1
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Wesselman HM, Arceri L, Nguyen TK, Lara CM, Wingert RA. Genetic mechanisms of multiciliated cell development: from fate choice to differentiation in zebrafish and other models. FEBS J 2024; 291:4159-4192. [PMID: 37997009 DOI: 10.1111/febs.17012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 10/17/2023] [Accepted: 11/21/2023] [Indexed: 11/25/2023]
Abstract
Multiciliated cells (MCCS) form bundles of cilia and their activities are essential for the proper development and physiology of many organ systems. Not surprisingly, defects in MCCs have profound consequences and are associated with numerous disease states. Here, we discuss the current understanding of MCC formation, with a special focus on the genetic and molecular mechanisms of MCC fate choice and differentiation. Furthermore, we cast a spotlight on the use of zebrafish to study MCC ontogeny and several recent advances made in understanding MCCs using this vertebrate model to delineate mechanisms of MCC emergence in the developing kidney.
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Affiliation(s)
| | - Liana Arceri
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Thanh Khoa Nguyen
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Caroline M Lara
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, University of Notre Dame, IN, USA
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2
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Ning M, Song L, Niu X, Wang Y, Liu W, Hu J, Cai H, Song W, Liu L, Li H, Gong D, Smith J, Huang Y. Multiscale 3D genome organization underlies duck fatty liver with no adipose inflammation or serious injury. Int J Biol Macromol 2024; 271:132452. [PMID: 38777007 DOI: 10.1016/j.ijbiomac.2024.132452] [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: 12/18/2023] [Revised: 04/22/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common form of chronic liver disease. Little is known about how gene expression and chromatin structure are regulated in NAFLD due to lack of suitable model. Ducks naturally develop fatty liver similar to serious human non-alcoholic fatty liver (NAFL) without adipose inflammation and liver fibrosis, thus serves as a good model for investigating molecular mechanisms of adipose metabolism and anti-inflammation. Here, we constructed a NAFLD model without adipose inflammation and liver fibrosis in ducks. By performing dynamic pathological and transcriptomic analyses, we identified critical genes involving in regulation of the NF-κB and MHCII signaling, which usually lead to adipose inflammation and liver fibrosis. We further generated dynamic three-dimensional chromatin maps during liver fatty formation and recovery. This showed that ducks enlarged hepatocyte cell nuclei to reduce inter-chromosomal interaction, decompress chromatin structure, and alter strength of intra-TAD and loop interactions during fatty liver formation. These changes partially contributed to the tight control the NF-κB and the MHCII signaling. Our analysis uncovers duck chromatin reorganization might be advantageous to maintain liver regenerative capacity and reduce adipose inflammation. These findings shed light on new strategies for NAFLD control.
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Affiliation(s)
- Mengfei Ning
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Linfei Song
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Xinyu Niu
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Yiming Wang
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Wenjie Liu
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Jiaxiang Hu
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Han Cai
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Weitao Song
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Long Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Huifang Li
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Yinhua Huang
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China.
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3
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Leggere JC, Hibbard JV, Papoulas O, Lee C, Pearson CG, Marcotte EM, Wallingford JB. Label-free proteomic comparison reveals ciliary and nonciliary phenotypes of IFT-A mutants. Mol Biol Cell 2024; 35:ar39. [PMID: 38170584 PMCID: PMC10916875 DOI: 10.1091/mbc.e23-03-0084] [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: 03/10/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
DIFFRAC is a powerful method for systematically comparing proteome content and organization between samples in a high-throughput manner. By subjecting control and experimental protein extracts to native chromatography and quantifying the contents of each fraction using mass spectrometry, it enables the quantitative detection of alterations to protein complexes and abundances. Here, we applied DIFFRAC to investigate the consequences of genetic loss of Ift122, a subunit of the intraflagellar transport-A (IFT-A) protein complex that plays a vital role in the formation and function of cilia and flagella, on the proteome of Tetrahymena thermophila. A single DIFFRAC experiment was sufficient to detect changes in protein behavior that mirrored known effects of IFT-A loss and revealed new biology. We uncovered several novel IFT-A-regulated proteins, which we validated through live imaging in Xenopus multiciliated cells, shedding new light on both the ciliary and non-ciliary functions of IFT-A. Our findings underscore the robustness of DIFFRAC for revealing proteomic changes in response to genetic or biochemical perturbation.
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Affiliation(s)
- Janelle C. Leggere
- Department of Molecular Biosciences, University of Texas at Austin, TX 78712
| | - Jaime V.K. Hibbard
- Department of Molecular Biosciences, University of Texas at Austin, TX 78712
| | - Ophelia Papoulas
- Department of Molecular Biosciences, University of Texas at Austin, TX 78712
| | - Chanjae Lee
- Department of Molecular Biosciences, University of Texas at Austin, TX 78712
| | - Chad G. Pearson
- Anschutz Medical Campus, Department of Cell and Developmental Biology, University of Colorado, Aurora, CO 80045
| | - Edward M. Marcotte
- Department of Molecular Biosciences, University of Texas at Austin, TX 78712
| | - John B. Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, TX 78712
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4
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Huber PB, LaBonne C. Small molecule-mediated reprogramming of Xenopus blastula stem cells to a neural crest state. Dev Biol 2024; 505:34-41. [PMID: 37890713 DOI: 10.1016/j.ydbio.2023.10.004] [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: 09/28/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
Neural crest cells are a stem cell population unique to vertebrates that give rise to a diverse array of derivatives, including much of the peripheral nervous system, pigment cells, cartilage, mesenchyme, and bone. Acquisition of these cells drove the evolution of vertebrates and defects in their development underlies a broad set of neurocristopathies. Moreover, studies of neural crest can inform differentiation protocols for pluripotent stem cells and regenerative medicine applications. Xenopus embryos are an important system for studies of the neural crest and have provided numerous insights into the signals and transcription factors that control the formation and later lineage diversification of these stem cells. Pluripotent animal pole explants are a particularly powerful tool in this system as they can be cultured in simple salt solution and instructed to give rise to any cell type including the neural crest. Here we report a protocol for small molecule-mediated induction of the neural crest state from blastula stem cells and validate it using transcriptome analysis and grafting experiments. This is an powerful new tool for generating this important cell type that will facilitate future studies of neural crest development and mutations and variants linked to neurocristopathies.
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Affiliation(s)
- Paul B Huber
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Carole LaBonne
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA.
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5
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Chae S, Park TJ, Kwon T. Convergent differentiation of multiciliated cells. Sci Rep 2023; 13:23028. [PMID: 38155158 PMCID: PMC10754865 DOI: 10.1038/s41598-023-50077-5] [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: 09/22/2023] [Accepted: 12/15/2023] [Indexed: 12/30/2023] Open
Abstract
Multiciliated cells (MCCs) are epithelial cells that control body fluid flow and contribute to the clearance of pathogenic microbes and other particles from the airways, egg transport in oviducts, and circulation of cerebrospinal fluid in the central nervous system. Although MCCs have shared functions to control fluid flow via coordinated motility of multiple ciliary structures, they are found in multiple mammalian tissues originating from distinct germ layers and differentiate via distinct developmental pathways. To understand the similarities and differences of MCCs in multiple tissues, we investigated single-cell transcriptome data of nasal epithelial cells, bronchial tubes, fallopian tubes, and ependymal cells in the subventricular zone from humans and mice by cross-species data integration. Expression of cilia-associated genes was indistinguishable between these MCCs, although cell populations had unique properties by the species and tissue, demonstrating that they share the same final differentiation status for ciliary functions. We further analyzed the final differentiation step of MCCs from their distinctive progenitors and confirmed their convergent gene set expression for ciliogenesis at the final step. These results may provide new insight into understanding ciliogenesis during the developmental process.
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Affiliation(s)
- Shinhyeok Chae
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Tae Joo Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
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6
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Sur A, Wang Y, Capar P, Margolin G, Prochaska MK, Farrell JA. Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development. Dev Cell 2023; 58:3028-3047.e12. [PMID: 37995681 PMCID: PMC11181902 DOI: 10.1016/j.devcel.2023.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/24/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
During development, animals generate distinct cell populations with specific identities, functions, and morphologies. We mapped transcriptionally distinct populations across 489,686 cells from 62 stages during wild-type zebrafish embryogenesis and early larval development (3-120 h post-fertilization). Using these data, we identified the limited catalog of gene expression programs reused across multiple tissues and their cell-type-specific adaptations. We also determined the duration each transcriptional state is present during development and identify unexpected long-term cycling populations. Focused clustering and transcriptional trajectory analyses of non-skeletal muscle and endoderm identified transcriptional profiles and candidate transcriptional regulators of understudied cell types and subpopulations, including the pneumatic duct, individual intestinal smooth muscle layers, spatially distinct pericyte subpopulations, and recently discovered best4+ cells. To enable additional discoveries, we make this comprehensive transcriptional atlas of early zebrafish development available through our website, Daniocell.
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Affiliation(s)
- Abhinav Sur
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Yiqun Wang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Paulina Capar
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Gennady Margolin
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Morgan Kathleen Prochaska
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Jeffrey A Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA.
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7
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Mizoguchi Y, Nakashima K, Sato A, Shindo A. β-adrenergic receptor regulates embryonic epithelial extensibility through actomyosin inhibition. iScience 2023; 26:108469. [PMID: 38213788 PMCID: PMC10783608 DOI: 10.1016/j.isci.2023.108469] [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: 04/25/2023] [Revised: 10/30/2023] [Accepted: 11/13/2023] [Indexed: 01/13/2024] Open
Abstract
During morphogenesis, epithelial tissues reshape and expand to cover the body and organs. The molecular mechanisms of this deformability remain elusive. Here, we investigate the role of the β-adrenergic receptor (ADRB) in orchestrating actomyosin contractility, pivotal for epithelial extensibility. Chemical screens on Xenopus laevis embryos pinpointed ADRB2 as a principal regulator. ADRB2 promotes actomyosin relaxation, facilitating apical cell area expansion during body elongation. In contrast, ADRB2 knockdown results in heightened cell contraction, marked by synchronous oscillation of F-actin and myosin, impeding body elongation. ADRB2 mutants with reduced affinity for ligand binding lack the function to induce cellular relaxation, highlighting the ligand's essential roles even in the developing epidermis. Our findings unveil ADRB2's critical contribution to extensibility of the epidermis and subsequent body elongation during development. This study also offers insights into the physiology of mature epithelial organs deformed by the smooth muscle response to the adrenergic autonomic nervous system.
