1
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Goh KY, Lee WX, Choy SM, Priyadarshini GK, Chua K, Tan QH, Low SY, Chin HS, Wong CS, Huang SY, Fu NY, Nishiyama J, Harmston N, Tang HW. FOXO-regulated DEAF1 controls muscle regeneration through autophagy. Autophagy 2024:1-23. [PMID: 38963021 DOI: 10.1080/15548627.2024.2374693] [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: 07/13/2023] [Accepted: 06/26/2024] [Indexed: 07/05/2024] Open
Abstract
The commonality between various muscle diseases is the loss of muscle mass, function, and regeneration, which severely restricts mobility and impairs the quality of life. With muscle stem cells (MuSCs) playing a key role in facilitating muscle repair, targeting regulators of muscle regeneration has been shown to be a promising therapeutic approach to repair muscles. However, the underlying molecular mechanisms driving muscle regeneration are complex and poorly understood. Here, we identified a new regulator of muscle regeneration, Deaf1 (Deformed epidermal autoregulatory factor-1) - a transcriptional factor downstream of foxo signaling. We showed that Deaf1 is transcriptionally repressed by FOXOs and that DEAF1 targets to Pik3c3 and Atg16l1 promoter regions and suppresses their expression. Deaf1 depletion therefore induces macroautophagy/autophagy, which in turn blocks MuSC survival and differentiation. In contrast, Deaf1 overexpression inactivates autophagy in MuSCs, leading to increased protein aggregation and cell death. The fact that Deaf1 depletion and its overexpression both lead to defects in muscle regeneration highlights the importance of fine tuning DEAF1-regulated autophagy during muscle regeneration. We further showed that Deaf1 expression is altered in aging and cachectic MuSCs. Manipulation of Deaf1 expression can attenuate muscle atrophy and restore muscle regeneration in aged mice or mice with cachectic cancers. Together, our findings unveil an evolutionarily conserved role for DEAF1 in muscle regeneration, providing insights into the development of new therapeutic strategies against muscle atrophy.Abbreviations: DEAF1: Deformed epidermal autoregulatory factor-1; FOXO: Forkhead box O; MuSC: Muscle Stem Cell; PAX7: Paired box 7; PIK3C3: Phosphatidylinositol 3-kinase catalytic subunit type 3.
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Affiliation(s)
- Kah Yong Goh
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Wen Xing Lee
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Sze Mun Choy
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | | | - Kenon Chua
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Department of Orthopaedic Surgery, Singapore General Hospital, Singapore, Singapore
- Programme in Musculoskeletal Sciences Academic Clinical Program, SingHealth/Duke-NUS, Singapore, Singapore
| | - Qian Hui Tan
- Division of Science, Yale-NUS College, Singapore, Singapore
| | - Shin Yi Low
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Hui San Chin
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Chee Seng Wong
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Shu-Yi Huang
- Department of Medical Research, National Taiwan University Hospital, Taipei City, Taiwan
| | - Nai Yang Fu
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Jun Nishiyama
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Nathan Harmston
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Division of Science, Yale-NUS College, Singapore, Singapore
- Molecular Biosciences Division, Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - Hong-Wen Tang
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
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2
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Piran Z, Nitzan M. SiFT: uncovering hidden biological processes by probabilistic filtering of single-cell data. Nat Commun 2024; 15:760. [PMID: 38278815 PMCID: PMC10817921 DOI: 10.1038/s41467-024-44757-7] [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: 10/23/2023] [Accepted: 01/03/2024] [Indexed: 01/28/2024] Open
Abstract
Cellular populations simultaneously encode multiple biological attributes, including spatial configuration, temporal trajectories, and cell-cell interactions. Some of these signals may be overshadowed by others and harder to recover, despite the great progress made to computationally reconstruct biological processes from single-cell data. To address this, we present SiFT, a kernel-based projection method for filtering biological signals in single-cell data, thus uncovering underlying biological processes. SiFT applies to a wide range of tasks, from the removal of unwanted variation in the data to revealing hidden biological structures. We demonstrate how SiFT enhances the liver circadian signal by filtering spatial zonation, recovers regenerative cell subpopulations in spatially-resolved liver data, and exposes COVID-19 disease-related cells, pathways, and dynamics by filtering healthy reference signals. SiFT performs the correction at the gene expression level, can scale to large datasets, and compares favorably to state-of-the-art methods.
