRABP1+ cells are lost during embryonic development in Mus ear pinna but are retained in Acomys to adulthood. Young neonatal Mus with abundant CRABP1+ cells still fail to execute regenerative healing. SUMMARY STATEMENT Comparing regenerative vs. fibrotic healing, we identify injury-induced cell states associated with persistent cell cycle progression and complex tissue regeneration in mammals.
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21
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Allen RS, Seifert AW. Spiny mice (Acomys) have evolved cellular features to support regenerative healing. Ann N Y Acad Sci 2025; 1544:5-26. [PMID: 39805008 PMCID: PMC11830558 DOI: 10.1111/nyas.15281] [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: 01/16/2025]
Abstract
Spiny mice (Acomys spp.) are warm-blooded (homeothermic) vertebrates whose ability to restore missing tissue through regenerative healing has coincided with the evolution of unique cellular and physiological adaptations across different tissue types. This review seeks to explore how these bizarre rodents deploy unique or altered injury response mechanisms to either enhance tissue repair or fully regenerate excised tissue compared to closely related, scar-forming mammals. First, we examine overall trends in healing Acomys tissues, including the cellular stress response, the ability to activate and maintain cell cycle progression, and the expression of certain features in reproductive adults that are normally associated with embryos. Second, we focus on specific cell types that exhibit precisely regulated proliferation to restore missing tissue. While Acomys utilize many of the same cell types involved in scar formation, these cells exhibit divergent activation profiles during regenerative healing. Considered together, current lines of evidence support sustained deployment of proregenerative pathways in conjunction with transient activation of fibrotic pathways to facilitate regeneration and improve tissue repair in Acomys.
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Affiliation(s)
- Robyn S. Allen
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Ashley W. Seifert
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
- The Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, Kentucky, USA
- Department of Veterinary Anatomy and Physiology, University of Nairobi, Nairobi, Kenya
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22
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Tam KT, Baar K. Using load to improve tendon/ligament tissue engineering and develop novel treatments for tendinopathy. Matrix Biol 2025; 135:39-54. [PMID: 39645093 DOI: 10.1016/j.matbio.2024.12.001] [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: 08/28/2024] [Revised: 11/15/2024] [Accepted: 12/01/2024] [Indexed: 12/09/2024]
Abstract
Tendon and ligament injuries are highly prevalent but heal poorly, even with proper care. Restoration of native tissue function is complicated by the fact that these tissues vary anatomically in terms of their mechanical properties, composition, and structure. These differences develop as adaptations to diverse mechanical demands; however, pathology may alter the loads placed on the tissue. Musculoskeletal loads can be generally categorized into tension, compression, and shear. Each of these regulate distinct molecular pathways that are involved in tissue remodeling, including many of the canonical tenogenic genes. In this review, we provide a perspective on the stage-specific regulation of mechanically sensitive pathways during development and maturation of tendon and ligament tissue, including scleraxis, mohawk, and others. Furthermore, we discuss structural features of healing and diseased tendon that may contribute to aberrant loading profiles, and how the associated disturbance in molecular signaling may contribute to incomplete healing or the formation of degenerative phenotypes. The perspectives provided here draw from studies spanning in vitro, animal, and human experiments of healthy and diseased tendon to propose a more targeted approach to advance rehabilitation, orthobiologics, and tissue engineering.
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Affiliation(s)
- Kenneth T Tam
- Biomedical Engineering Graduate Group, University of California Davis, Davis, CA 95616, USA; Department of Neurobiology, Physiology and Behavior, University of California Davis, Davis, CA 95616, USA
| | - Keith Baar
- Biomedical Engineering Graduate Group, University of California Davis, Davis, CA 95616, USA; Department of Neurobiology, Physiology and Behavior, University of California Davis, Davis, CA 95616, USA; Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; VA Northern California Health Care System, Mather, CA 95655, USA.
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23
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Chen Y, Hou Y, Zeng Q, Wang I, Shang M, Shin K, Hemauer C, Xing X, Kang J, Zhao G, Wang T. Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution. Genome Res 2025; 35:202-218. [PMID: 39809530 PMCID: PMC11789645 DOI: 10.1101/gr.279372.124] [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: 03/18/2024] [Accepted: 11/04/2024] [Indexed: 01/16/2025]
Abstract
Following amputation, zebrafish regenerate their injured caudal fin through lineage-restricted reprogramming. Although previous studies have charted various genetic and epigenetic dimensions of this process, the intricate gene regulatory programs shared by, or unique to, different regenerating cell types remain underinvestigated. Here, we mapped the regulatory landscape of fin regeneration by applying paired snRNA-seq and snATAC-seq on uninjured and regenerating fins. This map delineates the regulatory dynamics of predominant cell populations at multiple stages of regeneration. We observe a marked increase in the accessibility of chromatin regions associated with regenerative and developmental processes at 1 dpa, followed by a gradual closure across major cell types at later stages. This pattern is distinct from that of transcriptomic dynamics, which is characterized by several waves of gene upregulation and downregulation. We identified and in vivo validated cell-type-specific and position-specific regeneration-responsive enhancers and constructed regulatory networks by cell type and stage. Our single-cell resolution transcriptomic and chromatin accessibility map across regenerative stages provides new insights into regeneration regulatory mechanisms and serves as a valuable resource for the community.
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Affiliation(s)
- Yujie Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Yiran Hou
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Qinglin Zeng
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Irene Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Meiru Shang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Kwangdeok Shin
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin 53705, USA
| | - Christopher Hemauer
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin 53705, USA
| | - Guoyan Zhao
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
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24
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Nurhidayat L, Benes V, Blom S, Gomes I, Firdausi N, de Bakker MAG, Spaink HP, Richardson MK. Tokay gecko tail regeneration involves temporally collinear expression of HOXC genes and early expression of satellite cell markers. BMC Biol 2025; 23:6. [PMID: 39780185 PMCID: PMC11715542 DOI: 10.1186/s12915-024-02111-9] [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: 08/26/2024] [Accepted: 12/27/2024] [Indexed: 01/11/2025] Open
Abstract
BACKGROUND Regeneration is the replacement of lost or damaged tissue with a functional copy. In axolotls and zebrafish, regeneration involves stem cells produced by de-differentiation. These cells form a growth zone which expresses developmental patterning genes at its apex. This system resembles an embryonic developmental field where cells undergo pattern formation. Some lizards, including geckos, can regenerate their tails, but it is unclear whether they show a "development-like" regeneration pathway. RESULTS Using the tokay gecko (Gekko gecko) model species, we examined seven stages of tail regeneration, and three stages of embryonic tail bud development, using transcriptomics, single-cell sequencing, and in situ hybridization. We find no apical growth zone in the regenerating tail. The transcriptomes of the regenerating vs. embryonic tails are quite different with respect to developmental patterning genes. Posterior HOXC genes were activated in a temporally collinear sequence in the regenerating tail. The major precursor populations were stromal cells (regenerating tail) vs. pluripotent stem cells (embryonic tail). Segmented skeletal muscles were regenerated with no expression of classical segmentation genes, but with the early activation of satellite cell markers. CONCLUSIONS Our study suggests that tail regeneration in the tokay gecko-unlike tail development-might rely on the activation of resident stem cells, guided by pre-existing positional information.