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Affiliation(s)
- Yohei Mizoguchi
- Division of Biological Sciences, Department of Molecular Biology, Nagoya University Graduate School of Science, Nagoya 464-8602, Japan
| | - Kaoru Nakashima
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan
| | - Asako Shindo
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
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8
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Coyle MC, Tajima AM, Leon F, Choksi SP, Yang A, Espinoza S, Hughes TR, Reiter JF, Booth DS, King N. An RFX transcription factor regulates ciliogenesis in the closest living relatives of animals. Curr Biol 2023; 33:3747-3758.e9. [PMID: 37552984 PMCID: PMC10530576 DOI: 10.1016/j.cub.2023.07.022] [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: 01/07/2023] [Revised: 05/30/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Cilia allowed our protistan ancestors to sense and explore their environment, avoid predation, and capture bacterial prey.1,2,3 Regulated ciliogenesis was likely critical for early animal evolution,2,4,5,6 and in modern animals, deploying cilia in the right cells at the right time is crucial for development and physiology. Two transcription factors, RFX and FoxJ1, coordinate ciliogenesis in animals7,8,9 but are absent from the genomes of many other ciliated eukaryotes, raising the question of how the regulation of ciliogenesis in animals evolved.10,11 By comparing the genomes of animals with those of their closest living relatives, the choanoflagellates, we found that the genome of their last common ancestor encoded at least three RFX paralogs and a FoxJ1 homolog. Disruption of the RFX homolog cRFXa in the model choanoflagellate Salpingoeca rosetta resulted in delayed cell proliferation and aberrant ciliogenesis, marked by the collapse and resorption of nascent cilia. In cRFXa mutants, ciliogenesis genes and foxJ1 were significantly downregulated. Moreover, the promoters of S. rosetta ciliary genes are enriched for DNA motifs matching those bound by the cRFXa protein in vitro. These findings suggest that an ancestral cRFXa homolog coordinated ciliogenesis in the progenitors of animals and choanoflagellates and that the selective deployment of the RFX regulatory module may have been necessary to differentiate ciliated from non-ciliated cell types during early animal evolution.
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Affiliation(s)
- Maxwell C Coyle
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Adia M Tajima
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Fredrick Leon
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Semil P Choksi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ally Yang
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada
| | - Sarah Espinoza
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - David S Booth
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Nicole King
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
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9
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Ventrella R, Kim SK, Sheridan J, Grata A, Bresteau E, Hassan OA, Suva EE, Walentek P, Mitchell BJ. Bidirectional multiciliated cell extrusion is controlled by Notch-driven basal extrusion and Piezo1-driven apical extrusion. Development 2023; 150:dev201612. [PMID: 37602491 PMCID: PMC10482390 DOI: 10.1242/dev.201612] [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: 01/12/2023] [Accepted: 08/11/2023] [Indexed: 08/22/2023]
Abstract
Xenopus embryos are covered with a complex epithelium containing numerous multiciliated cells (MCCs). During late-stage development, there is a dramatic remodeling of the epithelium that involves the complete loss of MCCs. Cell extrusion is a well-characterized process for driving cell loss while maintaining epithelial barrier function. Normal cell extrusion is typically unidirectional, whereas bidirectional extrusion is often associated with disease (e.g. cancer). We describe two distinct mechanisms for MCC extrusion, a basal extrusion driven by Notch signaling and an apical extrusion driven by Piezo1. Early in the process there is a strong bias towards basal extrusion, but as development continues there is a shift towards apical extrusion. Importantly, response to the Notch signal is age dependent and governed by the maintenance of the MCC transcriptional program such that extension of this program is protective against cell loss. In contrast, later apical extrusion is regulated by Piezo1, such that premature activation of Piezo1 leads to early extrusion while blocking Piezo1 leads to MCC maintenance. Distinct mechanisms for MCC loss underlie the importance of their removal during epithelial remodeling.
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Affiliation(s)
- Rosa Ventrella
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL 60611, USA
- Precision Medicine Program, Midwestern University, Downers Grove, IL 60515, USA
| | - Sun K. Kim
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL 60611, USA
| | - Jennifer Sheridan
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL 60611, USA
| | - Aline Grata
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL 60611, USA
| | - Enzo Bresteau
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL 60611, USA
| | - Osama A. Hassan
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL 60611, USA
| | - Eve E. Suva
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL 60611, USA
| | - Peter Walentek
- University of Freiburg, Renal Division, Internal Medicine IV, Medical Center and CIBSS Centre for Integrative Biological Signalling Studies, 79104 Freiburg im Breisgau, Germany
| | - Brian J. Mitchell
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL 60611, USA
- Northwestern University, Lurie Cancer Center, Chicago, IL 60611, USA
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10
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Guo Q, Li Z, Jia S, Tong F, Ma L. Mechanism of Human Tubal Ectopic Pregnancy Caused by Cigarette Smoking. Reprod Sci 2023; 30:1074-1081. [PMID: 35962304 DOI: 10.1007/s43032-022-00947-6] [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: 05/18/2020] [Accepted: 04/14/2022] [Indexed: 10/15/2022]
Abstract
In the past few decades, the smoking rate of women of childbearing age has increased. Epidemiological data has repeatedly shown that smoking women have an increased risk of various reproductive diseases, including ectopic pregnancy (EP), decreased fertility, adverse pregnancy outcomes, and failure of assisted reproduction. The oviduct was the target of cigarette smoke in many in vivo and in vitro studies. The fallopian tube is a well-designed organ. Its function is to collect and transport the ova to the fertilized site and provide a suitable environment for fertilization and early embryonic development. Lastly, the fallopian tube transports the pre-implantation embryo to the uterus. Various biological processes can be studied in the fallopian tubes, making it an excellent model for toxicology. This paper reviews the roles of the fallopian tube in gametes and embryo transportation, and the possible mechanism tobacco smoke contributes to tubal EP. A possible signal pathway might be a model to develop intervention of EP for pregnant women exposed to smoking.
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Affiliation(s)
- Quan Guo
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Heping District Shenyang, 36 Sanhao Street, 110004, Shenyang, China.
| | - Zaiyi Li
- Reproductive Medicine Center, Seventh Affiliated Hospital, Sun Yat-Sen University, 628 Zhenyuan Road, Xinhu Street, Guangming District, Shenzhen, Guangdong, 510000, China
| | - Steve Jia
- RD Center, Pacificbio Inc. Irvine, Irvine, CA, 92602, USA
| | - Fangze Tong
- Murray Edwards College, University of Cambridge, Cambridge, CB3 0DF, UK
| | - Lin Ma
- Reproductive Medicine Center, Seventh Affiliated Hospital, Sun Yat-Sen University, 628 Zhenyuan Road, Xinhu Street, Guangming District, Shenzhen, Guangdong, 510000, China.
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11
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Lewis M, Terré B, Knobel PA, Cheng T, Lu H, Attolini CSO, Smak J, Coyaud E, Garcia-Cao I, Sharma S, Vineethakumari C, Querol J, Gil-Gómez G, Piergiovanni G, Costanzo V, Peiró S, Raught B, Zhao H, Salvatella X, Roy S, Mahjoub MR, Stracker TH. GEMC1 and MCIDAS interactions with SWI/SNF complexes regulate the multiciliated cell-specific transcriptional program. Cell Death Dis 2023; 14:201. [PMID: 36932059 PMCID: PMC10023806 DOI: 10.1038/s41419-023-05720-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023]
Abstract
Multiciliated cells (MCCs) project dozens to hundreds of motile cilia from their apical surface to promote the movement of fluids or gametes in the mammalian brain, airway or reproductive organs. Differentiation of MCCs requires the sequential action of the Geminin family transcriptional activators, GEMC1 and MCIDAS, that both interact with E2F4/5-DP1. How these factors activate transcription and the extent to which they play redundant functions remains poorly understood. Here, we demonstrate that the transcriptional targets and proximal proteomes of GEMC1 and MCIDAS are highly similar. However, we identified distinct interactions with SWI/SNF subcomplexes; GEMC1 interacts primarily with the ARID1A containing BAF complex while MCIDAS interacts primarily with BRD9 containing ncBAF complexes. Treatment with a BRD9 inhibitor impaired MCIDAS-mediated activation of several target genes and compromised the MCC differentiation program in multiple cell based models. Our data suggest that the differential engagement of distinct SWI/SNF subcomplexes by GEMC1 and MCIDAS is required for MCC-specific transcriptional regulation and mediated by their distinct C-terminal domains.
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Affiliation(s)
- Michael Lewis
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
| | - Berta Terré
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
- MRC Clinical Trials Unit at UCL, London, UK
| | - Philip A Knobel
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
- CDR-Life AG, Zurich, 8592, Switzerland
| | - Tao Cheng
- Washington University in St Louis, Departments of Medicine (Nephrology), Cell Biology and Physiology, St. Louis, MO, 20814, USA
| | - Hao Lu
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
| | - Jordann Smak
- National Cancer Institute, Radiation Oncology Branch, Bethesda, MD, 20892, USA
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Isabel Garcia-Cao
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
| | - Shalu Sharma
- National Cancer Institute, Radiation Oncology Branch, Bethesda, MD, 20892, USA
| | - Chithran Vineethakumari
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
| | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, 08035, Spain
| | - Gabriel Gil-Gómez
- Apoptosis Signalling Group, IMIM (Institut Hospital del Mar d'Investigacions Mediques), Barcelona, 08003, Spain
| | - Gabriele Piergiovanni
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, 20139, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, 20139, Italy
| | - Vincenzo Costanzo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, 20139, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, 20139, Italy
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, 08035, Spain
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Haotian Zhao
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, New York, NY, 11568, USA
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
- ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore
- Department of Biological Sciences, National University of Singapore, 117543, Singapore, Singapore
- Department of Pediatrics, National University of Singapore, 119288, Singapore, Singapore
| | - Moe R Mahjoub
- Washington University in St Louis, Departments of Medicine (Nephrology), Cell Biology and Physiology, St. Louis, MO, 20814, USA
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain.
- National Cancer Institute, Radiation Oncology Branch, Bethesda, MD, 20892, USA.
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12
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Leggere JC, Hibbard JVK, Papoulas O, Lee C, Pearson CG, Marcotte EM, Wallingford JB. Label-free proteomic comparison reveals ciliary and non-ciliary phenotypes of IFT-A mutants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531778. [PMID: 36945534 PMCID: PMC10028850 DOI: 10.1101/2023.03.08.531778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
DIFFRAC is a powerful method for systematically comparing proteome content and organization between samples in a high-throughput manner. By subjecting control and experimental protein extracts to native chromatography and quantifying the contents of each fraction using mass spectrometry, it enables the quantitative detection of alterations to protein complexes and abundances. Here, we applied DIFFRAC to investigate the consequences of genetic loss of Ift122, a subunit of the intraflagellar transport-A (IFT-A) protein complex that plays a vital role in the formation and function of cilia and flagella, on the proteome of Tetrahymena thermophila . A single DIFFRAC experiment was sufficient to detect changes in protein behavior that mirrored known effects of IFT-A loss and revealed new biology. We uncovered several novel IFT-A-regulated proteins, which we validated through live imaging in Xenopus multiciliated cells, shedding new light on both the ciliary and non-ciliary functions of IFT-A. Our findings underscore the robustness of DIFFRAC for revealing proteomic changes in response to genetic or biochemical perturbation.