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Affiliation(s)
- Zoe Piran
- School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel
| | - Mor Nitzan
- School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel.
- Racah Institute of Physics, The Hebrew University, Jerusalem, Israel.
- Faculty of Medicine, The Hebrew University, Jerusalem, Israel.
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3
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Sun C, Shao Y, Iqbal J. Insect Insights at the Single-Cell Level: Technologies and Applications. Cells 2023; 13:91. [PMID: 38201295 PMCID: PMC10777908 DOI: 10.3390/cells13010091] [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: 11/22/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Single-cell techniques are a promising way to unravel the complexity and heterogeneity of transcripts at the cellular level and to reveal the composition of different cell types and functions in a tissue or organ. In recent years, advances in single-cell RNA sequencing (scRNA-seq) have further changed our view of biological systems. The application of scRNA-seq in insects enables the comprehensive characterization of both common and rare cell types and cell states, the discovery of new cell types, and revealing how cell types relate to each other. The recent application of scRNA-seq techniques to insect tissues has led to a number of exciting discoveries. Here we provide an overview of scRNA-seq and its application in insect research, focusing on biological applications, current challenges, and future opportunities to make new discoveries with scRNA-seq in insects.
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Affiliation(s)
- Chao Sun
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Yongqi Shao
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Junaid Iqbal
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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4
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Enomoto M, Igaki T. Cell-cell interactions that drive tumorigenesis in Drosophila. Fly (Austin) 2022; 16:367-381. [PMID: 36413374 PMCID: PMC9683056 DOI: 10.1080/19336934.2022.2148828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cell-cell interactions within tumour microenvironment play crucial roles in tumorigenesis. Genetic mosaic techniques available in Drosophila have provided a powerful platform to study the basic principles of tumour growth and progression via cell-cell communications. This led to the identification of oncogenic cell-cell interactions triggered by endocytic dysregulation, mitochondrial dysfunction, cell polarity defects, or Src activation in Drosophila imaginal epithelia. Such oncogenic cooperations can be caused by interactions among epithelial cells, mesenchymal cells, and immune cells. Moreover, microenvironmental factors such as nutrients, local tissue structures, and endogenous growth signalling activities critically affect tumorigenesis. Dissecting various types of oncogenic cell-cell interactions at the single-cell level in Drosophila will greatly increase our understanding of how tumours progress in living animals.
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Affiliation(s)
- Masato Enomoto
- Laboratory of Genetics, Graduate School of Biostudies, Kyoto University, Yoshida-Konoecho, Kyoto, Japan
| | - Tatsushi Igaki
- Laboratory of Genetics, Graduate School of Biostudies, Kyoto University, Yoshida-Konoecho, Kyoto, Japan,CONTACT Tatsushi Igaki
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5
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Katti P, Ajayi PT, Aponte A, Bleck CKE, Glancy B. Identification of evolutionarily conserved regulators of muscle mitochondrial network organization. Nat Commun 2022; 13:6622. [PMID: 36333356 PMCID: PMC9636386 DOI: 10.1038/s41467-022-34445-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial networks provide coordinated energy distribution throughout muscle cells. However, pathways specifying mitochondrial networks are incompletely understood and it is unclear how they might affect contractile fiber-type. Here, we show that natural energetic demands placed on Drosophila melanogaster muscles yield native cell-types among which contractile and mitochondrial network-types are regulated differentially. Proteomic analyses of indirect flight, jump, and leg muscles, together with muscles misexpressing known fiber-type specification factor salm, identified transcription factors H15 and cut as potential mitochondrial network regulators. We demonstrate H15 operates downstream of salm regulating flight muscle contractile and mitochondrial network-type. Conversely, H15 regulates mitochondrial network configuration but not contractile type in jump and leg muscles. Further, we find that cut regulates salm expression in flight muscles and mitochondrial network configuration in leg muscles. These data indicate cell type-specific regulation of muscle mitochondrial network organization through evolutionarily conserved transcription factors cut, salm, and H15.