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Affiliation(s)
- Luthfi Nurhidayat
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Faculty of Biology, Universitas Gadjah Mada, Jalan Teknika Selatan Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory Heidelberg, Meyerhofstraße 1, Heidelberg, 69117, Germany
| | - Sira Blom
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Inês Gomes
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Nisrina Firdausi
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Merijn A G de Bakker
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Herman P Spaink
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Michael K Richardson
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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25
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Medina-Feliciano JG, Valentín-Tirado G, Luna-Martínez K, Beltran-Rivera A, Miranda-Negrón Y, García-Arrarás JE. Single-cell RNA sequencing of the holothurian regenerating intestine reveals the pluripotency of the coelomic epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601561. [PMID: 39005414 PMCID: PMC11244903 DOI: 10.1101/2024.07.01.601561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
In holothurians, the regenerative process following evisceration involves the development of a "rudiment" or "anlage" at the injured end of the mesentery. This regenerating anlage plays a pivotal role in the formation of a new intestine. Despite its significance, our understanding of the molecular characteristics inherent to the constituent cells of this structure has remained limited. To address this gap, we employed state-of-the-art scRNA-seq and HCR-FISH analyses to discern the distinct cellular populations associated with the regeneration anlage. Through this approach, we successfully identified thirteen distinct cell clusters. Among these, two clusters exhibit characteristics consistent with putative mesenchymal cells, while another four show features akin to coelomocyte cell populations. The remaining seven cell clusters collectively form a large group encompassing the coelomic epithelium of the regenerating anlage and mesentery. Within this large group of clusters, we recognized previously documented cell populations such as muscle precursors, neuroepithelial cells and actively proliferating cells. Strikingly, our analysis provides data for identifying at least four other cellular populations that we define as the precursor cells of the growing anlage. Consequently, our findings strengthen the hypothesis that the coelomic epithelium of the anlage is a pluripotent tissue that gives rise to diverse cell types of the regenerating intestinal organ. Moreover, our results provide the initial view into the transcriptomic analysis of cell populations responsible for the amazing regenerative capabilities of echinoderms.
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26
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Fashemi BE, Rougeau AK, Salazar AM, Bark SJ, Chappidi R, Brown JW, Cho CJ, Mills JC, Mysorekar IU. IFRD1 is required for maintenance of bladder epithelial homeostasis. iScience 2024; 27:111282. [PMID: 39628564 PMCID: PMC11613175 DOI: 10.1016/j.isci.2024.111282] [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] [Received: 01/25/2024] [Revised: 06/21/2024] [Accepted: 10/25/2024] [Indexed: 12/06/2024] Open
Abstract
The maintenance of homeostasis and rapid regeneration of the urothelium following stress are critical for bladder function. Here, we identify a key role for IFRD1 in maintaining urothelial homeostasis in a mouse model. We demonstrate that the murine bladder expresses IFRD1 at homeostasis, particularly in the urothelium, and its loss alters the global transcriptome with significant accumulation of endolysosomes and dysregulated uroplakin expression pattern. We show that IFRD1 interacts with mRNA-translation-regulating factors in human urothelial cells. Loss of Ifrd1 leads to disrupted proteostasis, enhanced endoplasmic reticulum (ER stress) with activation of the PERK arm of the unfolded protein response pathway, and increased oxidative stress. Ifrd1-deficient bladders exhibit urothelial cell apoptosis/exfoliation, enhanced basal cell proliferation, reduced differentiation into superficial cells, increased urothelial permeability, and aberrant voiding behavior. These findings highlight a crucial role for IFRD1 in urothelial homeostasis, suggesting its potential as a therapeutic target for bladder dysfunction.
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Affiliation(s)
- Bisiayo E. Fashemi
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amala K. Rougeau
- Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Arnold M. Salazar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Steven J. Bark
- Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Rayvanth Chappidi
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey W. Brown
- Department of Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Charles J. Cho
- Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Jason C. Mills
- Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Indira U. Mysorekar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
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27
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Masselink W, Murawala P. The evolutionary origin and mechanism of chordate tail regeneration. An ancient tale? Cells Dev 2024:203988. [PMID: 39706570 DOI: 10.1016/j.cdev.2024.203988] [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: 11/13/2024] [Revised: 12/15/2024] [Accepted: 12/17/2024] [Indexed: 12/23/2024]
Abstract
Chordate tail regeneration represents the remarkable ability of some chordates to partially or completely regenerate a significant portion of their primary body axis. In this review we will discuss the chordate regenerative ability, what is known about the cellular sources which contribute to the regenerating tail, how various structures such as the spinal cord and vertebral column are re-established, and how scaling of the regenerating tail is regulated. Finally, we propose that tail regeneration is evolutionarily conserved and is fundamentally different from tail development however the origin and mechanism of this process remain elusive.
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Affiliation(s)
- Wouter Masselink
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria.
| | - Prayag Murawala
- MDI Biological laboratory (MDIBL), Bar Harbor, ME 04609, USA; Department of Nephrology and Hypertension, Hannover Medical School, 30625 Hannover, Germany.
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28
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Pan X, Zhao Y, Li Y, Chen J, Zhang W, Yang L, Xiong YZ, Ying Y, Xu H, Zhang Y, Gao C, Sun Y, Li N, Chen L, Chen Z, Lei K. Mitochondrial dynamics govern whole-body regeneration through stem cell pluripotency and mitonuclear balance. Nat Commun 2024; 15:10681. [PMID: 39672898 PMCID: PMC11645412 DOI: 10.1038/s41467-024-54720-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 11/19/2024] [Indexed: 12/15/2024] Open
Abstract
Tissue regeneration is a complex process involving large changes in cell proliferation, fate determination, and differentiation. Mitochondrial dynamics and metabolism play a crucial role in development and wound repair, but their function in large-scale regeneration remains poorly understood. Planarians offer an excellent model to investigate this process due to their remarkable regenerative abilities. In this study, we examine mitochondrial dynamics during planarian regeneration. We find that knockdown of the mitochondrial fusion gene, opa1, impairs both tissue regeneration and stem cell pluripotency. Interestingly, the regeneration defects caused by opa1 knockdown are rescued by simultaneous knockdown of the mitochondrial fission gene, drp1, which partially restores mitochondrial dynamics. Furthermore, we discover that Mitolow stem cells exhibit an enrichment of pluripotency due to their fate choices at earlier stages. Transcriptomic analysis reveals the delicate mitonuclear balance in metabolism and mitochondrial proteins in regeneration, controlled by mitochondrial dynamics. These findings highlight the importance of maintaining mitochondrial dynamics in large-scale tissue regeneration and suggest the potential for manipulating these dynamics to enhance stem cell functionality and regenerative processes.
