1
|
Poss KD, Tanaka EM. Hallmarks of regeneration. Cell Stem Cell 2024; 31:1244-1261. [PMID: 39163854 DOI: 10.1016/j.stem.2024.07.007] [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: 04/10/2024] [Revised: 06/12/2024] [Accepted: 07/24/2024] [Indexed: 08/22/2024]
Abstract
Regeneration is a heroic biological process that restores tissue architecture and function in the face of day-to-day cell loss or the aftershock of injury. Capacities and mechanisms for regeneration can vary widely among species, organs, and injury contexts. Here, we describe "hallmarks" of regeneration found in diverse settings of the animal kingdom, including activation of a cell source, initiation of regenerative programs in the source, interplay with supporting cell types, and control of tissue size and function. We discuss these hallmarks with an eye toward major challenges and applications of regenerative biology.
Collapse
Affiliation(s)
- Kenneth D Poss
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Elly M Tanaka
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Adrain C, Badenes M. Can the HB-EGF/EGFR pathway restore injured neurons? FEBS J 2024; 291:2094-2097. [PMID: 38680125 DOI: 10.1111/febs.17143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
Heparin-binding epidermal growth factor-like growth factor (HB-EGF) is a transmembrane protein that, when cleaved by metalloproteases through a process called ectodomain shedding, binds to the EGF receptor (EGFR), activating downstream signaling. The HB-EGF/EGFR pathway is crucial in development and is involved in numerous pathophysiological processes. In this issue of The FEBS Journal, Sireci et al. reveal a previously unexplored function of the HB-EGF/EGFR pathway in promoting neuronal progenitor proliferation and sensory neuron regeneration in the zebrafish olfactory epithelium in response to injury.
Collapse
Affiliation(s)
- Colin Adrain
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
- Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, UK
| | - Marina Badenes
- Veterinary and Animal Research Center (CECAV), Faculty of Veterinary Medicine, Lusófona University-Lisbon University Centre, Portugal
- Superior School of Health, Protection and Animal Welfare, Polytechnic Institute of Lusophony, Lisbon, Portugal
| |
Collapse
|
4
|
Sireci S, Kocagöz Y, Alkiraz AS, Güler K, Dokuzluoglu Z, Balcioglu E, Meydanli S, Demirler MC, Erdogan NS, Fuss SH. HB-EGF promotes progenitor cell proliferation and sensory neuron regeneration in the zebrafish olfactory epithelium. FEBS J 2024; 291:2098-2133. [PMID: 38088047 DOI: 10.1111/febs.17033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Maintenance and regeneration of the zebrafish olfactory epithelium (OE) are supported by two distinct progenitor cell populations that occupy spatially discrete stem cell niches and respond to different tissue conditions. Globose basal cells (GBCs) reside at the inner and peripheral margins of the sensory OE and are constitutively active to replace sporadically dying olfactory sensory neurons (OSNs). In contrast, horizontal basal cells (HBCs) are uniformly distributed across the sensory tissue and are selectively activated by acute injury conditions. Here we show that expression of the heparin-binding epidermal growth factor-like growth factor (HB-EGF) is strongly and transiently upregulated in response to OE injury and signals through the EGF receptor (EGFR), which is expressed by HBCs. Exogenous stimulation of the OE with recombinant HB-EGF promotes HBC expansion and OSN neurogenesis in a pattern that resembles the tissue response to injury. In contrast, pharmacological inhibition of HB-EGF membrane shedding, HB-EGF availability, and EGFR signaling strongly attenuate or delay injury-induced HBC activity and OSN restoration without affecting maintenance neurogenesis by GBCs. Thus, HB-EGF/EGFR signaling appears to be a critical component of the signaling network that controls HBC activity and, consequently, repair neurogenesis in the zebrafish OE.