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13
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Kwon KY, Jeong H, Jang DG, Kwon T, Park TJ. Ckb and Ybx2 interact with Ribc2 and are necessary for the ciliary beating of multi-cilia. Genes Genomics 2023; 45:157-167. [PMID: 36508087 DOI: 10.1007/s13258-022-01350-w] [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: 10/25/2022] [Accepted: 11/26/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Motile cilia in a vertebrate are important to sustaining activities of life. Fluid flow on the apical surface of several tissues, including bronchial epithelium, ependymal epithelium, and fallopian tubules is generated by the ciliary beating of motile cilia. Multi-ciliated cells in ependymal tissue are responsible for the circulation of cerebrospinal fluid (CSF), which is essential for the development and homeostasis of the central nervous system, and airway tissues are protected from external contaminants by cilia-driven mucosal flow over the top of the airway epithelium. OBJECTIVE A previous study reported that reduction of Ribc2 protein leads to disruption of ciliary beating in multi-ciliated cells. However, knowledge regarding the molecular function of Ribc2 is limited, thus currently available information is also limited. Therefore, we evaluated the importance of proteins involved in the interaction with Ribc2 in the process of ciliary beating. METHODS Immunoprecipitation and mass spectrometry analysis was performed for the discovery of proteins involved in the interaction with Ribc2. Expression of the target gene was inhibited by injection of antisense morpholinos and measurement of the fluid flow on the embryonic epidermis of Xenopus was performed using fluorescent beads for examination of the ciliary beating of multi cilia. In addition, the flag-tagged protein was expressed by injection of mRNA and the changes in protein localization in the cilia were measured by immunostaining and western blot analysis for analysis of the molecular interaction between Ribc2 and Ribc2 binding proteins in multi-cilia. RESULTS The IP/MS analysis identified Ckb and Ybx2 as Ribc2 binding proteins and our results showed that localization of both Ckb and Ybx2 occurs at the axoneme of multi-cilia on the embryonic epithelium of Xenopus laevis. In addition, our findings confirmed that knock-down of Ckb or Ybx2 resulted in abnormal ciliary beating and reduction of cilia-driven fluid flow on multi-cilia of Xenopus laevis. In addition, significantly decreased localization of Ckb or Ybx2 in the ciliary axoneme was observed in Ribc2-depleted multi-cilia. CONCLUSION Ckb and Ybx2 are involved in the interaction with Ribc2 and are necessary for the ciliary beating of multi-cilia.
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Affiliation(s)
- Keun Yeong Kwon
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Hyeongsun Jeong
- Department of Biological Medical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Dong Gil Jang
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Taejoon Kwon
- Department of Biological Medical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| | - Tae Joo Park
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
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14
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Ventrella R, Kim SK, Sheridan J, Grata A, Bresteau E, Hassan O, Suva EE, Walentek P, Mitchell B. Bidirectional multiciliated cell extrusion is controlled by Notch driven basal extrusion and Piezo 1 driven apical extrusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523838. [PMID: 36711534 PMCID: PMC9882179 DOI: 10.1101/2023.01.12.523838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Xenopus embryos are covered with a complex epithelium containing numerous multiciliated cells (MCCs). During late stage development there is a dramatic remodeling of the epithelium that involves the complete loss of MCCs. Cell extrusion is a well-characterized process for driving cell loss while maintaining epithelial barrier function. Normal cell extrusion is typically unidirectional whereas bidirectional extrusion is often associated with disease (e.g. cancer). We describe two distinct mechanisms for MCC extrusion, a basal extrusion driven by Notch signaling and an apical extrusion driven by Piezo1. Early in the process there is a strong bias towards basal extrusion, but as development continues there is a shift towards apical extrusion. Importantly, receptivity to the Notch signal is age-dependent and governed by the maintenance of the MCC transcriptional program such that extension of this program is protective against cell loss. In contrast, later apical extrusion is regulated by Piezo 1 such that premature activation of Piezo 1 leads to early extrusion while blocking Piezo 1 leads to MCC maintenance. Distinct mechansms for MCC loss underlie the importance of their removal during epithelial remodeling. Summay Statement Cell extrusion typically occurs unidirectionally. We have identified a single population of multiciliated cells that extrudes bidirectionally: Notch-driven basal extrusion and Piezo 1-mediated apical extrusion.
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Affiliation(s)
- Rosa Ventrella
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
- Current position; Assistant professor, Precision Medicine Program, Midwestern University
| | - Sun K. Kim
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
| | - Jennifer Sheridan
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
| | - Aline Grata
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
| | - Enzo Bresteau
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
| | - Osama Hassan
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
| | - Eve E. Suva
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
| | - Peter Walentek
- University of Freiburg, Renal Division, Internal Medicine IV, Medical Center and CIBSS Centre for Integrative Biological Signalling Studies
| | - Brian Mitchell
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
- Northwestern University, Lurie Cancer Center
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15
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Wesselman HM, Nguyen TK, Chambers JM, Drummond BE, Wingert RA. Advances in Understanding the Genetic Mechanisms of Zebrafish Renal Multiciliated Cell Development. J Dev Biol 2022; 11:1. [PMID: 36648903 PMCID: PMC9844391 DOI: 10.3390/jdb11010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Cilia are microtubule-based organelles that project from the cell surface. In humans and other vertebrates, possession of a single cilium structure enables an assortment of cellular processes ranging from mechanosensation to fluid propulsion and locomotion. Interestingly, cells can possess a single cilium or many more, where so-called multiciliated cells (MCCs) possess apical membrane complexes with several dozen or even hundreds of motile cilia that beat in a coordinated fashion. Development of MCCs is, therefore, integral to control fluid flow and/or cellular movement in various physiological processes. As such, MCC dysfunction is associated with numerous pathological states. Understanding MCC ontogeny can be used to address congenital birth defects as well as acquired disease conditions. Today, researchers used both in vitro and in vivo experimental models to address our knowledge gaps about MCC specification and differentiation. In this review, we summarize recent discoveries from our lab and others that have illuminated new insights regarding the genetic pathways that direct MCC ontogeny in the embryonic kidney using the power of the zebrafish animal model.
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Affiliation(s)
| | | | | | | | - Rebecca A. Wingert
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556, USA
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16
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Wang J, Wang W, Shen L, Zheng A, Meng Q, Li H, Yang S. Clinical detection, diagnosis and treatment of morphological abnormalities of sperm flagella: A review of literature. Front Genet 2022; 13:1034951. [PMID: 36425067 PMCID: PMC9679630 DOI: 10.3389/fgene.2022.1034951] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/28/2022] [Indexed: 11/12/2023] Open
Abstract
Sperm carries male genetic information, and flagella help move the sperm to reach oocytes. When the ultrastructure of the flagella is abnormal, the sperm is unable to reach the oocyte and achieve insemination. Multiple morphological abnormalities of sperm flagella (MMAF) is a relatively rare idiopathic condition that is mainly characterized by multiple defects in sperm flagella. In the last decade, with the development of high-throughput DNA sequencing approaches, many genes have been revealed to be related to MMAF. However, the differences in sperm phenotypes and reproductive outcomes in many cases are attributed to different pathogenic genes or different pathogenic mutations in the same gene. Here, we will review information about the various phenotypes resulting from different pathogenic genes, including sperm ultrastructure and encoding proteins with their location and functions as well as assisted reproductive technology (ART) outcomes. We will share our clinical detection and diagnosis experience to provide additional clinical views and broaden the understanding of this disease.
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Affiliation(s)
| | | | | | | | | | | | - Shenmin Yang
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China
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17
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Dai S, Liang Y, Liu M, Yang Y, Liu H, Shen Y. Novel biallelic mutations in TTC29 cause asthenoteratospermia and male infertility. Mol Genet Genomic Med 2022; 10:e2078. [PMID: 36346162 PMCID: PMC9747556 DOI: 10.1002/mgg3.2078] [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] [Received: 06/30/2022] [Revised: 09/27/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiple morphological abnormalities of the sperm flagella (MMAF), which is characterized as asthenoteratospermia involving absent, short, bent, coiled, and/or irregular-caliber flagella, is a rare recessive inherited disorder associated with male infertility. To date, genetic causes of MMAF cases are not fully explored. METHODS Whole-exome sequencing was conducted to identify pathogenic variants in a patient with MMAF. The functional effect of the identified mutations was investigated by immunofluorescence staining and western blotting. Intracytoplasmic sperm injection was used to assist fertilization for the patient with MMAF. RESULTS We identified novel biallelic mutations, a splicing variant NC_000004.12:g.146937593C>T (c.254+1G>A), and a nonsense mutation NM_001300761.4:c.1185C>G (NP_001287690.1:p.Tyr395*), in TTC29 from an infertile patient. In addition to the typical MMAF phenotype, the patient also presented aberrant morphology of sperm heads. Further functional experiments confirmed the absence of TTC29 expression in the spermatozoa. We also explored the specific expression pattern of TTC29 in human and mouse spermatogenesis. The outcome of intracytoplasmic sperm injection in the patient was unsuccessful, while additional female risk factors should not be excluded. CONCLUSIONS Our study revealed the novel biallelic mutations in TTC29 in a MMAF patient, which findings expand the mutational spectrum of TTC29 and further contribute to the diagnosis, genetic counseling, and prognosis of male infertility.
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Affiliation(s)
- Siyu Dai
- Core FacilityWest China Hospital, Sichuan UniversityChengduChina,Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina,Medical Genetics Department, Prenatal Diagnostic CenterWest China Second University Hospital, Sichuan UniversityChengduChina,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of EducationSichuan UniversityChengduChina
| | - Yan Liang
- Core FacilityWest China Hospital, Sichuan UniversityChengduChina
| | - Mohan Liu
- State Key Laboratory of Biotherapy and Cancer CenterSichuan UniversityChengduChina
| | - Yanting Yang
- Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina,Medical Genetics Department, Prenatal Diagnostic CenterWest China Second University Hospital, Sichuan UniversityChengduChina,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of EducationSichuan UniversityChengduChina
| | - Hongqian Liu
- Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina,Medical Genetics Department, Prenatal Diagnostic CenterWest China Second University Hospital, Sichuan UniversityChengduChina,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of EducationSichuan UniversityChengduChina
| | - Ying Shen
- Department of Obstetrics/Gynecology, Joint Laboratory of Reproductive Medicine (SCU‐CUHK), Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of EducationWest China Second University Hospital, Sichuan UniversityChengduChina
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18
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Multiciliated cells use filopodia to probe tissue mechanics during epithelial integration in vivo. Nat Commun 2022; 13:6423. [PMID: 36307428 PMCID: PMC9616887 DOI: 10.1038/s41467-022-34165-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 10/17/2022] [Indexed: 12/25/2022] Open
Abstract
During embryonic development, regeneration, and homeostasis, cells have to migrate and physically integrate into the target tissues where they ultimately execute their function. While much is known about the biochemical pathways driving cell migration in vivo, we are only beginning to understand the mechanical interplay between migrating cells and their surrounding tissue. Here, we reveal that multiciliated cell precursors in the Xenopus embryo use filopodia to pull at the vertices of the overlying epithelial sheet. This pulling is effectively used to sense vertex stiffness and identify the preferred positions for cell integration into the tissue. Notably, we find that pulling forces equip multiciliated cells with the ability to remodel the epithelial junctions of the neighboring cells, enabling them to generate a permissive environment that facilitates integration. Our findings reveal the intricate physical crosstalk at the cell-tissue interface and uncover previously unknown functions for mechanical forces in orchestrating cell integration.