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Affiliation(s)
- Xue Pan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yun Zhao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Fudan University, Shanghai, China
| | - Yucong Li
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Fudan University, Shanghai, China
| | - Jiajia Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Wenya Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Fudan University, Shanghai, China
| | - Ling Yang
- HPC Center, Westlake University, Hangzhou, Zhejiang, China
| | - Yuanyi Zhou Xiong
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Fudan University, Shanghai, China
| | - Yuqing Ying
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Hao Xu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yuhong Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Chong Gao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yuhan Sun
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Nan Li
- HPC Center, Westlake University, Hangzhou, Zhejiang, China
| | - Liangyi Chen
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, National Biomedical Imaging Center, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- State Key Laboratory of Membrane Biology, Peking University, Beijing, China.
- PKU-Nanjing Institute of Translational Medicine, Nanjing, China.
| | - Zhixing Chen
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, National Biomedical Imaging Center, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| | - Kai Lei
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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29
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Blumenkrantz M, Woron F, Gagarin E, Weinstein E, Kamel MH, Campos L, Geras A, Anderson T, Mo J, Sherwood D, Gwin M, Dumitrascu B, Chahine NO, Smeeton J. Dynamic cell fate plasticity and tissue integration drive functional synovial joint regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.12.628180. [PMID: 39713398 PMCID: PMC11661154 DOI: 10.1101/2024.12.12.628180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
Adult mammalian synovial joints have limited regenerative capacity, where injuries heal with mechanically inferior fibrotic tissues. Here we developed a unilateral whole-joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using a combination of microCT, histological, live imaging, and single-cell RNA sequencing (scRNAseq) approaches after complete removal of all joint tissues, we find de novo regeneration of articular cartilage, ligament, and synovium into a functional joint. Clonal lineage tracing and scRNAseq implicate a multipotent, neural crest-derived population in the adult skeleton as a cell source for these regenerating tissues. Together, our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage.
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30
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Zhu J, Zhong X, He H, Cao J, Zhou Z, Dong J, Li H, Zhang A, Lyu Y, Li C, Guan J, Deng H. Generation of human expandable limb-bud-like progenitors via chemically induced dedifferentiation. Cell Stem Cell 2024; 31:1732-1740.e6. [PMID: 39442525 DOI: 10.1016/j.stem.2024.10.001] [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: 06/01/2024] [Revised: 08/15/2024] [Accepted: 10/01/2024] [Indexed: 10/25/2024]
Abstract
In certain highly regenerative animals, cellular dedifferentiation occurs after injury, allowing specialized cells to become progenitor cells for regeneration. However, this capacity is restricted in human cells due to reduced plasticity. Here, we introduce a chemical-induced dedifferentiation approach that reverts the differentiated cells to a progenitor-like state, conferring the features of human limb bud cells from human adult somatic cells. These chemically induced human limb-bud-like progenitors (hCiLBP cells) show a high degree of transcriptomic similarity to human embryonic limb bud progenitors. Importantly, we established culture conditions that allow hCiLBP cells to undergo extensive expansion while maintaining population homogeneity and long-term self-renewal capacity. Moreover, hCiLBP cells exhibit increased osteochondrogenic differentiation ability, providing an innovative platform for generation of skeletal lineage cell types. These results highlight a potential therapeutic approach for repairing damaged human tissues through reversal of developmental pathways from mature cells to expandable progenitor cells.
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Affiliation(s)
- Jialiang Zhu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; BeiCell Therapeutics, Beijing, China; BeiCell Therapeutics, Suzhou, China
| | - Xinxing Zhong
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Huanjing He
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jingxiao Cao
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | - Zhengyang Zhou
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jiebin Dong
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Honggang Li
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Anqi Zhang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yulin Lyu
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | - Cheng Li
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | - Jingyang Guan
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Ningbo Institute of Marine Medicine, Peking University, Beijing, China.
| | - Hongkui Deng
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China; Changping Laboratory, Beijing, China.
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Qin T, Han J, Fan C, Sun H, Rauf N, Wang T, Yin Z, Chen X. Unveiling axolotl transcriptome for tissue regeneration with high-resolution annotation via long-read sequencing. Comput Struct Biotechnol J 2024; 23:3186-3198. [PMID: 39263210 PMCID: PMC11388199 DOI: 10.1016/j.csbj.2024.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 08/08/2024] [Accepted: 08/14/2024] [Indexed: 09/13/2024] Open
Abstract
Axolotls are known for their remarkable regeneration ability. Exploring their transcriptome provides insight into regenerative mechanisms. However, the current annotation of the axolotl transcriptome is limited, leaving the role of unannotated transcripts in regeneration unknown. To discourse this challenge, we exploited long-read sequencing technology, which enables direct observation of full-length RNA transcripts, greatly enhancing the coverage and accuracy of axolotl transcriptome annotation. By utilizing this method, we identified 222 novel gene loci and 4775 novel transcripts, which were quantified using short-read sequencing data. Through the inclusive analysis, we discovered novel homologs, potential functional proteins, noncoding RNAs, and alternative splicing events in key regeneration pathways. In particular, we identified novel transcripts with high protein-coding potential implicated in cell cycle regulation and musculoskeletal development, and regeneration were identified. Interestingly, alternative splice variants were also detected across diverse pathways critical to regeneration. This specifies that these novel transcripts potentially play vital roles underpinning the robust regenerative capacities of axolotls. Single-cell transcriptomic analysis further revealed these isoforms to predominantly exist in axolotl limb chondrocytes and mature tissue cell populations. Overall, the findings significantly advanced consideration of the axolotl transcriptome and provided a new perspective for understanding the mechanisms of regenerative abilities of axolotls.
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Affiliation(s)
- Tian Qin
- Department of Orthopedic Surgery of Sir Run Run Shaw Hospital, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, China
| | - Jie Han
- Department of Sports Medicine & Orthopedic Surgery, The Second Affiliated Hospital, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Chunmei Fan
- Department of Sports Medicine & Orthopedic Surgery, The Second Affiliated Hospital, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Heng Sun
- Medical 3D Printing Center, Orthopedic Institute, Department of Orthopedic Surgery, The First Affiliated Hospital, School of Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu 215000, China
| | - Naveed Rauf
- Department of Sports Medicine & Orthopedic Surgery, The Second Affiliated Hospital, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Zi Yin
- Department of Orthopedic Surgery of Sir Run Run Shaw Hospital, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, China
| | - Xiao Chen
- Department of Sports Medicine & Orthopedic Surgery, The Second Affiliated Hospital, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, China
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Stockinger AW, Adelmann L, Fahrenberger M, Ruta C, Özpolat BD, Milivojev N, Balavoine G, Raible F. Molecular profiles, sources and lineage restrictions of stem cells in an annelid regeneration model. Nat Commun 2024; 15:9882. [PMID: 39557833 PMCID: PMC11574210 DOI: 10.1038/s41467-024-54041-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 10/30/2024] [Indexed: 11/20/2024] Open
Abstract
Regeneration of missing body parts can be observed in diverse animal phyla, but it remains unclear to which extent these capacities rely on shared or divergent principles. Research into this question requires detailed knowledge about the involved molecular and cellular principles in suitable reference models. By combining single-cell RNA sequencing and mosaic transgenesis in the marine annelid Platynereis dumerilii, we map cellular profiles and lineage restrictions during posterior regeneration. Our data reveal cell-type specific injury responses, re-expression of positional identity factors, and the re-emergence of stem cell signatures in multiple cell populations. Epidermis and mesodermal coelomic tissue produce distinct putative posterior stem cells (PSCs) in the emerging blastema. A novel mosaic transgenesis strategy reveals both developmental compartments and lineage restrictions during regenerative growth. Our work supports the notion that posterior regeneration involves dedifferentiation, and reveals molecular and mechanistic parallels between annelid and vertebrate regeneration.