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Affiliation(s)
- Prasanna Katti
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Peter T Ajayi
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Angel Aponte
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christopher K E Bleck
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Brian Glancy
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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6
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Worley MI, Everetts NJ, Yasutomi R, Chang RJ, Saretha S, Yosef N, Hariharan IK. Ets21C sustains a pro-regenerative transcriptional program in blastema cells of Drosophila imaginal discs. Curr Biol 2022; 32:3350-3364.e6. [PMID: 35820420 PMCID: PMC9387119 DOI: 10.1016/j.cub.2022.06.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 04/06/2022] [Accepted: 06/14/2022] [Indexed: 12/11/2022]
Abstract
An important unanswered question in regenerative biology is to what extent regeneration is accomplished by the reactivation of gene regulatory networks used during development versus the activation of regeneration-specific transcriptional programs. Following damage, Drosophila imaginal discs, the larval precursors of adult structures, can regenerate missing portions by localized proliferation of damage-adjacent tissue. Using single-cell transcriptomics in regenerating wing discs, we have obtained a comprehensive view of the transcriptome of regenerating discs and identified two regeneration-specific cell populations within the blastema, Blastema1 and Blastema2. Collectively, these cells upregulate multiple genes encoding secreted proteins that promote regeneration including Pvf1, upd3, asperous, Mmp1, and the maturation delaying factor Ilp8. Expression of the transcription factor Ets21C is restricted to this regenerative secretory zone; it is not expressed in undamaged discs. Ets21C expression is activated by the JNK/AP-1 pathway, and it can function in a type 1 coherent feedforward loop with AP-1 to sustain expression of downstream genes. Without Ets21C function, the blastema cells fail to maintain the expression of a number of genes, which leads to premature differentiation and severely compromised regeneration. As Ets21C is dispensable for normal development, these observations indicate that Ets21C orchestrates a regeneration-specific gene regulatory network. We have also identified cells resembling both Blastema1 and Blastema2 in scribble tumorous discs. They express the Ets21C-dependent gene regulatory network, and eliminating Ets21C function reduces tumorous growth. Thus, mechanisms that function during regeneration can be co-opted by tumors to promote aberrant growth.
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Affiliation(s)
- Melanie I Worley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Nicholas J Everetts
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Department of Electrical Engineering and Computer Science, Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Riku Yasutomi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Rebecca J Chang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Shrey Saretha
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science, Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Iswar K Hariharan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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7
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Tse J, Li TH, Zhang J, Lee ACK, Lee I, Qu Z, Lin X, Hui J, Chan TF. Single-Cell Atlas of the Drosophila Leg Disc Identifies a Long Non-Coding RNA in Late Development. Int J Mol Sci 2022; 23:ijms23126796. [PMID: 35743238 PMCID: PMC9224501 DOI: 10.3390/ijms23126796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/05/2023] Open
Abstract
The Drosophila imaginal disc has been an excellent model for the study of developmental gene regulation. In particular, long non-coding RNAs (lncRNAs) have gained widespread attention in recent years due to their important role in gene regulation. Their specific spatiotemporal expressions further support their role in developmental processes and diseases. In this study, we explored the role of a novel lncRNA in Drosophila leg development by dissecting and dissociating w1118 third-instar larval third leg (L3) discs into single cells and single nuclei, and performing single-cell RNA-sequencing (scRNA-seq) and single-cell assays for transposase-accessible chromatin (scATAC-seq). Single-cell transcriptomics analysis of the L3 discs across three developmental timepoints revealed different cell types and identified lncRNA:CR33938 as a distal specific gene with high expression in late development. This was further validated by fluorescence in-situ hybridization (FISH). The scATAC-seq results reproduced the single-cell transcriptomics landscape and elucidated the distal cell functions at different timepoints. Furthermore, overexpression of lncRNA:CR33938 in the S2 cell line increased the expression of leg development genes, further elucidating its potential role in development.
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Affiliation(s)
- Joyce Tse
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (J.T.); (T.H.L.); (J.Z.); (A.C.K.L.); (I.L.); (Z.Q.); (X.L.); (J.H.)