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19
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Zahn N, James-Zorn C, Ponferrada VG, Adams DS, Grzymkowski J, Buchholz DR, Nascone-Yoder NM, Horb M, Moody SA, Vize PD, Zorn AM. Normal Table of Xenopus development: a new graphical resource. Development 2022; 149:dev200356. [PMID: 35833709 PMCID: PMC9445888 DOI: 10.1242/dev.200356] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/17/2022] [Indexed: 12/26/2022]
Abstract
Normal tables of development are essential for studies of embryogenesis, serving as an important resource for model organisms, including the frog Xenopus laevis. Xenopus has long been used to study developmental and cell biology, and is an increasingly important model for human birth defects and disease, genomics, proteomics and toxicology. Scientists utilize Nieuwkoop and Faber's classic 'Normal Table of Xenopus laevis (Daudin)' and accompanying illustrations to enable experimental reproducibility and reuse the illustrations in new publications and teaching. However, it is no longer possible to obtain permission for these copyrighted illustrations. We present 133 new, high-quality illustrations of X. laevis development from fertilization to metamorphosis, with additional views that were not available in the original collection. All the images are available on Xenbase, the Xenopus knowledgebase (http://www.xenbase.org/entry/zahn.do), for download and reuse under an attributable, non-commercial creative commons license. Additionally, we have compiled a 'Landmarks Table' of key morphological features and marker gene expression that can be used to distinguish stages quickly and reliably (https://www.xenbase.org/entry/landmarks-table.do). This new open-access resource will facilitate Xenopus research and teaching in the decades to come.
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Affiliation(s)
| | - Christina James-Zorn
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Ave, Cincinnati, OH 45229, USA
| | - Virgilio G. Ponferrada
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Ave, Cincinnati, OH 45229, USA
| | - Dany S. Adams
- Lucell Diagnostics Inc, 16 Stearns Street, Cambridge, MA 02138, USA
| | - Julia Grzymkowski
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27695, USA
| | - Daniel R. Buchholz
- Department of Biology Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Nanette M. Nascone-Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27695, USA
| | - Marko Horb
- National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Sally A. Moody
- Department of Anatomy and Cell Biology, George Washington University Medical Center, Washington, DC 20037, USA
| | - Peter D. Vize
- Xenbase, Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Aaron M. Zorn
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Ave, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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20
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Martinez G, Coutton C, Loeuillet C, Cazin C, Muroňová J, Boguenet M, Lambert E, Dhellemmes M, Chevalier G, Hograindleur JP, Vilpreux C, Neirijnck Y, Kherraf ZE, Escoffier J, Nef S, Ray PF, Arnoult C. Oligogenic heterozygous inheritance of sperm abnormalities in mouse. eLife 2022; 11:75373. [PMID: 35451961 PMCID: PMC9071268 DOI: 10.7554/elife.75373] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Male infertility is an important health concern that is expected to have a major genetic etiology. Although high-throughput sequencing has linked gene defects to more than 50% of rare and severe sperm anomalies, less than 20% of common and moderate forms are explained. We hypothesized that this low success rate could at least be partly due to oligogenic defects – the accumulation of several rare heterozygous variants in distinct, but functionally connected, genes. Here, we compared fertility and sperm parameters in male mice harboring one to four heterozygous truncating mutations of genes linked to multiple morphological anomalies of the flagellum (MMAF) syndrome. Results indicated progressively deteriorating sperm morphology and motility with increasing numbers of heterozygous mutations. This first evidence of oligogenic inheritance in failed spermatogenesis strongly suggests that oligogenic heterozygosity could explain a significant proportion of asthenoteratozoospermia cases. The findings presented pave the way to further studies in mice and man.
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Affiliation(s)
| | | | - Corinne Loeuillet
- Institute for Advanced Biosciences, INSERM, CNRS, University Grenoble-Alpes, Grenoble, France
| | | | - Jana Muroňová
- Institute for Advanced Biosciences, INSERM, CNRS, University Grenoble-Alpes, Grenoble, France
| | - Magalie Boguenet
- Institute for Advanced Biosciences, INSERM, CNRS, University Grenoble-Alpes, Grenoble, France
| | - Emeline Lambert
- Institute for Advanced Biosciences, INSERM, CNRS, University Grenoble-Alpes, Grenoble, France
| | - Magali Dhellemmes
- Institute for Advanced Biosciences, INSERM, CNRS, University Grenoble-Alpes, Grenoble, France
| | - Geneviève Chevalier
- Institute for Advanced Biosciences, INSERM, CNRS, University Grenoble-Alpes, Grenoble, France
| | | | - Charline Vilpreux
- Institute for Advanced Biosciences, INSERM, CNRS, University Grenoble-Alpes, Grenoble, France
| | - Yasmine Neirijnck
- Department of Genetic Medicine and Development, University of Geneva Medical School, Genève, Switzerland
| | - Zine Eddine Kherraf
- Institute for Advanced Biosciences, INSERM, CNRS, University Grenoble-Alpes, Grenoble, France
| | - Jessica Escoffier
- Institute for Advanced Biosciences, INSERM, CNRS, University Grenoble-Alpes, Grenoble, France
| | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Pierre F Ray
- Institute for Advanced Biosciences, INSERM, CNRS, University Grenoble-Alpes, Grenoble, France
| | - Christophe Arnoult
- Institute for Advanced Biosciences, INSERM, CNRS, University Grenoble-Alpes, Grenoble, France
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21
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Langel SN, Kelly FL, Brass DM, Nagler AE, Carmack D, Tu JJ, Travieso T, Goswami R, Permar SR, Blasi M, Palmer SM. E-cigarette and food flavoring diacetyl alters airway cell morphology, inflammatory and antiviral response, and susceptibility to SARS-CoV-2. Cell Death Dis 2022; 8:64. [PMID: 35169120 PMCID: PMC8847558 DOI: 10.1038/s41420-022-00855-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 11/09/2022]
Abstract
Diacetyl (DA) is an α-diketone that is used to flavor microwave popcorn, coffee, and e-cigarettes. Occupational exposure to high levels of DA causes impaired lung function and obstructive airway disease. Additionally, lower levels of DA exposure dampen host defenses in vitro. Understanding DA’s impact on lung epithelium is important for delineating exposure risk on lung health. In this study, we assessed the impact of DA on normal human bronchial epithelial cell (NHBEC) morphology, transcriptional profiles, and susceptibility to SARS-CoV-2 infection. Transcriptomic analysis demonstrated cilia dysregulation, an increase in hypoxia and sterile inflammation associated pathways, and decreased expression of interferon-stimulated genes after DA exposure. Additionally, DA exposure resulted in cilia loss and increased hyaluronan production. After SARS-CoV-2 infection, both genomic and subgenomic SARS-CoV-2 RNA were increased in DA vapor- compared to vehicle-exposed NHBECs. This work suggests that transcriptomic and physiologic changes induced by DA vapor exposure damage cilia and increase host susceptibility to SARS-CoV-2.
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Affiliation(s)
- Stephanie N Langel
- Duke Center for Human Systems Immunology and Department of Surgery, Durham, NC, USA
| | - Francine L Kelly
- Duke Clinical Research Institute and Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - David M Brass
- Duke Clinical Research Institute and Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Andrew E Nagler
- Duke Clinical Research Institute and Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Dylan Carmack
- Duke Clinical Research Institute and Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Joshua J Tu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA.,Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Tatianna Travieso
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA.,Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Ria Goswami
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Sallie R Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Maria Blasi
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA. .,Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA.
| | - Scott M Palmer
- Duke Clinical Research Institute and Department of Medicine, Duke University Medical Center, Durham, NC, USA
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22
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Turn RE, Hu Y, Dewees SI, Devi N, East MP, Hardin KR, Khatib T, Linnert J, Wolfrum U, Lim MJ, Casanova JE, Caspary T, Kahn RA. The ARF GAPs ELMOD1 and ELMOD3 act at the Golgi and cilia to regulate ciliogenesis and ciliary protein traffic. Mol Biol Cell 2022; 33:ar13. [PMID: 34818063 PMCID: PMC9236152 DOI: 10.1091/mbc.e21-09-0443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/11/2022] Open
Abstract
ELMODs are a family of three mammalian paralogues that display GTPase-activating protein (GAP) activity toward a uniquely broad array of ADP-ribosylation factor (ARF) family GTPases that includes ARF-like (ARL) proteins. ELMODs are ubiquitously expressed in mammalian tissues, highly conserved across eukaryotes, and ancient in origin, being present in the last eukaryotic common ancestor. We described functions of ELMOD2 in immortalized mouse embryonic fibroblasts (MEFs) in the regulation of cell division, microtubules, ciliogenesis, and mitochondrial fusion. Here, using similar strategies with the paralogues ELMOD1 and ELMOD3, we identify novel functions and locations of these cell regulators and compare them to those of ELMOD2, allowing the determination of functional redundancy among the family members. We found strong similarities in phenotypes resulting from deletion of either Elmod1 or Elmod3 and marked differences from those arising in Elmod2 deletion lines. Deletion of either Elmod1 or Elmod3 results in the decreased ability of cells to form primary cilia, loss of a subset of proteins from cilia, and accumulation of some ciliary proteins at the Golgi, predicted to result from compromised traffic from the Golgi to cilia. These phenotypes are reversed upon activating mutant expression of either ARL3 or ARL16, linking their roles to ELMOD1/3 actions.
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Affiliation(s)
- Rachel E. Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA 94305
| | - Yihan Hu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan, China
| | - Skylar I. Dewees
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Narra Devi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Michael P. East
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Katherine R. Hardin
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Tala Khatib
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Joshua Linnert
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Michael J. Lim
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - James E. Casanova
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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23
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Khan SA, Khan S, Muhammad N, Rehman ZU, Khan MA, Nasir A, Kalsoom UE, Khan AK, Khan H, Wasif N. The First Report of a Missense Variant in RFX2 Causing Non-Syndromic Tooth Agenesis in a Consanguineous Pakistani Family. Front Genet 2022; 12:782653. [PMID: 35145545 PMCID: PMC8822170 DOI: 10.3389/fgene.2021.782653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background: The syndromic and non-syndromic congenital missing teeth phenotype is termed tooth agenesis. Since tooth agenesis is a heterogeneous disorder hence, the patients show diverse absent teeth phenotypes. Thus identifying novel genes involved in the morphogenesis of ectodermal appendages, including teeth, paves the way for establishing signaling pathways.Methods and Results: We have recruited an autosomal recessive non-syndromic tooth agenesis family with two affected members. The exome sequencing technology identified a novel missense sequence variant c.1421T > C; p.(Ile474Thr) in a regulatory factor X (RFX) family member (RFX2, OMIM: 142,765). During the data analysis eight rare variants on various chromosomal locations were identified, but the co-segregation analysis using Sanger sequencing confirmed the segregation of only two variants RFX2: c.1421T > C; p.(Ile474Thr), DOHH: c.109C > G; p.(Pro37Ala) lying in a common 7.1 MB region of homozygosity on chromosome 19p13.3. Furthermore, the online protein prediction algorithms and protein modeling analysis verified the RFX2 variant as a damaging genetic alteration and ACMG pathogenicity criteria classified it as likely pathogenic. On the other hand, the DOHH variant showed benign outcomes.Conclusion:RFX2 regulates the Hedgehog and fibroblast growth factor signaling pathways, which are involved in the epithelial and mesenchymal interactions during tooth development. Prior animal model studies have confirmed the expression of rfx2 at a developmental stage governing mouth formation. Moreover, its regulatory role and close association with ciliary and non-ciliary genes causing various dental malformations makes it a potential candidate gene for tooth agenesis phenotype. Further studies will contribute to exploring the direct role of RFX2 in human tooth development.