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Affiliation(s)
- Alexander W Stockinger
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Genetics and Microbiology, Vienna, Austria
- Research Platform Single-Cell Regulation of Stem Cells (SinCeReSt), University of Vienna, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria
- PhD Programme Stem Cells, Tissues, Organoids - Dissecting Regulators of Potency and Pattern Formation (SCORPION), University of Vienna, Vienna, Austria
| | - Leonie Adelmann
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Genetics and Microbiology, Vienna, Austria
- Research Platform Single-Cell Regulation of Stem Cells (SinCeReSt), University of Vienna, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria
- PhD Programme Stem Cells, Tissues, Organoids - Dissecting Regulators of Potency and Pattern Formation (SCORPION), University of Vienna, Vienna, Austria
| | - Martin Fahrenberger
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Research Platform Single-Cell Regulation of Stem Cells (SinCeReSt), University of Vienna, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria
- Center for Integrative Bioinformatics Vienna (CIBIV), University of Vienna and Medical University of Vienna, Vienna, Austria
- Medical University of Vienna, Max Perutz Labs, Vienna, Austria
| | - Christine Ruta
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - B Duygu Özpolat
- Université de Paris Cité, CNRS, Institut Jacques Monod, Paris, France
- Department of Biology, Washington University in Saint Louis, St. Louis, MO, USA
| | - Nadja Milivojev
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Genetics and Microbiology, Vienna, Austria
- Research Platform Single-Cell Regulation of Stem Cells (SinCeReSt), University of Vienna, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria
- PhD Programme Stem Cells, Tissues, Organoids - Dissecting Regulators of Potency and Pattern Formation (SCORPION), University of Vienna, Vienna, Austria
| | - Guillaume Balavoine
- Université de Paris Cité, CNRS, Institut Jacques Monod, Paris, France.
- Institute of Neuroscience, CNRS, Université Paris-Saclay, Saclay, France.
| | - Florian Raible
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- University of Vienna, Center for Molecular Biology, Department of Genetics and Microbiology, Vienna, Austria.
- Research Platform Single-Cell Regulation of Stem Cells (SinCeReSt), University of Vienna, Vienna, Austria.
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Del Moral-Morales A, Sámano C, Ocampo-Cervantes JA, Topf M, Baumbach J, Hernández J, Torres-Arciga K, González-Barrios R, Soto-Reyes E. Key Proteins for Regeneration in A. mexicanum: Transcriptomic Insights From Aged and Juvenile Limbs. SCIENTIFICA 2024; 2024:5460694. [PMID: 39575453 PMCID: PMC11581807 DOI: 10.1155/2024/5460694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 10/10/2024] [Indexed: 11/24/2024]
Abstract
The axolotl, known for its remarkable regenerative abilities, is an excellent model for studying regenerative therapies. Nevertheless, the precise molecular mechanisms governing its regenerative potential remain uncertain. In this study, we collected samples from axolotls of different ages, including 8-year-old individuals and 8-month-old juveniles, obtaining their blastemas 10 days after amputation. Subsequently, we conducted a transcriptomic analysis comparing our samples to a set of previously published experiments. Our analysis unveiled a distinctive transcriptional response in the blastema, characterized by differential gene expression associated with processes such as bone and tissue remodeling, transcriptional regulation, angiogenesis, and intercellular communication. To gain deeper insights, we compared these findings with those from aged axolotls that showed no signs of regeneration 10 days after amputation. We identified four genes-FSTL1, ADAMTS17, GPX7, and CTHRC1-that showed higher expression in regenerating tissue compared to aged axolotls. Further scrutiny, including structural and homology analysis, revealed that these genes are conserved across vertebrate species. Our discoveries point to a group of proteins relevant to tissue regeneration, with their conservation in vertebrates suggesting critical roles in development. These findings also propose a novel gene set involved in axolotl regeneration, laying a promising foundation for future investigations across vertebrates.
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Affiliation(s)
- Aylin Del Moral-Morales
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
| | - Cynthia Sámano
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
| | - José Antonio Ocampo-Cervantes
- Centro de Investigaciones Biológicas y Acuícolas de Cuemanco (CIBAC), Universidad Autónoma Metropolitana-Xochimilco (UAM-X), Mexico City, Mexico
| | - Maya Topf
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Leibniz-Institut für Virologie (LIV), Hamburg, Germany
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational BioMedicine Lab., University of Southern Denmark, Odense, Denmark
| | - Jossephlyn Hernández
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
| | - Karla Torres-Arciga
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Ernesto Soto-Reyes
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
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Erickson JR, Walker SE, Arenas Gomez CM, Echeverri K. Sall4 regulates downstream patterning genes during limb regeneration. Dev Biol 2024; 515:151-159. [PMID: 39067503 PMCID: PMC11325254 DOI: 10.1016/j.ydbio.2024.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Many salamanders can completely regenerate a fully functional limb. Limb regeneration is a carefully coordinated process involving several defined stages. One key event during the regeneration process is the patterning of the blastema to inform cells of what they must differentiate into. Although it is known that many genes involved in the initial development of the limb are re-used during regeneration, the exact molecular circuitry involved in this process is not fully understood. Several large-scale transcriptional profiling studies of axolotl limb regeneration have identified many transcription factors that are up-regulated after limb amputation. Sall4 is a transcription factor that has been identified to play essential roles in maintaining cells in an undifferentiated state during development and also plays a unique role in limb development. Inactivation of Sall4 during limb bud development results in defects in anterior-posterior patterning of the limb. Sall4 has been found to be up-regulated during limb regeneration in both Xenopus and salamanders, but to date it function has been untested. We confirmed that Sall4 is up-regulated during limb regeneration in the axolotl using qRT-PCR and identified that it is present in the skin cells and also in cells within the blastema. Using CRISPR technology we microinjected gRNAs specific for Sall4 complexed with cas9 protein into the blastema to specifically knockout Sall4 in blastema cells only. This resulted in limb regenerate defects, including missing digits, fusion of digit elements, and defects in the radius and ulna. This suggests that during regeneration Sall4 may play a similar role in regulating the specification of anterior-proximal skeletal elements.
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Affiliation(s)
- J R Erickson
- Department of Genetics, Dell Biology and Development, Stell Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - S E Walker
- Marine Biological Laboratory, University of Chicago, Eugene Bell Center for Regeneration Biology and Tissue Engineering, Woods Hole, MA, USA
| | - C M Arenas Gomez
- Marine Biological Laboratory, University of Chicago, Eugene Bell Center for Regeneration Biology and Tissue Engineering, Woods Hole, MA, USA
| | - K Echeverri
- Department of Genetics, Dell Biology and Development, Stell Cell Institute, University of Minnesota, Minneapolis, MN, USA; Marine Biological Laboratory, University of Chicago, Eugene Bell Center for Regeneration Biology and Tissue Engineering, Woods Hole, MA, USA.