- State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Tsz Ho Li
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (J.T.); (T.H.L.); (J.Z.); (A.C.K.L.); (I.L.); (Z.Q.); (X.L.); (J.H.)
- State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Jizhou Zhang
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (J.T.); (T.H.L.); (J.Z.); (A.C.K.L.); (I.L.); (Z.Q.); (X.L.); (J.H.)
- State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Alan Chun Kit Lee
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (J.T.); (T.H.L.); (J.Z.); (A.C.K.L.); (I.L.); (Z.Q.); (X.L.); (J.H.)
- State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Ivy Lee
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (J.T.); (T.H.L.); (J.Z.); (A.C.K.L.); (I.L.); (Z.Q.); (X.L.); (J.H.)
- State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Zhe Qu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (J.T.); (T.H.L.); (J.Z.); (A.C.K.L.); (I.L.); (Z.Q.); (X.L.); (J.H.)
- State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Xiao Lin
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (J.T.); (T.H.L.); (J.Z.); (A.C.K.L.); (I.L.); (Z.Q.); (X.L.); (J.H.)
- State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Jerome Hui
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (J.T.); (T.H.L.); (J.Z.); (A.C.K.L.); (I.L.); (Z.Q.); (X.L.); (J.H.)
- State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (J.T.); (T.H.L.); (J.Z.); (A.C.K.L.); (I.L.); (Z.Q.); (X.L.); (J.H.)
- State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
- Correspondence:
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8
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Deng M, Wang Y, Yan Y. Mining cell–cell signaling in single-cell transcriptomics atlases. Curr Opin Cell Biol 2022; 76:102101. [DOI: 10.1016/j.ceb.2022.102101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 03/16/2022] [Accepted: 04/24/2022] [Indexed: 12/22/2022]
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9
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Yousefian S, Musillo MJ, Bageritz J. Analysis of Single-Cell Transcriptome Data in Drosophila. Methods Mol Biol 2022; 2540:93-111. [PMID: 35980574 DOI: 10.1007/978-1-0716-2541-5_4] [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] [Indexed: 06/15/2023]
Abstract
The fly Drosophila is a versatile model organism that has led to fascinating biological discoveries. In the past few years, Drosophila researchers have used single-cell RNA-sequencing (scRNA-seq) to gain insights into the cellular composition, and developmental processes of various tissues and organs. Given the success of single-cell technologies a variety of computational tools and software packages were developed to enable and facilitate the analysis of scRNA-seq data. In this book chapter we want to give guidance on analyzing droplet-based scRNA-seq data from Drosophila. We will initially describe the preprocessing commonly done for Drosophila, point out possible downstream analyses, and finally highlight computational methods developed using Drosophila scRNA-seq data.
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Affiliation(s)
- Schayan Yousefian
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maria Jelena Musillo
- Centre for Organismal Studies Heidelberg (COS), Universität Heidelberg, Heidelberg, Germany
| | - Josephine Bageritz
- Centre for Organismal Studies Heidelberg (COS), Universität Heidelberg, Heidelberg, Germany.
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10
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Sun X, Li L, Wu B, Ge J, Zheng Y, Yu T, Zhou L, Zhang T, Yang A, Liu Z. Cell type diversity in scallop adductor muscles revealed by single-cell RNA-Seq. Genomics 2021; 113:3582-3598. [PMID: 34425225 DOI: 10.1016/j.ygeno.2021.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/26/2021] [Accepted: 08/18/2021] [Indexed: 11/28/2022]
Abstract
Studies on cell atlas in marine invertebrates provide a better understanding of cell types, stem cell maintenance, and lineages of cell differentiation. To investigate the molecular features of various cell types in molluscan muscles, we performed single-cell RNA sequencing (scRNA-seq) to map cell types in scallop adductor muscles. We uncovered the cell type-specific features of 20 cell clusters defined by the expression of multiple specific molecular markers. These cell clusters are mainly classified into four broad classes, including mesenchymal stem cells, muscle cells, neurons, and haemolymph cells. In particular, we identified a diverse repertoire of neurons in the striated adductor muscle, but not in the smooth muscle. We further reconstructed the cell differentiation events using all the cell clusters by single-cell pseudotemporal trajectories. By integrating dual BrdU-PCNA immunodetection, neuron-specific staining and electron microscopy observation, we showed the spatial distribution of mesenchymal stem cells and neurons in striated adductor muscle of scallops. The present findings will not only be useful to address the cell type-specific gene expression profiles in scallop muscles, but also provide valuable resources for cross-species comparison of marine organisms.