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Affiliation(s)
- Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
- *Correspondence: Saadullah Khan, ; Naveed Wasif,
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Zia Ur Rehman
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Muhammad Adnan Khan
- Dental Material, Institute of Basic Medical Sciences, Khyber Medical University Peshawar, Peshawar, Pakistan
| | - Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Umm-e- Kalsoom
- Department of Biochemistry, Hazara University, Mansehra, Pakistan
| | - Anwar Kamal Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Hassan Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Naveed Wasif
- Institute of Human Genetics, University of Ulm, Ulm, Germany
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
- *Correspondence: Saadullah Khan, ; Naveed Wasif,
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24
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Nommick A, Boutin C, Rosnet O, Schirmer C, Bazellières E, Thomé V, Loiseau E, Viallat A, Kodjabachian L. Lrrcc1 and Ccdc61 are conserved effectors of multiciliated cell function. J Cell Sci 2022; 135:274401. [DOI: 10.1242/jcs.258960] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022] Open
Abstract
Ciliated epithelia perform essential functions across animal evolution, ranging from locomotion of marine organisms to mucociliary clearance of airways in mammals. These epithelia are composed of multiciliated cells (MCCs) harbouring myriads of motile cilia, which rest on modified centrioles called basal bodies (BBs), and beat coordinately to generate directed fluid flows. Thus, BB biogenesis and organization is central to MCC function. In basal eukaryotes, the coiled-coil domain proteins Lrrcc1 and Ccdc61 were shown to be required for proper BB construction and function. Here, we used the Xenopus embryonic ciliated epidermis to characterize Lrrcc1 and Ccdc61 in vertebrate MCCs. We found that they both encode BB components, localized proximally at the junction with striated rootlets. Knocking down either gene caused defects in BB docking, spacing, and polarization. Moreover, their depletion impaired the apical cytoskeleton, and altered ciliary beating. Consequently, cilia-powered fluid flow was greatly reduced in morphant tadpoles, which displayed enhanced mortality when exposed to pathogenic bacteria. This work illustrates how integration across organizational scales make elementary BB components essential for the emergence of the physiological function of ciliated epithelia.
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Affiliation(s)
- Aude Nommick
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Camille Boutin
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Olivier Rosnet
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Claire Schirmer
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Elsa Bazellières
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Virginie Thomé
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Etienne Loiseau
- Aix Marseille Univ, CNRS, CINaM, Turing Center for Living Systems, Marseille, France
| | - Annie Viallat
- Aix Marseille Univ, CNRS, CINaM, Turing Center for Living Systems, Marseille, France
| | - Laurent Kodjabachian
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
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25
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Reverdatto S, Prasad A, Belrose JL, Zhang X, Sammons MA, Gibbs KM, Szaro BG. Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate Central Nervous System. BMC Genomics 2022; 23:2. [PMID: 34979916 PMCID: PMC8725369 DOI: 10.1186/s12864-021-08247-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Because some of its CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this capacity as tadpoles metamorphose into frogs, the South African claw-toed frog, Xenopus laevis, offers unique opportunities for exploring differences between regenerative and non-regenerative responses to CNS injury within the same organism. An earlier, three-way RNA-seq study (frog ONC eye, tadpole SCI hindbrain, frog SCI hindbrain) identified genes that regulate chromatin accessibility among those that were differentially expressed in regenerative vs non-regenerative CNS [11]. The current study used whole genome bisulfite sequencing (WGBS) of DNA collected from these same animals at the peak period of axon regeneration to study the extent to which DNA methylation could potentially underlie differences in chromatin accessibility between regenerative and non-regenerative CNS. RESULTS Consistent with the hypothesis that DNA of regenerative CNS is more accessible than that of non-regenerative CNS, DNA from both the regenerative tadpole hindbrain and frog eye was less methylated than that of the non-regenerative frog hindbrain. Also, consistent with observations of CNS injury in mammals, DNA methylation in non-regenerative frog hindbrain decreased after SCI. However, contrary to expectations that the level of DNA methylation would decrease even further with axotomy in regenerative CNS, DNA methylation in these regions instead increased with injury. Injury-induced differences in CpG methylation in regenerative CNS became especially enriched in gene promoter regions, whereas non-CpG methylation differences were more evenly distributed across promoter regions, intergenic, and intragenic regions. In non-regenerative CNS, tissue-related (i.e., regenerative vs. non-regenerative CNS) and injury-induced decreases in promoter region CpG methylation were significantly correlated with increased RNA expression, but the injury-induced, increased CpG methylation seen in regenerative CNS across promoter regions was not, suggesting it was associated with increased rather than decreased chromatin accessibility. This hypothesis received support from observations that in regenerative CNS, many genes exhibiting increased, injury-induced, promoter-associated CpG-methylation also exhibited increased RNA expression and association with histone markers for active promoters and enhancers. DNA immunoprecipitation for 5hmC in optic nerve regeneration found that the promoter-associated increases seen in CpG methylation were distinct from those exhibiting changes in 5hmC. CONCLUSIONS Although seemingly paradoxical, the increased injury-associated DNA methylation seen in regenerative CNS has many parallels in stem cells and cancer. Thus, these axotomy-induced changes in DNA methylation in regenerative CNS provide evidence for a novel epigenetic state favoring successful over unsuccessful CNS axon regeneration. The datasets described in this study should help lay the foundations for future studies of the molecular and cellular mechanisms involved. The insights gained should, in turn, help point the way to novel therapeutic approaches for treating CNS injury in mammals.
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Affiliation(s)
- Sergei Reverdatto
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Aparna Prasad
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Jamie L Belrose
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xiang Zhang
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Morgan A Sammons
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kurt M Gibbs
- Department of Biology & Chemistry, Morehead State University, Morehead, KY, 40351, USA
| | - Ben G Szaro
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA.
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA.
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.
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26
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Chuyen A, Daian F, Pasini A, Kodjabachian L. A live-imaging protocol to track cell movement in the Xenopus embryo. STAR Protoc 2021; 2:100928. [PMID: 34778847 PMCID: PMC8577151 DOI: 10.1016/j.xpro.2021.100928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Tracking individual cell movement during development is challenging, particularly in tissues subjected to major remodeling. Currently, most live imaging techniques in Xenopus are limited to tissue explants and/or to superficial cells. We describe here a protocol to track immature multiciliated cells (MCCs) moving within the inner epidermal layer of a whole embryo. In addition, we present a data processing protocol to uncouple the movements of individual cells from the coplanar drifts of the tissue in which they are embedded. For complete details on the use and execution of this protocol, please refer to Chuyen et al. (2021).
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Affiliation(s)
- Alexandre Chuyen
- Aix-Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Fabrice Daian
- Aix-Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Andrea Pasini
- Aix-Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Laurent Kodjabachian
- Aix-Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
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27
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Genome-Wide RNAi Screening Identifies Novel Pathways/Genes Involved in Oxidative Stress and Repurposable Drugs to Preserve Cystic Fibrosis Airway Epithelial Cell Integrity. Antioxidants (Basel) 2021; 10:antiox10121936. [PMID: 34943039 PMCID: PMC8750174 DOI: 10.3390/antiox10121936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 12/20/2022] Open
Abstract
Recurrent infection-inflammation cycles in cystic fibrosis (CF) patients generate a highly oxidative environment, leading to progressive destruction of the airway epithelia. The identification of novel modifier genes involved in oxidative stress susceptibility in the CF airways might contribute to devise new therapeutic approaches. We performed an unbiased genome-wide RNAi screen using a randomized siRNA library to identify oxidative stress modulators in CF airway epithelial cells. We monitored changes in cell viability after a lethal dose of hydrogen peroxide. Local similarity and protein-protein interaction network analyses uncovered siRNA target genes/pathways involved in oxidative stress. Further mining against public drug databases allowed identifying and validating commercially available drugs conferring oxidative stress resistance. Accordingly, a catalog of 167 siRNAs able to confer oxidative stress resistance in CF submucosal gland cells targeted 444 host genes and multiple circuitries involved in oxidative stress. The most significant processes were related to alternative splicing and cell communication, motility, and remodeling (impacting cilia structure/function, and cell guidance complexes). Other relevant pathways included DNA repair and PI3K/AKT/mTOR signaling. The mTOR inhibitor everolimus, the α1-adrenergic receptor antagonist doxazosin, and the Syk inhibitor fostamatinib significantly increased the viability of CF submucosal gland cells under strong oxidative stress pressure. Thus, novel therapeutic strategies to preserve airway cell integrity from the harsh oxidative milieu of CF airways could stem from a deep understanding of the complex consequences of oxidative stress at the molecular level, followed by a rational repurposing of existing "protective" drugs. This approach could also prove useful to other respiratory pathologies.
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28
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Vasquez SSV, van Dam J, Wheway G. An updated SYSCILIA gold standard (SCGSv2) of known ciliary genes, revealing the vast progress that has been made in the cilia research field. Mol Biol Cell 2021; 32:br13. [PMID: 34613793 PMCID: PMC8694072 DOI: 10.1091/mbc.e21-05-0226] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cilia are microtubule-based organelles with important functions in motility and sensation. They contribute to a broad spectrum of developmental disorders called ciliopathies and have recently been linked to common conditions such as cancers and congenital heart disease. There has been increasing interest in the biology of cilia and their contribution to disease over the past two decades. In 2013 we published a "Gold Standard" list of genes confirmed to be associated with cilia. This was published as part of the SYSCILIA consortium for systems biology study dissecting the contribution of cilia to human health and disease, and was named the Syscilia Gold Standard (SCGS). Since this publication, interest in cilia and understanding of their functions have continued to grow, and we now present an updated SCGS version 2. This includes an additional 383 genes, more than doubling the size of SCGSv1. We use this dataset to conduct a review of advances in understanding of cilia biology 2013- 2021 and offer perspectives on the future of cilia research. We hope that this continues to be a useful resource for the cilia community.