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Sindelka R, Naraine R, Abaffy P, Zucha D, Kraus D, Netusil J, Smetana K, Lacina L, Endaya BB, Neuzil J, Psenicka M, Kubista M. Characterization of regeneration initiating cells during Xenopus laevis tail regeneration. Genome Biol 2024; 25:251. [PMID: 39350302 PMCID: PMC11443866 DOI: 10.1186/s13059-024-03396-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 09/19/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Embryos are regeneration and wound healing masters. They rapidly close wounds and scarlessly remodel and regenerate injured tissue. Regeneration has been extensively studied in many animal models using new tools such as single-cell analysis. However, until now, they have been based primarily on experiments assessing from 1 day post injury. RESULTS In this paper, we reveal that critical steps initiating regeneration occur within hours after injury. We discovered the regeneration initiating cells (RICs) using single-cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells, and their expression signature suggests they are important for modifying the surrounding extracellular matrix thus regulating development. The absence or deregulation of RICs leads to excessive extracellular matrix deposition and defective regeneration. CONCLUSION RICs represent a newly discovered transient cell state involved in the initiation of the regeneration process.
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Affiliation(s)
- Radek Sindelka
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, 252 50, Czech Republic.
| | - Ravindra Naraine
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, 252 50, Czech Republic
| | - Pavel Abaffy
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, 252 50, Czech Republic
| | - Daniel Zucha
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, 252 50, Czech Republic
| | - Daniel Kraus
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, 252 50, Czech Republic
| | - Jiri Netusil
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, 252 50, Czech Republic
| | - Karel Smetana
- First Faculty of Medicine, Institute of Anatomy, Charles University, Prague 2, 128 00, Czech Republic
| | - Lukas Lacina
- First Faculty of Medicine, Institute of Anatomy, Charles University, Prague 2, 128 00, Czech Republic
- Department Dermatovenereology, First Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | - Berwini Beduya Endaya
- Laboratory of Molecular Therapy, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, 252 50, Czech Republic
| | - Jiri Neuzil
- Laboratory of Molecular Therapy, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, 252 50, Czech Republic
- School of Pharmacy and Medical Science, Griffith University, Southport, QLD, Australia
- Faculty of Science, Charles University, Prague 2, Czech Republic
- First Faculty of Medicine, Charles University, Prague 2, Czech Republic
| | - Martin Psenicka
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Vodnany, 389 25, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, 252 50, Czech Republic
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Zaraisky AG, Araslanova KR, Shitikov AD, Tereshina MB. Loss of the ability to regenerate body appendages in vertebrates: from side effects of evolutionary innovations to gene loss. Biol Rev Camb Philos Soc 2024; 99:1868-1888. [PMID: 38817123 DOI: 10.1111/brv.13102] [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: 10/24/2023] [Revised: 05/04/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024]
Abstract
The ability to regenerate large body appendages is an ancestral trait of vertebrates, which varies across different animal groups. While anamniotes (fish and amphibians) commonly possess this ability, it is notably restricted in amniotes (reptiles, birds, and mammals). In this review, we explore the factors contributing to the loss of regenerative capabilities in amniotes. First, we analyse the potential negative impacts on appendage regeneration caused by four evolutionary innovations: advanced immunity, skin keratinization, whole-body endothermy, and increased body size. These innovations emerged as amniotes transitioned to terrestrial habitats and were correlated with a decline in regeneration capability. Second, we examine the role played by the loss of regeneration-related enhancers and genes initiated by these innovations in the fixation of an inability to regenerate body appendages at the genomic level. We propose that following the cessation of regenerative capacity, the loss of highly specific regeneration enhancers could represent an evolutionarily neutral event. Consequently, the loss of such enhancers might promptly follow the suppression of regeneration as a side effect of evolutionary innovations. By contrast, the loss of regeneration-related genes, due to their pleiotropic functions, would only take place if such loss was accompanied by additional evolutionary innovations that compensated for the loss of pleiotropic functions unrelated to regeneration, which would remain even after participation of these genes in regeneration was lost. Through a review of the literature, we provide evidence that, in many cases, the loss in amniotes of genes associated with body appendage regeneration in anamniotes was significantly delayed relative to the time when regenerative capability was lost. We hypothesise that this delay may be attributed to the necessity for evolutionary restructuring of developmental mechanisms to create conditions where the loss of these genes was a beneficial innovation for the organism. Experimental investigation of the downregulation of genes involved in the regeneration of body appendages in anamniotes but absent in amniotes offers a promising avenue to uncover evolutionary innovations that emerged from the loss of these genes. We propose that the vast majority of regeneration-related genes lost in amniotes (about 150 in humans) may be involved in regulating the early stages of limb and tail regeneration in anamniotes. Disruption of this stage, rather than the late stage, may not interfere with the mechanisms of limb and tail bud development during embryogenesis, as these mechanisms share similarities with those operating in the late stage of regeneration. Consequently, the most promising approach to restoring regeneration in humans may involve creating analogs of embryonic limb buds using stem cell-based tissue-engineering methods, followed by their transfer to the amputation stump. Due to the loss of many genes required specifically during the early stage of regeneration, this approach may be more effective than attempting to induce both early and late stages of regeneration directly in the stump itself.
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Affiliation(s)
- Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow, 117997, Russia
- Pirogov Russian National Research Medical University, 1 Ostrovityanova str., Moscow, 117997, Russia
| | - Karina R Araslanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow, 117997, Russia
| | - Alexander D Shitikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow, 117997, Russia
| | - Maria B Tereshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow, 117997, Russia
- Pirogov Russian National Research Medical University, 1 Ostrovityanova str., Moscow, 117997, Russia
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Barutia I, Sombke A. Explosive regeneration and anamorphic development of legs in the house centipede Scutigera coleoptrata. Front Zool 2024; 21:23. [PMID: 39294713 PMCID: PMC11412016 DOI: 10.1186/s12983-024-00544-0] [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: 07/11/2024] [Accepted: 09/11/2024] [Indexed: 09/21/2024] Open
Abstract
BACKGROUND Regenerating legs is advantageous for arthropods as their appendages exhibit crucial functional specializations. Many arthropods possess a 'preferred breakage point', where the appendage is most likely to break and where regeneration likely to occur, however, different taxa exhibit different levels of regenerative potential. Centipede appendage regeneration is categorized as 'progressive' or 'explosive'. In the later, the appendage is fully regenerated after one molt. This term was used for house centipedes that frequently lose their long legs. We chose Scutigera coleoptrata as a model to comprehensively investigate the process of leg appendotomy and regeneration as well as compare it with leg development in anamorphic instars. RESULTS The trochanter exhibits a preferred breakage point. Internally, it houses a three-layered diaphragm that effectively seals the lumen. In case of leg loss, the wound is quickly sealed. The epidermis detaches from the cuticle and muscles of the coxa get compacted, giving sufficient space for the regenerating leg. A blastema forms and the leg then grows in a coiled manner. The regenerating leg is innervated and syncytial muscles form. If the leg is lost in an early intermolt phase, progression of regeneration is slower than when a specimen is closer to the next molt. Instars of house centipedes can simultaneously develop and regenerate legs. The legs develop laterally on the posterior segments under the cuticle. As opposed to regeneration, the progression of leg development always follows the same temporal pattern throughout the entire intermolt phase. CONCLUSION Several factors are of major significance in house centipede leg regeneration. First, the ease with which they lose legs: the diaphragm represents an efficient tool for appendotomy. Moreover, the functional extension of the coxa provides space for a leg to be regenerated in. Lastly, the genetic predisposition allows them to regenerate legs within one molting cycle. This "package" is unique among land arthropods, and to this degree rare in marine taxa. Furthermore, observing leg regeneration and anamorphic leg development in parallel suggest that regeneration is most likely an epiphenomenon of development, and the differences are a requirement for the novel context in which re-development occurs.