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Affiliation(s)
- Xiujun Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Li Li
- Marine Biology Institute of Shandong Province, Qingdao 266104, China
| | - Biao Wu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Jianlong Ge
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Yanxin Zheng
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Yantai 265800, China
| | - Tao Yu
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Yantai 265800, China
| | - Liqing Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Tianshi Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Aiguo Yang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Zhihong Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China.
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11
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Drosophila, an Integrative Model to Study the Features of Muscle Stem Cells in Development and Regeneration. Cells 2021; 10:cells10082112. [PMID: 34440881 PMCID: PMC8394675 DOI: 10.3390/cells10082112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/17/2022] Open
Abstract
Muscle stem cells (MuSCs) are essential for muscle growth, maintenance and repair. Over the past decade, experiments in Drosophila have been instrumental in understanding the molecular and cellular mechanisms regulating MuSCs (also known as adult muscle precursors, AMPs) during development. A large number of genetic tools available in fruit flies provides an ideal framework to address new questions which could not be addressed with other model organisms. This review reports the main findings revealed by the study of Drosophila AMPs, with a specific focus on how AMPs are specified and properly positioned, how they acquire their identity and which are the environmental cues controlling their behavior and fate. The review also describes the recent identification of the Drosophila adult MuSCs that have similar characteristics to vertebrates MuSCs. Integration of the different levels of MuSCs analysis in flies is likely to provide new fundamental knowledge in muscle stem cell biology largely applicable to other systems.
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12
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Hu Y, Tattikota SG, Liu Y, Comjean A, Gao Y, Forman C, Kim G, Rodiger J, Papatheodorou I, dos Santos G, Mohr SE, Perrimon N. DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species. Comput Struct Biotechnol J 2021; 19:2018-2026. [PMID: 33995899 PMCID: PMC8085783 DOI: 10.1016/j.csbj.2021.04.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/24/2021] [Accepted: 04/07/2021] [Indexed: 12/27/2022] Open
Abstract
With the advent of single-cell RNA sequencing (scRNA-seq) technologies, there has been a spike in studies involving scRNA-seq of several tissues across diverse species including Drosophila. Although a few databases exist for users to query genes of interest within the scRNA-seq studies, search tools that enable users to find orthologous genes and their cell type-specific expression patterns across species are limited. Here, we built a new search database, DRscDB (https://www.flyrnai.org/tools/single_cell/web/), to address this need. DRscDB serves as a comprehensive repository for published scRNA-seq datasets for Drosophila and relevant datasets from human and other model organisms. DRscDB is based on manual curation of Drosophila scRNA-seq studies of various tissue types and their corresponding analogous tissues in vertebrates including zebrafish, mouse, and human. Of note, our search database provides most of the literature-derived marker genes, thus preserving the original analysis of the published scRNA-seq datasets. Finally, DRscDB serves as a web-based user interface that allows users to mine gene expression data from scRNA-seq studies and perform cell cluster enrichment analyses pertaining to various scRNA-seq studies, both within and across species.
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Affiliation(s)
- Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Sudhir Gopal Tattikota
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Yue Gao
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Corey Forman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Grace Kim
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jonathan Rodiger
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Gilberto dos Santos
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Stephanie E. Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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13
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Everetts NJ, Worley MI, Yasutomi R, Yosef N, Hariharan IK. Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions. eLife 2021; 10:61276. [PMID: 33749594 PMCID: PMC8021398 DOI: 10.7554/elife.61276] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/21/2021] [Indexed: 12/20/2022] Open
Abstract
In both vertebrates and invertebrates, generating a functional appendage requires interactions between ectoderm-derived epithelia and mesoderm-derived cells. To investigate such interactions, we used single-cell transcriptomics to generate a temporal cell atlas of the Drosophila wing disc from two developmental time points. Using these data, we visualized gene expression using a multilayered model of the wing disc and cataloged ligand–receptor pairs that could mediate signaling between epithelial cells and adult muscle precursors (AMPs). We found that localized expression of the fibroblast growth factor ligands, Thisbe and Pyramus, in the disc epithelium regulates the number and location of the AMPs. In addition, Hedgehog ligand from the epithelium activates a specific transcriptional program within adjacent AMP cells, defined by AMP-specific targets Neurotactin and midline, that is critical for proper formation of direct flight muscles. More generally, our annotated temporal cell atlas provides an organ-wide view of potential cell–cell interactions between epithelial and myogenic cells.