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Affiliation(s)
| | - John van Dam
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, 3584 CH Utrecht, Netherlands
| | - Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, United Kingdom
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29
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Chuyen A, Rulquin C, Daian F, Thomé V, Clément R, Kodjabachian L, Pasini A. The Scf/Kit pathway implements self-organized epithelial patterning. Dev Cell 2021; 56:795-810.e7. [PMID: 33756121 DOI: 10.1016/j.devcel.2021.02.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 12/22/2020] [Accepted: 02/22/2021] [Indexed: 01/11/2023]
Abstract
How global patterns emerge from individual cell behaviors is poorly understood. In the Xenopus embryonic epidermis, multiciliated cells (MCCs) are born in a random pattern within an inner mesenchymal layer and subsequently intercalate at regular intervals into an outer epithelial layer. Using video microscopy and mathematical modeling, we found that regular pattern emergence involves mutual repulsion among motile immature MCCs and affinity toward outer-layer intercellular junctions. Consistently, Arp2/3-mediated actin remodeling is required for MCC patterning. Mechanistically, we show that the Kit tyrosine kinase receptor, expressed in MCCs, and its ligand Scf, expressed in outer-layer cells, are both required for regular MCC distribution. Membrane-associated Scf behaves as a potent adhesive cue for MCCs, while its soluble form promotes their mutual repulsion. Finally, Kit expression is sufficient to confer order to a disordered heterologous cell population. This work reveals how a single signaling system can implement self-organized large-scale patterning.
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30
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Wu YJ, Liu Y, Hu YQ, Wang L, Bai FR, Xu C, Wu JW. Control of multiciliogenesis by miR-34/449 in the male reproductive tract through enforcing cell cycle exit. J Cell Sci 2021; 134:261955. [PMID: 33973639 PMCID: PMC8182409 DOI: 10.1242/jcs.253450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Multiciliated cells (MCCs) are terminally differentiated postmitotic cells that possess hundreds of motile cilia on their apical surface. Defects in cilia formation are associated with ciliopathies that affect many organs. In this study, we tested the role and mechanism of the miR-34/449 family in the regulation of multiciliogenesis in EDs using an miR-34b/c−/−; miR-449−/− double knockout (dKO) mouse model. MiR-34b/c and miR-449 depletion led to a reduced number of MCCs and abnormal cilia structure in the EDs starting from postnatal day (P)14. However, abnormal MCC differentiation in the dKO EDs could be observed as early as P7. RNA-seq analyses revealed that the aberrant development of MCCs in the EDs of dKO mice was associated with the upregulation of genes involved in cell cycle control. Using a cyclin-dependent kinase inhibitor to force cell cycle exit promoted MCC differentiation, and partially rescued the defective multiciliogenesis in the EDs of dKO mice. Taken together, our results suggest that miR-34b/c and miR-449 play an essential role in multiciliogenesis in EDs by regulating cell cycle exit. Summary: Mutagenic, expression and histological analyses reveal an essential role for miR-34b/c and miR-449 in multiciliogenesis in efferent ductules of the male reproductive tract by regulating cell cycle exit.
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Affiliation(s)
- Yu-Jie Wu
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Yue Liu
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Yan-Qin Hu
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Li Wang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Fu-Rong Bai
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Chen Xu
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Jing-Wen Wu
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
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31
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Kim H, Lee YS, Kim SM, Jang S, Choi H, Lee JW, Kim TD, Kim VN. RNA demethylation by FTO stabilizes the FOXJ1 mRNA for proper motile ciliogenesis. Dev Cell 2021; 56:1118-1130.e6. [PMID: 33761320 DOI: 10.1016/j.devcel.2021.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 12/10/2020] [Accepted: 02/27/2021] [Indexed: 12/29/2022]
Abstract
Adenosine N6-methylation (m6A) is one of the most pervasive mRNA modifications, and yet the physiological significance of m6A removal (demethylation) remains elusive. Here, we report that the m6A demethylase FTO functions as a conserved regulator of motile ciliogenesis. Mechanistically, FTO demethylates and thereby stabilizes the mRNA that encodes the master ciliary transcription factor FOXJ1. Depletion of Fto in Xenopus laevis embryos caused widespread motile cilia defects, and Foxj1 was identified as one of the major phenocritical targets. In primary human airway epithelium, FTO depletion also led to FOXJ1 mRNA destabilization and a severe loss of ciliated cells with an increase of neighboring goblet cells. Consistently, Fto knockout mice showed strong asthma-like phenotypes upon allergen challenge, a result owing to defective ciliated cells in the airway epithelium. Altogether, our study reveals a conserved role of the FTO-FOXJ1 axis in embryonic and homeostatic motile ciliogenesis.
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Affiliation(s)
- Hyunjoon Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of the Biological Sciences, Seoul National University, Seoul 08826, Korea.
| | - Young-Suk Lee
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of the Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Seok-Min Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Soohyun Jang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Hyunji Choi
- School of the Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jae-Won Lee
- Natural Medicine Research Center, KRIBB, Cheongju, Korea
| | - Tae-Don Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Korea.
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of the Biological Sciences, Seoul National University, Seoul 08826, Korea.
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32
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Tasca A, Helmstädter M, Brislinger MM, Haas M, Mitchell B, Walentek P. Notch signaling induces either apoptosis or cell fate change in multiciliated cells during mucociliary tissue remodeling. Dev Cell 2021; 56:525-539.e6. [PMID: 33400913 PMCID: PMC7904641 DOI: 10.1016/j.devcel.2020.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/13/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
Multiciliated cells (MCCs) are extremely highly differentiated, presenting >100 cilia and basal bodies. Therefore, MCC fate is thought to be terminal and irreversible. We analyzed how MCCs are removed from the airway-like mucociliary Xenopus epidermis during developmental tissue remodeling. We found that a subset of MCCs undergoes lateral line-induced apoptosis, but that the majority coordinately trans-differentiate into goblet secretory cells. Both processes are dependent on Notch signaling, while the cellular response to Notch is modulated by Jak/STAT, thyroid hormone, and mTOR signaling. At the cellular level, trans-differentiation is executed through the loss of ciliary gene expression, including foxj1 and pcm1, altered proteostasis, cilia retraction, basal body elimination, as well as the initiation of mucus production and secretion. Our work describes two modes for MCC loss during vertebrate development, the signaling regulation of these processes, and demonstrates that even cells with extreme differentiation features can undergo direct fate conversion.
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Affiliation(s)
- Alexia Tasca
- Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, 79106 Freiburg, Germany; Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
| | - Martin Helmstädter
- Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, 79106 Freiburg, Germany
| | - Magdalena Maria Brislinger
- Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, 79106 Freiburg, Germany; Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Maximilian Haas
- Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, 79106 Freiburg, Germany; Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Brian Mitchell
- Department of Cell and Developmental Biology, Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Peter Walentek
- Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, 79106 Freiburg, Germany; Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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33
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Rao VG, Kulkarni SS. Xenopus to the rescue: A model to validate and characterize candidate ciliopathy genes. Genesis 2021; 59:e23414. [PMID: 33576572 DOI: 10.1002/dvg.23414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022]
Abstract
Cilia are present on most vertebrate cells and play a central role in development, growth, and homeostasis. Thus, cilia dysfunction can manifest into an array of diseases, collectively termed ciliopathies, affecting millions of lives worldwide. Yet, our understanding of the gene regulatory networks that control cilia assembly and functions remain incomplete. With the advances in next-generation sequencing technologies, we can now rapidly predict pathogenic variants from hundreds of ciliopathy patients. While the pace of candidate gene discovery is exciting, most of these genes have never been previously implicated in cilia assembly or function. This makes assigning the disease causality difficult. This review discusses how Xenopus, a genetically tractable and high-throughput vertebrate model, has played a central role in identifying, validating, and characterizing candidate ciliopathy genes. The review is focused on multiciliated cells (MCCs) and diseases associated with MCC dysfunction. MCCs harbor multiple motile cilia on their apical surface to generate extracellular fluid flow inside the airway, the brain ventricles, and the oviduct. In Xenopus, these cells are external and present on the embryonic epidermal epithelia, facilitating candidate genes analysis in MCC development in vivo. The ability to introduce patient variants to study their effects on disease progression makes Xenopus a powerful model to improve our understanding of the underlying disease mechanisms and explain the patient phenotype.
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Affiliation(s)
- Venkatramanan G Rao
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Saurabh S Kulkarni
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA.,Department of Biology, University of Virginia, Charlottesville, Virginia, USA
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34
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Lewis M, Stracker TH. Transcriptional regulation of multiciliated cell differentiation. Semin Cell Dev Biol 2021; 110:51-60. [DOI: 10.1016/j.semcdb.2020.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/25/2020] [Accepted: 04/13/2020] [Indexed: 01/01/2023]
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Adivitiya, Kaushik MS, Chakraborty S, Veleri S, Kateriya S. Mucociliary Respiratory Epithelium Integrity in Molecular Defense and Susceptibility to Pulmonary Viral Infections. BIOLOGY 2021; 10:95. [PMID: 33572760 PMCID: PMC7911113 DOI: 10.3390/biology10020095] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 01/08/2023]
Abstract
Mucociliary defense, mediated by the ciliated and goblet cells, is fundamental to respiratory fitness. The concerted action of ciliary movement on the respiratory epithelial surface and the pathogen entrapment function of mucus help to maintain healthy airways. Consequently, genetic or acquired defects in lung defense elicit respiratory diseases and secondary microbial infections that inflict damage on pulmonary function and may even be fatal. Individuals living with chronic and acute respiratory diseases are more susceptible to develop severe coronavirus disease-19 (COVID-19) illness and hence should be proficiently managed. In light of the prevailing pandemic, we review the current understanding of the respiratory system and its molecular components with a major focus on the pathophysiology arising due to collapsed respiratory epithelium integrity such as abnormal ciliary movement, cilia loss and dysfunction, ciliated cell destruction, and changes in mucus rheology. The review includes protein interaction networks of coronavirus infection-manifested implications on the molecular machinery that regulates mucociliary clearance. We also provide an insight into the alteration of the transcriptional networks of genes in the nasopharynx associated with the mucociliary clearance apparatus in humans upon infection by severe acute respiratory syndrome coronavirus-2.
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Affiliation(s)
- Adivitiya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Manish Singh Kaushik
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Soura Chakraborty
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Shobi Veleri
- Drug Safety Division, ICMR-National Institute of Nutrition, Hyderabad 500007, India;
| | - Suneel Kateriya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
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36
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Lee C, Cox RM, Papoulas O, Horani A, Drew K, Devitt CC, Brody SL, Marcotte EM, Wallingford JB. Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins. eLife 2020; 9:e58662. [PMID: 33263282 PMCID: PMC7785291 DOI: 10.7554/elife.58662] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 12/01/2020] [Indexed: 12/20/2022] Open
Abstract
Ciliary motility is driven by axonemal dyneins that are assembled in the cytoplasm before deployment to cilia. Motile ciliopathy can result from defects in the dyneins themselves or from defects in factors required for their cytoplasmic pre-assembly. Recent work demonstrates that axonemal dyneins, their specific assembly factors, and broadly-acting chaperones are concentrated in liquid-like organelles in the cytoplasm called DynAPs (Dynein Axonemal Particles). Here, we use in vivo imaging in Xenopus to show that inner dynein arm (IDA) and outer dynein arm (ODA) subunits are partitioned into non-overlapping sub-regions within DynAPs. Using affinity- purification mass-spectrometry of in vivo interaction partners, we also identify novel partners for inner and outer dynein arms. Among these, we identify C16orf71/Daap1 as a novel axonemal dynein regulator. Daap1 interacts with ODA subunits, localizes specifically to the cytoplasm, is enriched in DynAPs, and is required for the deployment of ODAs to axonemes. Our work reveals a new complexity in the structure and function of a cell-type specific liquid-like organelle that is directly relevant to human genetic disease.