Collapse
Affiliation(s)
- Siran Sireci
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogaziçi University, Istanbul, Türkiye
| | - Yigit Kocagöz
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogaziçi University, Istanbul, Türkiye
| | - Aysu Sevval Alkiraz
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogaziçi University, Istanbul, Türkiye
| | - Kardelen Güler
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogaziçi University, Istanbul, Türkiye
| | - Zeynep Dokuzluoglu
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogaziçi University, Istanbul, Türkiye
| | - Ecem Balcioglu
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogaziçi University, Istanbul, Türkiye
| | - Sinem Meydanli
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogaziçi University, Istanbul, Türkiye
| | - Mehmet Can Demirler
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogaziçi University, Istanbul, Türkiye
| | | | - Stefan Herbert Fuss
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogaziçi University, Istanbul, Türkiye
| |
Collapse
|
5
|
Peterson EA, Sun J, Chen X, Wang J. Neutrophils facilitate the epicardial regenerative response after zebrafish heart injury. Dev Biol 2024; 508:93-106. [PMID: 38286185 PMCID: PMC10923159 DOI: 10.1016/j.ydbio.2024.01.011] [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: 07/29/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 01/31/2024]
Abstract
Despite extensive studies on endogenous heart regeneration within the past 20 years, the players involved in initiating early regeneration events are far from clear. Here, we assessed the function of neutrophils, the first-responder cells to tissue damage, during zebrafish heart regeneration. We detected rapid neutrophil mobilization to the injury site after ventricular amputation, peaking at 1-day post-amputation (dpa) and resolving by 3 dpa. Further analyses indicated neutrophil mobilization coincides with peak epicardial cell proliferation, and recruited neutrophils associated with activated, expanding epicardial cells at 1 dpa. Neutrophil depletion inhibited myocardial regeneration and significantly reduced epicardial cell expansion, proliferation, and activation. To explore the molecular mechanism of neutrophils on the epicardial regenerative response, we performed scRNA-seq analysis of 1 dpa neutrophils and identified enrichment of the FGF and MAPK/ERK signaling pathways. Pharmacological inhibition of FGF signaling indicated its' requirement for epicardial expansion, while neutrophil depletion blocked MAPK/ERK signaling activation in epicardial cells. Ligand-receptor analysis indicated the EGF ligand, hbegfa, is released from neutrophils and synergizes with other FGF and MAPK/ERK factors for induction of epicardial regeneration. Altogether, our studies revealed that neutrophils quickly motivate epicardial cells, which later accumulate at the injury site and contribute to heart regeneration.
Collapse
Affiliation(s)
- Elizabeth A Peterson
- Division of Cardiology, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Jisheng Sun
- Division of Cardiology, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Xin Chen
- Division of Cardiology, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Jinhu Wang
- Division of Cardiology, School of Medicine, Emory University, Atlanta, GA, 30322, USA.
| |
Collapse
|
6
|
Ando K, Ou J, Thompson JD, Welsby J, Bangru S, Shen J, Wei X, Diao Y, Poss KD. A screen for regeneration-associated silencer regulatory elements in zebrafish. Dev Cell 2024; 59:676-691.e5. [PMID: 38290519 PMCID: PMC10939760 DOI: 10.1016/j.devcel.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 11/03/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Regeneration involves gene expression changes explained in part by context-dependent recruitment of transcriptional activators to distal enhancers. Silencers that engage repressive transcriptional complexes are less studied than enhancers and more technically challenging to validate, but they potentially have profound biological importance for regeneration. Here, we identified candidate silencers through a screening process that examined the ability of DNA sequences to limit injury-induced gene expression in larval zebrafish after fin amputation. A short sequence (s1) on chromosome 5 near several genes that reduce expression during adult fin regeneration could suppress promoter activity in stable transgenic lines and diminish nearby gene expression in knockin lines. High-resolution analysis of chromatin organization identified physical associations of s1 with gene promoters occurring preferentially during fin regeneration, and genomic deletion of s1 elevated the expression of these genes after fin amputation. Our study provides methods to identify "tissue regeneration silencer elements" (TRSEs) with the potential to reduce unnecessary or deleterious gene expression during regeneration.
Collapse
Affiliation(s)
- Kazunori Ando
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jianhong Ou
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John D Thompson
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John Welsby
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sushant Bangru
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jingwen Shen
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaolin Wei
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yarui Diao
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth D Poss
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA.
| |
Collapse
|
7
|
Bobrovskikh AV, Zubairova US, Doroshkov AV. Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of Teleostei. BIOLOGY 2023; 12:1516. [PMID: 38132342 PMCID: PMC10740722 DOI: 10.3390/biology12121516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other Teleostei from the GEO NCBI and the Single-Cell Expression Atlas. We found a considerable number of scRNAseq experiments at different stages of zebrafish development in organs such as the kidney, liver, stomach, heart, and brain. These datasets could be further used to conduct large-scale meta-analyses and to compare the IIS of zebrafish with the mammalian one. However, only a small number of scRNAseq datasets are available for other fish (turbot, salmon, cavefish, and dark sleeper). Since fish biology is very diverse, it would be a major mistake to use zebrafish alone in fish immunology studies. In particular, there is a special need for new scRNAseq experiments involving nonmodel Teleostei, e.g., long-lived species, cancer-resistant fish, and various fish ecotypes.
Collapse
Affiliation(s)
- Aleksandr V. Bobrovskikh
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
| | - Ulyana S. Zubairova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
- Department of Information Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexey V. Doroshkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
- Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia
| |
Collapse
|