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Affiliation(s)
- Iulia Barutia
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Institute for Zoology and Evolutionary Research, Animal Physiology, Friedrich-Schiller-University Jena, Erbertstrasse 1, 07743, Jena, Germany.
- Max-Planck-Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745, Jena, Germany.
| | - Andy Sombke
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Center for Anatomy and Cell Biology, Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, 1090, Vienna, Austria.
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Kramer J, Aires R, Keeley SD, Schröder TA, Lauer G, Sandoval-Guzmán T. Axolotl mandible regeneration occurs through mechanical gap closure and a shared regenerative program with the limb. Dis Model Mech 2024; 17:dmm050743. [PMID: 39206627 PMCID: PMC11449444 DOI: 10.1242/dmm.050743] [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: 02/14/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
The mandible plays an essential part in human life and, thus, defects in this structure can dramatically impair the quality of life in patients. Axolotls, unlike humans, are capable of regenerating their lower jaws; however, the underlying mechanisms and their similarities to those in limb regeneration are unknown. In this work, we used morphological, histological and transcriptomic approaches to analyze the regeneration of lateral resection defects in the axolotl mandible. We found that this structure can regenerate all missing tissues in 90 days through gap minimization, blastema formation and, finally, tissue growth, differentiation and integration. Moreover, transcriptomic comparisons of regenerating mandibles and limbs showed that they share molecular phases of regeneration, that these similarities peak during blastema stages and that mandible regeneration occurs at a slower pace. Altogether, our study demonstrates the existence of a shared regenerative program used in two different regenerating body structures with different embryonic origins in the axolotl and contributes to our understanding of the minimum requirements for a successful regeneration in vertebrates, bringing us closer to understand similar lesions in human mandibles.
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Affiliation(s)
- Julia Kramer
- Clinic of Oral and Maxillofacial Surgery, University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Rita Aires
- Department of Internal Medicine III, Center for Healthy Aging, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Sean D. Keeley
- Department of Internal Medicine III, Center for Healthy Aging, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Tom Alexander Schröder
- Clinic of Oral and Maxillofacial Surgery, University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Günter Lauer
- Clinic of Oral and Maxillofacial Surgery, University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Tatiana Sandoval-Guzmán
- Department of Internal Medicine III, Center for Healthy Aging, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Paul Langerhans Institute Dresden, Helmholtz Centre Munich, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
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Sparta B, Hamilton T, Natesan G, Aragones SD, Deeds EJ. Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing. PLoS Comput Biol 2024; 20:e1012386. [PMID: 39241106 PMCID: PMC11410258 DOI: 10.1371/journal.pcbi.1012386] [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: 01/30/2024] [Revised: 09/18/2024] [Accepted: 08/05/2024] [Indexed: 09/08/2024] Open
Abstract
Effective analysis of single-cell RNA sequencing (scRNA-seq) data requires a rigorous distinction between technical noise and biological variation. In this work, we propose a simple feature selection model, termed "Differentially Distributed Genes" or DDGs, where a binomial sampling process for each mRNA species produces a null model of technical variation. Using scRNA-seq data where cell identities have been established a priori, we find that the DDG model of biological variation outperforms existing methods. We demonstrate that DDGs distinguish a validated set of real biologically varying genes, minimize neighborhood distortion, and enable accurate partitioning of cells into their established cell-type groups.
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Affiliation(s)
- Breanne Sparta
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
| | - Timothy Hamilton
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California, United States of America
| | - Gunalan Natesan
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
| | - Samuel D Aragones
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
| | - Eric J Deeds
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
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40
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Youssef KK, Nieto MA. Epithelial-mesenchymal transition in tissue repair and degeneration. Nat Rev Mol Cell Biol 2024; 25:720-739. [PMID: 38684869 DOI: 10.1038/s41580-024-00733-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 05/02/2024]
Abstract
Epithelial-mesenchymal transitions (EMTs) are the epitome of cell plasticity in embryonic development and cancer; during EMT, epithelial cells undergo dramatic phenotypic changes and become able to migrate to form different tissues or give rise to metastases, respectively. The importance of EMTs in other contexts, such as tissue repair and fibrosis in the adult, has become increasingly recognized and studied. In this Review, we discuss the function of EMT in the adult after tissue damage and compare features of embryonic and adult EMT. Whereas sustained EMT leads to adult tissue degeneration, fibrosis and organ failure, its transient activation, which confers phenotypic and functional plasticity on somatic cells, promotes tissue repair after damage. Understanding the mechanisms and temporal regulation of different EMTs provides insight into how some tissues heal and has the potential to open new therapeutic avenues to promote repair or regeneration of tissue damage that is currently irreversible. We also discuss therapeutic strategies that modulate EMT that hold clinical promise in ameliorating fibrosis, and how precise EMT activation could be harnessed to enhance tissue repair.
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Affiliation(s)
| | - M Angela Nieto
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, Spain.
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.
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41
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Fujita T, Aoki N, Mori C, Homma KJ, Yamaguchi S. SoxC and MmpReg promote blastema formation in whole-body regeneration of fragmenting potworms Enchytraeus japonensis. Nat Commun 2024; 15:6659. [PMID: 39174502 PMCID: PMC11341731 DOI: 10.1038/s41467-024-50865-1] [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: 10/03/2022] [Accepted: 07/22/2024] [Indexed: 08/24/2024] Open
Abstract
Regeneration in many animals involves the formation of a blastema, which differentiates and organizes into the appropriate missing body parts. Although the mechanisms underlying blastema formation are often fundamental to regeneration biology, information on the cellular and molecular basis of blastema formation remains limited. Here, we focus on a fragmenting potworm (Enchytraeus japonensis), which can regenerate its whole body from small fragments. We find soxC and mmpReg as upregulated genes in the blastema. RNAi of soxC and mmpReg reduce the number of blastema cells, indicating that soxC and mmpReg promote blastema formation. Expression analyses show that soxC-expressing cells appear to gradually accumulate in blastema and constitute a large part of the blastema. Additionally, similar expression dynamics of SoxC orthologue genes in frog (Xenopus laevis) are found in the regeneration blastema of tadpole tail. Our findings provide insights into the cellular and molecular mechanisms underlying blastema formation across species.