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Affiliation(s)
- Chanjae Lee
- Department of Molecular Biosciences, University of TexasAustinUnited States
| | - Rachael M Cox
- Department of Molecular Biosciences, University of TexasAustinUnited States
| | - Ophelia Papoulas
- Department of Molecular Biosciences, University of TexasAustinUnited States
| | - Amjad Horani
- Department of Pediatrics, Washington University School of MedicineSt. LouisUnited States
| | - Kevin Drew
- Department of Molecular Biosciences, University of TexasAustinUnited States
| | - Caitlin C Devitt
- Department of Molecular Biosciences, University of TexasAustinUnited States
| | - Steven L Brody
- Department of Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Edward M Marcotte
- Department of Molecular Biosciences, University of TexasAustinUnited States
| | - John B Wallingford
- Department of Molecular Biosciences, University of TexasAustinUnited States
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Lemeille S, Paschaki M, Baas D, Morlé L, Duteyrat JL, Ait-Lounis A, Barras E, Soulavie F, Jerber J, Thomas J, Zhang Y, Holtzman MJ, Kistler WS, Reith W, Durand B. Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis. Nucleic Acids Res 2020; 48:9019-9036. [PMID: 32725242 PMCID: PMC7498320 DOI: 10.1093/nar/gkaa625] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022] Open
Abstract
Cilia assembly is under strict transcriptional control during animal development. In vertebrates, a hierarchy of transcription factors (TFs) are involved in controlling the specification, differentiation and function of multiciliated epithelia. RFX TFs play key functions in the control of ciliogenesis in animals. Whereas only one RFX factor regulates ciliogenesis in C. elegans, several distinct RFX factors have been implicated in this process in vertebrates. However, a clear understanding of the specific and redundant functions of different RFX factors in ciliated cells remains lacking. Using RNA-seq and ChIP-seq approaches we identified genes regulated directly and indirectly by RFX1, RFX2 and RFX3 in mouse ependymal cells. We show that these three TFs have both redundant and specific functions in ependymal cells. Whereas RFX1, RFX2 and RFX3 occupy many shared genomic loci, only RFX2 and RFX3 play a prominent and redundant function in the control of motile ciliogenesis in mice. Our results provide a valuable list of candidate ciliary genes. They also reveal stunning differences between compensatory processes operating in vivo and ex vivo.
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Affiliation(s)
- Sylvain Lemeille
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Marie Paschaki
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Dominique Baas
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Laurette Morlé
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Jean-Luc Duteyrat
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Aouatef Ait-Lounis
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Emmanuèle Barras
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Fabien Soulavie
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Julie Jerber
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Joëlle Thomas
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Yong Zhang
- Department of Medicine and Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Michael J Holtzman
- Department of Medicine and Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri
| | - W Stephen Kistler
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
| | - Walter Reith
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Bénédicte Durand
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
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38
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Collins C, Ventrella R, Mitchell BJ. Building a ciliated epithelium: Transcriptional regulation and radial intercalation of multiciliated cells. Curr Top Dev Biol 2020; 145:3-39. [PMID: 34074533 DOI: 10.1016/bs.ctdb.2020.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The epidermis of the Xenopus embryo has emerged as a powerful tool for studying the development of a ciliated epithelium. Interspersed throughout the epithelium are multiciliated cells (MCCs) with 100+ motile cilia that beat in a coordinated manner to generate fluid flow over the surface of the cell. MCCs are essential for various developmental processes and, furthermore, ciliary dysfunction is associated with numerous pathologies. Therefore, understanding the cellular mechanisms involved in establishing a ciliated epithelium are of particular interest. MCCs originate in the inner epithelial layer of Xenopus skin, where Notch signaling plays a critical role in determining which progenitors will adopt a ciliated cell fate. Then, activation of various transcriptional regulators, such as GemC1 and MCIDAS, initiate the MCC transcriptional program, resulting in centriole amplification and the formation of motile cilia. Following specification and differentiation, MCCs undergo the process of radial intercalation, where cells apically migrate from the inner layer to the outer epithelial layer. This process involves the cooperation of various cytoskeletal networks, activation of various signaling molecules, and changes in cell-ECM and cell-cell adhesion. Coordination of these cellular processes is required for complete incorporation into the outer epithelial layer and generation of a functional ciliated epithelium. Here, we highlight recent advances made in understanding the transcriptional cascades required for MCC specification and differentiation and the coordination of cellular processes that facilitate radial intercalation. Proper regulation of these signaling pathways and processes are the foundation for developing a ciliated epithelium.
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Affiliation(s)
- Caitlin Collins
- Department of Cell and Developmental Biology, Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL, United States
| | - Rosa Ventrella
- Department of Cell and Developmental Biology, Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL, United States
| | - Brian J Mitchell
- Department of Cell and Developmental Biology, Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL, United States.
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Drew K, Lee C, Cox RM, Dang V, Devitt CC, McWhite CD, Papoulas O, Huizar RL, Marcotte EM, Wallingford JB. A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery. Dev Biol 2020; 467:108-117. [PMID: 32898505 DOI: 10.1016/j.ydbio.2020.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 08/18/2020] [Indexed: 01/06/2023]
Abstract
Cell-type specific RNA-associated proteins are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RNA-associated proteins, we currently have few comprehensive rosters of cell-type specific RNA-associated proteins in vertebrate tissues. Here, we demonstrate the feasibility of determining the RNA-associated proteome of a defined vertebrate embryonic tissue using DIF-FRAC, a systematic and universal (i.e., label-free) method. Application of DIF-FRAC to cultured tissue explants of Xenopus mucociliary epithelium identified dozens of known RNA-associated proteins as expected, but also several novel RNA-associated proteins, including proteins related to assembly of the mitotic spindle and regulation of ciliary beating. In particular, we show that the inner dynein arm tether Cfap44 is an RNA-associated protein that localizes not only to axonemes, but also to liquid-like organelles in the cytoplasm called DynAPs. This result led us to discover that DynAPs are generally enriched for RNA. Together, these data provide a useful resource for a deeper understanding of mucociliary epithelia and demonstrate that DIF-FRAC will be broadly applicable for systematic identification of RNA-associated proteins from embryonic tissues.
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Affiliation(s)
- Kevin Drew
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Chanjae Lee
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Rachael M Cox
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Vy Dang
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Caitlin C Devitt
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Claire D McWhite
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Ophelia Papoulas
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Ryan L Huizar
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Edward M Marcotte
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA.
| | - John B Wallingford
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA.
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40
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Belrose JL, Prasad A, Sammons MA, Gibbs KM, Szaro BG. Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons. BMC Genomics 2020; 21:540. [PMID: 32758133 PMCID: PMC7430912 DOI: 10.1186/s12864-020-06954-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The South African claw-toed frog, Xenopus laevis, is uniquely suited for studying differences between regenerative and non-regenerative responses to CNS injury within the same organism, because some CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this capacity as tadpoles metamorphose into frogs. Tissues from these CNS regions (frog ONC eye, tadpole SCI hindbrain, frog SCI hindbrain) were used in a three-way RNA-seq study of axotomized CNS axons to identify potential core gene expression programs for successful CNS axon regeneration. RESULTS Despite tissue-specific changes in expression dominating the injury responses of each tissue, injury-induced changes in gene expression were nonetheless shared between the two axon-regenerative CNS regions that were not shared with the non-regenerative region. These included similar temporal patterns of gene expression and over 300 injury-responsive genes. Many of these genes and their associated cellular functions had previously been associated with injury responses of multiple tissues, both neural and non-neural, from different species, thereby demonstrating deep phylogenetically conserved commonalities between successful CNS axon regeneration and tissue regeneration in general. Further analyses implicated the KEGG adipocytokine signaling pathway, which links leptin with metabolic and gene regulatory pathways, and a novel gene regulatory network with genes regulating chromatin accessibility at its core, as important hubs in the larger network of injury response genes involved in successful CNS axon regeneration. CONCLUSIONS This study identifies deep, phylogenetically conserved commonalities between CNS axon regeneration and other examples of successful tissue regeneration and provides new targets for studying the molecular underpinnings of successful CNS axon regeneration, as well as a guide for distinguishing pro-regenerative injury-induced changes in gene expression from detrimental ones in mammals.
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Affiliation(s)
- Jamie L Belrose
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Aparna Prasad
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Morgan A Sammons
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Kurt M Gibbs
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, 40351, USA
| | - Ben G Szaro
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.
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41
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Gojo J, Englinger B, Jiang L, Hübner JM, Shaw ML, Hack OA, Madlener S, Kirchhofer D, Liu I, Pyrdol J, Hovestadt V, Mazzola E, Mathewson ND, Trissal M, Lötsch D, Dorfer C, Haberler C, Halfmann A, Mayr L, Peyrl A, Geyeregger R, Schwalm B, Mauermann M, Pajtler KW, Milde T, Shore ME, Geduldig JE, Pelton K, Czech T, Ashenberg O, Wucherpfennig KW, Rozenblatt-Rosen O, Alexandrescu S, Ligon KL, Pfister SM, Regev A, Slavc I, Berger W, Suvà ML, Kool M, Filbin MG. Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma. Cancer Cell 2020; 38:44-59.e9. [PMID: 32663469 PMCID: PMC7479515 DOI: 10.1016/j.ccell.2020.06.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/26/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023]
Abstract
Ependymoma is a heterogeneous entity of central nervous system tumors with well-established molecular groups. Here, we apply single-cell RNA sequencing to analyze ependymomas across molecular groups and anatomic locations to investigate their intratumoral heterogeneity and developmental origins. Ependymomas are composed of a cellular hierarchy initiating from undifferentiated populations, which undergo impaired differentiation toward three lineages of neuronal-glial fate specification. While prognostically favorable groups of ependymoma predominantly harbor differentiated cells, aggressive groups are enriched for undifferentiated cell populations. The delineated transcriptomic signatures correlate with patient survival and define molecular dependencies for targeted treatment approaches. Taken together, our analyses reveal a developmental hierarchy underlying ependymomas relevant to biological and clinical behavior.