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Affiliation(s)
- Nicholas J Everetts
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Electrical Engineering & Computer Science, Center for Computational Biology, UC Berkeley, University of California, Berkeley, Berkeley, United States
| | - Melanie I Worley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Riku Yasutomi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Nir Yosef
- Department of Electrical Engineering & Computer Science, Center for Computational Biology, UC Berkeley, University of California, Berkeley, Berkeley, United States
| | - Iswar K Hariharan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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14
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Mohr SE, Tattikota SG, Xu J, Zirin J, Hu Y, Perrimon N. Methods and tools for spatial mapping of single-cell RNAseq clusters in Drosophila. Genetics 2021; 217:6156631. [PMID: 33713129 DOI: 10.1093/genetics/iyab019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/02/2021] [Indexed: 01/26/2023] Open
Abstract
Single-cell RNA sequencing (scRNAseq) experiments provide a powerful means to identify clusters of cells that share common gene expression signatures. A major challenge in scRNAseq studies is to map the clusters to specific anatomical regions along the body and within tissues. Existing data, such as information obtained from large-scale in situ RNA hybridization studies, cell type specific transcriptomics, gene expression reporters, antibody stainings, and fluorescent tagged proteins, can help to map clusters to anatomy. However, in many cases, additional validation is needed to precisely map the spatial location of cells in clusters. Several approaches are available for spatial resolution in Drosophila, including mining of existing datasets, and use of existing or new tools for direct or indirect detection of RNA, or direct detection of proteins. Here, we review available resources and emerging technologies that will facilitate spatial mapping of scRNAseq clusters at high resolution in Drosophila. Importantly, we discuss the need, available approaches, and reagents for multiplexing gene expression detection in situ, as in most cases scRNAseq clusters are defined by the unique coexpression of sets of genes.
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Affiliation(s)
- Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sudhir Gopal Tattikota
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
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15
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Zappia MP, de Castro L, Ariss MM, Jefferson H, Islam AB, Frolov MV. A cell atlas of adult muscle precursors uncovers early events in fibre-type divergence in Drosophila. EMBO Rep 2020; 21:e49555. [PMID: 32815271 PMCID: PMC7534622 DOI: 10.15252/embr.201949555] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 07/12/2020] [Accepted: 07/24/2020] [Indexed: 12/31/2022] Open
Abstract
In Drosophila, the wing disc‐associated muscle precursor cells give rise to the fibrillar indirect flight muscles (IFM) and the tubular direct flight muscles (DFM). To understand early transcriptional events underlying this muscle diversification, we performed single‐cell RNA‐sequencing experiments and built a cell atlas of myoblasts associated with third instar larval wing disc. Our analysis identified distinct transcriptional signatures for IFM and DFM myoblasts that underlie the molecular basis of their divergence. The atlas further revealed various states of differentiation of myoblasts, thus illustrating previously unappreciated spatial and temporal heterogeneity among them. We identified and validated novel markers for both IFM and DFM myoblasts at various states of differentiation by immunofluorescence and genetic cell‐tracing experiments. Finally, we performed a systematic genetic screen using a panel of markers from the reference cell atlas as an entry point and found a novel gene, Amalgam which is functionally important in muscle development. Our work provides a framework for leveraging scRNA‐seq for gene discovery and details a strategy that can be applied to other scRNA‐seq datasets.
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Affiliation(s)
- Maria Paula Zappia
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Lucia de Castro
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Majd M Ariss
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Holly Jefferson
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Abul Bmmk Islam
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Maxim V Frolov
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
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