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Affiliation(s)
- Toshiyuki Fujita
- Department of Biological Sciences, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Naoya Aoki
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Chihiro Mori
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Koichi J Homma
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Shinji Yamaguchi
- Department of Biological Sciences, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan.
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42
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Kawaguchi A, Wang J, Knapp D, Murawala P, Nowoshilow S, Masselink W, Taniguchi-Sugiura Y, Fei JF, Tanaka EM. A chromatin code for limb segment identity in axolotl limb regeneration. Dev Cell 2024; 59:2239-2253.e9. [PMID: 38788714 DOI: 10.1016/j.devcel.2024.05.002] [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: 01/15/2023] [Revised: 07/25/2023] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
The salamander limb correctly regenerates missing limb segments because connective tissue cells have segment-specific identities, termed "positional information". How positional information is molecularly encoded at the chromatin level has been unknown. Here, we performed genome-wide chromatin profiling in mature and regenerating axolotl limb connective tissue cells. We find segment-specific levels of histone H3K27me3 as the major positional mark, especially at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. In the hand, the permissive chromatin state of the homeoprotein gene HoxA13 engages with the regeneration program bypassing the upper limb program. Comparison of regeneration regulatory elements with those found in other regenerative animals identified a core shared set of transcription factors, supporting an ancient, conserved regeneration program.
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Affiliation(s)
- Akane Kawaguchi
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Dunja Knapp
- DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Prayag Murawala
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Sergej Nowoshilow
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Wouter Masselink
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Yuka Taniguchi-Sugiura
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
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43
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Duerr TJ, Miller M, Kumar S, Bakr D, Griffiths JR, Gautham AK, Douglas D, Voss SR, Monaghan JR. Retinoic acid breakdown is required for proximodistal positional identity during amphibian limb regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.07.607055. [PMID: 39149228 PMCID: PMC11326211 DOI: 10.1101/2024.08.07.607055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Regenerating limbs retain their proximodistal (PD) positional identity following amputation. This positional identity is genetically encoded by PD patterning genes that instruct blastema cells to regenerate the appropriate PD limb segment. Retinoic acid (RA) is known to specify proximal limb identity, but how RA signaling levels are established in the blastema is unknown. Here, we show that RA breakdown via CYP26B1 is essential for determining RA signaling levels within blastemas. CYP26B1 inhibition molecularly reprograms distal blastemas into a more proximal identity, phenocopying the effects of administering excess RA. We identify Shox as an RA-responsive gene that is differentially expressed between proximally and distally amputated limbs. Ablation of Shox results in shortened limbs with proximal skeletal elements that fail to initiate endochondral ossification. These results suggest that PD positional identity is determined by RA degradation and RA-responsive genes that regulate PD skeletal element formation during limb regeneration.
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Affiliation(s)
- Timothy J. Duerr
- Northeastern University, Department of Biology, Boston, MA
- Northeastern University, Institute for Chemical Imaging of Living Systems, Boston, MA
| | - Melissa Miller
- Northeastern University, Department of Biology, Boston, MA
| | - Sage Kumar
- Northeastern University, Institute for Chemical Imaging of Living Systems, Boston, MA
| | - Dareen Bakr
- Northeastern University, Department of Biology, Boston, MA
| | | | | | | | - S. Randal Voss
- University of Kentucky, Spinal Cord and Brain Injury Research Center, Department of Neuroscience, Ambystoma Genetic Stock Center, Lexington, KY
| | - James R. Monaghan
- Northeastern University, Department of Biology, Boston, MA
- Northeastern University, Institute for Chemical Imaging of Living Systems, Boston, MA
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44
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Huang L, Ho C, Ye X, Gao Y, Guo W, Chen J, Sun J, Wen D, Liu Y, Liu Y, Zhang Y, Li Q. Mechanisms and translational applications of regeneration in limbs: From renewable animals to humans. Ann Anat 2024; 255:152288. [PMID: 38823491 DOI: 10.1016/j.aanat.2024.152288] [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: 10/02/2023] [Revised: 04/08/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND The regenerative capacity of organisms declines throughout evolution, and mammals lack the ability to regenerate limbs after injury. Past approaches to achieving successful restoration through pharmacological intervention, tissue engineering, and cell therapies have faced significant challenges. OBJECTIVES This review aims to provide an overview of the current understanding of the mechanisms behind animal limb regeneration and the successful translation of these mechanisms for human tissue regeneration. RESULTS Particular attention was paid to the Mexican axolotl (Ambystoma mexicanum), the only adult tetrapod capable of limb regeneration. We will explore fundamental questions surrounding limb regeneration, such as how amputation initiates regeneration, how the limb knows when to stop and which parts to regenerate, and how these findings can apply to mammalian systems. CONCLUSIONS Given the urgent need for regenerative therapies to treat conditions like diabetic foot ulcers and trauma survivors, this review provides valuable insights and ideas for researchers, clinicians, and biomedical engineers seeking to facilitate the regeneration process or elicit full regeneration from partial regeneration events.
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Affiliation(s)
- Lu Huang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China; Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA.
| | - Chiakang Ho
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Xinran Ye
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Ya Gao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Weiming Guo
- Shanghai Key Laboratory of Stomatology, 639 Zhizaoju Road, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai 200011, China; National Center for Stomatology, Shanghai 200011, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai 200011, China; Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Julie Chen
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Jiaming Sun
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Dongsheng Wen
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Yangdan Liu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Yuxin Liu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Yifan Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China.
| | - Qingfeng Li
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China.
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45
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Tomasso A, Disela V, Longaker MT, Bartscherer K. Marvels of spiny mouse regeneration: cellular players and their interactions in restoring tissue architecture in mammals. Curr Opin Genet Dev 2024; 87:102228. [PMID: 39047585 DOI: 10.1016/j.gde.2024.102228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/12/2024] [Accepted: 06/30/2024] [Indexed: 07/27/2024]
Abstract
Understanding the cellular and molecular determinants of mammalian tissue regeneration and repair is crucial for developing effective therapies that restore tissue architecture and function. In this review, we focus on the cell types involved in scarless wound response and regeneration of spiny mice (Acomys). Comparative -omics approaches with scar-prone mammals have revealed species-specific peculiarities in cellular behavior during the divergent healing trajectories. We discuss the developing views on which cell types engage in restoring the architecture of spiny mouse tissues through a co-ordinated spatiotemporal response to injury. While yet at the beginning of understanding how cells interact in these fascinating animals to regenerate tissues, spiny mice hold great promise for scar prevention and anti-fibrotic treatments.
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Affiliation(s)
- Antonio Tomasso
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University - School of Medicine, Department of Surgery, Stanford, CA 94305, USA; Department of Biology/Chemistry, Osnabrück University, Osnabrück 49076, Germany; Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht 3584CT, the Netherlands. https://twitter.com/@anto_tomasso
| | - Vanessa Disela
- Department of Biology/Chemistry, Osnabrück University, Osnabrück 49076, Germany; Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht 3584CT, the Netherlands. https://twitter.com/@VDisela
| | - Michael T Longaker
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University - School of Medicine, Department of Surgery, Stanford, CA 94305, USA. https://twitter.com/@LongakerLab
| | - Kerstin Bartscherer
- Department of Biology/Chemistry, Osnabrück University, Osnabrück 49076, Germany.
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46
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Maynard A, Soretić M, Treutlein B. Single-cell genomic profiling to study regeneration. Curr Opin Genet Dev 2024; 87:102231. [PMID: 39053027 DOI: 10.1016/j.gde.2024.102231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/28/2024] [Accepted: 07/04/2024] [Indexed: 07/27/2024]
Abstract
Regenerative capacities and strategies vary dramatically across animals, as well as between cell types, organs, and with age. In recent years, high-throughput single-cell transcriptomics and other single-cell profiling technologies have been applied to many animal models to gain an understanding of the cellular and molecular mechanisms underlying regeneration. Here, we review recent single-cell studies of regeneration in diverse contexts and summarize key concepts that have emerged. The immense regenerative capacity of some invertebrates, exemplified by planarians, is driven mainly by the differentiation of abundant adult pluripotent stem cells, whereas in many other cases, regeneration involves the reactivation of embryonic or developmental gene-regulatory networks in differentiated cell types. However, regeneration also differs from development in many ways, including the use of regeneration-specific cell types and gene regulatory networks.
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Affiliation(s)
- Ashley Maynard
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - Mateja Soretić
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - Barbara Treutlein
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland.
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47
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Trompet D, Melis S, Chagin AS, Maes C. Skeletal stem and progenitor cells in bone development and repair. J Bone Miner Res 2024; 39:633-654. [PMID: 38696703 DOI: 10.1093/jbmr/zjae069] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/04/2024]
Abstract
Bone development, growth, and repair are complex processes involving various cell types and interactions, with central roles played by skeletal stem and progenitor cells. Recent research brought new insights into the skeletal precursor populations that mediate intramembranous and endochondral bone development. Later in life, many of the cellular and molecular mechanisms determining development are reactivated upon fracture, with powerful trauma-induced signaling cues triggering a variety of postnatal skeletal stem/progenitor cells (SSPCs) residing near the bone defect. Interestingly, in this injury context, the current evidence suggests that the fates of both SSPCs and differentiated skeletal cells can be considerably flexible and dynamic, and that multiple cell sources can be activated to operate as functional progenitors generating chondrocytes and/or osteoblasts. The combined implementation of in vivo lineage tracing, cell surface marker-based cell selection, single-cell molecular analyses, and high-resolution in situ imaging has strongly improved our insights into the diversity and roles of developmental and reparative stem/progenitor subsets, while also unveiling the complexity of their dynamics, hierarchies, and relationships. Albeit incompletely understood at present, findings supporting lineage flexibility and possibly plasticity among sources of osteogenic cells challenge the classical dogma of a single primitive, self-renewing, multipotent stem cell driving bone tissue formation and regeneration from the apex of a hierarchical and strictly unidirectional differentiation tree. We here review the state of the field and the newest discoveries in the origin, identity, and fates of skeletal progenitor cells during bone development and growth, discuss the contributions of adult SSPC populations to fracture repair, and reflect on the dynamism and relationships among skeletal precursors and differentiated cell lineages. Further research directed at unraveling the heterogeneity and capacities of SSPCs, as well as the regulatory cues determining their fate and functioning, will offer vital new options for clinical translation toward compromised fracture healing and bone regenerative medicine.
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Affiliation(s)
- Dana Trompet
- Laboratory of Skeletal Cell Biology and Physiology (SCEBP), Skeletal Biology and Engineering Research Center (SBE), Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, 40530 Gothenburg, Sweden
- Department of Physiology and Pharmacology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Seppe Melis
- Laboratory of Skeletal Cell Biology and Physiology (SCEBP), Skeletal Biology and Engineering Research Center (SBE), Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Andrei S Chagin
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, 40530 Gothenburg, Sweden
- Department of Physiology and Pharmacology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Christa Maes
- Laboratory of Skeletal Cell Biology and Physiology (SCEBP), Skeletal Biology and Engineering Research Center (SBE), Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
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48
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Aztekin C. Mechanisms of regeneration: to what extent do they recapitulate development? Development 2024; 151:dev202541. [PMID: 39045847 DOI: 10.1242/dev.202541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
One of the enduring debates in regeneration biology is the degree to which regeneration mirrors development. Recent technical advances, such as single-cell transcriptomics and the broad applicability of CRISPR systems, coupled with new model organisms in research, have led to the exploration of this longstanding concept from a broader perspective. In this Review, I outline the historical parallels between development and regeneration before focusing on recent research that highlights how dissecting the divergence between these processes can uncover previously unreported biological mechanisms. Finally, I discuss how these advances position regeneration as a more dynamic and variable process with expanded possibilities for morphogenesis compared with development. Collectively, these insights into mechanisms that orchestrate morphogenesis may reshape our understanding of the evolution of regeneration, reveal hidden biology activated by injury, and offer non-developmental strategies for restoring lost or damaged organs and tissues.
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Affiliation(s)
- Can Aztekin
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne, EPFL, 1015 Lausanne, Switzerland
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49
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Liberali P, Schier AF. The evolution of developmental biology through conceptual and technological revolutions. Cell 2024; 187:3461-3495. [PMID: 38906136 DOI: 10.1016/j.cell.2024.05.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Developmental biology-the study of the processes by which cells, tissues, and organisms develop and change over time-has entered a new golden age. After the molecular genetics revolution in the 80s and 90s and the diversification of the field in the early 21st century, we have entered a phase when powerful technologies provide new approaches and open unexplored avenues. Progress in the field has been accelerated by advances in genomics, imaging, engineering, and computational biology and by emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary technologies have led to remarkable progress in understanding animal development. We describe how classic questions in gene regulation, pattern formation, morphogenesis, organogenesis, and stem cell biology are being revisited. We discuss the connections of development with evolution, self-organization, metabolism, time, and ecology. We speculate how developmental biology might evolve in an era of synthetic biology, artificial intelligence, and human engineering.
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Affiliation(s)
- Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland.
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50
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Viragova S, Li D, Klein OD. Activation of fetal-like molecular programs during regeneration in the intestine and beyond. Cell Stem Cell 2024; 31:949-960. [PMID: 38971147 PMCID: PMC11235077 DOI: 10.1016/j.stem.2024.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/10/2024] [Accepted: 05/24/2024] [Indexed: 07/08/2024]
Abstract
Tissue regeneration after damage is generally thought to involve the mobilization of adult stem cells that divide and differentiate into progressively specialized progeny. However, recent studies indicate that tissue regeneration can be accompanied by reversion to a fetal-like state. During this process, cells at the injury site reactivate programs that operate during fetal development but are typically absent in adult homeostasis. Here, we summarize our current understanding of the molecular signals and epigenetic mediators that orchestrate "fetal-like reversion" during intestinal regeneration. We also explore evidence for this phenomenon in other organs and species and highlight open questions that merit future examination.
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Affiliation(s)
- Sara Viragova
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Dong Li
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA
| | - Ophir D Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA.
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