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Affiliation(s)
- Johannes Gojo
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jens M Hübner
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - McKenzie L Shaw
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Olivia A Hack
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Dominik Kirchhofer
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Ilon Liu
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jason Pyrdol
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Volker Hovestadt
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Emanuele Mazzola
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nathan D Mathewson
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Maria Trissal
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Daniela Lötsch
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Angela Halfmann
- Clinical Cell Biology, Children's Cancer Research Institute (CCRI), 1090 Vienna, Austria
| | - Lisa Mayr
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Rene Geyeregger
- Clinical Cell Biology, Children's Cancer Research Institute (CCRI), 1090 Vienna, Austria
| | - Benjamin Schwalm
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Monica Mauermann
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Marni E Shore
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jack E Geduldig
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kristine Pelton
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Orr Ashenberg
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Keith L Ligon
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Aviv Regev
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Walter Berger
- Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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42
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Patir A, Fraser AM, Barnett MW, McTeir L, Rainger J, Davey MG, Freeman TC. The transcriptional signature associated with human motile cilia. Sci Rep 2020; 10:10814. [PMID: 32616903 PMCID: PMC7331728 DOI: 10.1038/s41598-020-66453-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/15/2020] [Indexed: 02/06/2023] Open
Abstract
Cilia are complex microtubule-based organelles essential to a range of processes associated with embryogenesis and tissue homeostasis. Mutations in components of these organelles or those involved in their assembly may result in a diverse set of diseases collectively known as ciliopathies. Accordingly, many cilia-associated proteins have been described, while those distinguishing cilia subtypes are poorly defined. Here we set out to define genes associated with motile cilia in humans based on their transcriptional signature. To define the signature, we performed network deconvolution of transcriptomics data derived from tissues possessing motile ciliated cell populations. For each tissue, genes coexpressed with the motile cilia-associated transcriptional factor, FOXJ1, were identified. The consensus across tissues provided a transcriptional signature of 248 genes. To validate these, we examined the literature, databases (CilDB, CentrosomeDB, CiliaCarta and SysCilia), single cell RNA-Seq data, and the localisation of mRNA and proteins in motile ciliated cells. In the case of six poorly characterised signature genes, we performed new localisation experiments on ARMC3, EFCAB6, FAM183A, MYCBPAP, RIBC2 and VWA3A. In summary, we report a set of motile cilia-associated genes that helps shape our understanding of these complex cellular organelles.
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Affiliation(s)
- Anirudh Patir
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Amy M Fraser
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Mark W Barnett
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Lynn McTeir
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Joe Rainger
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Megan G Davey
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Tom C Freeman
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK.
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43
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Kakebeen AD, Chitsazan AD, Williams MC, Saunders LM, Wills AE. Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors. eLife 2020; 9:e52648. [PMID: 32338593 PMCID: PMC7250574 DOI: 10.7554/elife.52648] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/25/2020] [Indexed: 12/24/2022] Open
Abstract
Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable the growth and differentiation of new tissue, a process executed over multiple days and across dozens of cell types. The heterogeneity of tissues and temporally-sensitive fate decisions involved has made it difficult to articulate the gene regulatory programs enabling regeneration of individual cell types. To better understand how a regenerative program is fulfilled by neural progenitor cells (NPCs) of the spinal cord, we analyzed pax6-expressing NPCs isolated from regenerating Xenopus tropicalis tails. By intersecting chromatin accessibility data with single-cell transcriptomics, we find that NPCs place an early priority on neuronal differentiation. Late in regeneration, the priority returns to proliferation. Our analyses identify Pbx3 and Meis1 as critical regulators of tail regeneration and axon organization. Overall, we use transcriptional regulatory dynamics to present a new model for cell fate decisions and their regulators in NPCs during regeneration.
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Affiliation(s)
| | | | | | - Lauren M Saunders
- Department of Genome Sciences, University of WashingtonSeattleUnited States
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44
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Beeby M, Ferreira JL, Tripp P, Albers SV, Mitchell DR. Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia. FEMS Microbiol Rev 2020; 44:253-304. [DOI: 10.1093/femsre/fuaa006] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
Echoing the repeated convergent evolution of flight and vision in large eukaryotes, propulsive swimming motility has evolved independently in microbes in each of the three domains of life. Filamentous appendages – archaella in Archaea, flagella in Bacteria and cilia in Eukaryotes – wave, whip or rotate to propel microbes, overcoming diffusion and enabling colonization of new environments. The implementations of the three propulsive nanomachines are distinct, however: archaella and flagella rotate, while cilia beat or wave; flagella and cilia assemble at their tips, while archaella assemble at their base; archaella and cilia use ATP for motility, while flagella use ion-motive force. These underlying differences reflect the tinkering required to evolve a molecular machine, in which pre-existing machines in the appropriate contexts were iteratively co-opted for new functions and whose origins are reflected in their resultant mechanisms. Contemporary homologies suggest that archaella evolved from a non-rotary pilus, flagella from a non-rotary appendage or secretion system, and cilia from a passive sensory structure. Here, we review the structure, assembly, mechanism and homologies of the three distinct solutions as a foundation to better understand how propulsive nanomachines evolved three times independently and to highlight principles of molecular evolution.
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Affiliation(s)
- Morgan Beeby
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Josie L Ferreira
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Patrick Tripp
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - David R Mitchell
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 E. Adams St., Syracuse, NY 13210, USA
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45
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Gigante ED, Caspary T. Signaling in the primary cilium through the lens of the Hedgehog pathway. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 9:e377. [PMID: 32084300 DOI: 10.1002/wdev.377] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/22/2020] [Accepted: 01/25/2020] [Indexed: 12/14/2022]
Abstract
Cilia are microtubule-based, cell-surface projections whose machinery is evolutionarily conserved. In vertebrates, cilia are observed on almost every cell type and are either motile or immotile. Immotile sensory, or primary cilia, are responsive to extracellular ligands and signals. Cilia can be thought of as compartments, functionally distinct from the cell that provides an environment for signaling cascades. Hedgehog is a critical developmental signaling pathway which is functionally linked to primary cilia in vertebrates. The major components of the vertebrate Hedgehog signaling pathway dynamically localize to the ciliary compartment and ciliary membrane. Critically, G-protein coupled receptor (GPCR) Smoothened, the obligate transducer of the pathway, is enriched and activated in the cilium. While Smoothened is the most intensely studied ciliary receptor, many GPCRs localize within cilia. Understanding the link between Smoothened and cilia defines common features, and distinctions, of GPCR signaling within the primary cilium. This article is categorized under: Signaling Pathways > Global Signaling Mechanisms Signaling Pathways > Cell Fate Signaling.
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Affiliation(s)
- Eduardo D Gigante
- Graduate Program in Neuroscience, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
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46
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Touré A, Martinez G, Kherraf ZE, Cazin C, Beurois J, Arnoult C, Ray PF, Coutton C. The genetic architecture of morphological abnormalities of the sperm tail. Hum Genet 2020; 140:21-42. [PMID: 31950240 DOI: 10.1007/s00439-020-02113-x] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/06/2020] [Indexed: 12/29/2022]
Abstract
Spermatozoa contain highly specialized structural features reflecting unique functions required for fertilization. Among them, the flagellum is a sperm-specific organelle required to generate the motility, which is essential to reach the egg. The flagellum integrity is, therefore, critical for normal sperm function and flagellum defects consistently lead to male infertility due to reduced or absent sperm motility defined as asthenozoospermia. Multiple morphological abnormalities of the flagella (MMAF), also called short tails, is among the most severe forms of sperm flagellum defects responsible for male infertility and is characterized by the presence in the ejaculate of spermatozoa being short, coiled, absent and of irregular caliber. Recent studies have demonstrated that MMAF is genetically heterogeneous which is consistent with the large number of proteins (over one thousand) localized in the human sperm flagella. In the past 5 years, genomic investigation of the MMAF phenotype allowed the identification of 18 genes whose mutations induce MMAF and infertility. Here we will review information about those genes including their expression pattern, the features of the encoded proteins together with their localization within the different flagellar protein complexes (axonemal or peri-axonemal) and their potential functions. We will categorize the identified MMAF genes following the protein complexes, functions or biological processes they may be associated with, based on the current knowledge in the field.
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Affiliation(s)
- Aminata Touré
- Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, 75014, Paris, France.,INSERM U1016, Institut Cochin, 75014, Paris, France.,Centre National de La Recherche Scientifique UMR8104, 75014, Paris, France
| | - Guillaume Martinez
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Univ. Grenoble Alpes, 38000, Grenoble, France.,CHU Grenoble Alpes, UM de Génétique Chromosomique, 38000, Grenoble, France
| | - Zine-Eddine Kherraf
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Univ. Grenoble Alpes, 38000, Grenoble, France.,CHU Grenoble Alpes, UM GI-DPI, 38000, Grenoble, France
| | - Caroline Cazin
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Univ. Grenoble Alpes, 38000, Grenoble, France
| | - Julie Beurois
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Univ. Grenoble Alpes, 38000, Grenoble, France
| | - Christophe Arnoult
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Univ. Grenoble Alpes, 38000, Grenoble, France
| | - Pierre F Ray
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Univ. Grenoble Alpes, 38000, Grenoble, France.,CHU Grenoble Alpes, UM GI-DPI, 38000, Grenoble, France
| | - Charles Coutton
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Univ. Grenoble Alpes, 38000, Grenoble, France. .,CHU Grenoble Alpes, UM de Génétique Chromosomique, 38000, Grenoble, France.
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47
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Paraiso KD, Blitz IL, Zhou JJ, Cho KWY. Morpholinos Do Not Elicit an Innate Immune Response during Early Xenopus Embryogenesis. Dev Cell 2020; 49:643-650.e3. [PMID: 31112700 DOI: 10.1016/j.devcel.2019.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/14/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023]
Abstract
It has recently been reported that a common side effect of translation-blocking morpholino antisense oligonucleotides is the induction of a set of innate immune response genes in Xenopus embryos and that splicing-blocking morpholinos lead to unexpected off-target mis-splicing events. Here, we present an analysis of all publicly available Xenopus RNA sequencing (RNA-seq) data in a reexamination of the effects of translation-blocking morpholinos on the innate immune response. Our analysis does not support the authors' general conclusion, which was based on a limited number of RNA-seq datasets. Moreover, the strong induction of an immune response appears to be specific to the tbxt/tbxt2 morpholinos. The more comprehensive study presented here indicates that using morpholinos for targeted gene knockdowns remains of considerable value for the rapid identification of gene function.
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Affiliation(s)
- Kitt D Paraiso
- Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ira L Blitz
- Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Jeff J Zhou
- Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Ken W Y Cho
- Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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48
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Lorès P, Dacheux D, Kherraf ZE, Nsota Mbango JF, Coutton C, Stouvenel L, Ialy-Radio C, Amiri-Yekta A, Whitfield M, Schmitt A, Cazin C, Givelet M, Ferreux L, Fourati Ben Mustapha S, Halouani L, Marrakchi O, Daneshipour A, El Khouri E, Do Cruzeiro M, Favier M, Guillonneau F, Chaudhry M, Sakheli Z, Wolf JP, Patrat C, Gacon G, Savinov SN, Hosseini SH, Robinson DR, Zouari R, Ziyyat A, Arnoult C, Dulioust E, Bonhivers M, Ray PF, Touré A. Mutations in TTC29, Encoding an Evolutionarily Conserved Axonemal Protein, Result in Asthenozoospermia and Male Infertility. Am J Hum Genet 2019; 105:1148-1167. [PMID: 31735292 DOI: 10.1016/j.ajhg.2019.10.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/11/2019] [Indexed: 12/30/2022] Open
Abstract
In humans, structural or functional defects of the sperm flagellum induce asthenozoospermia, which accounts for the main sperm defect encountered in infertile men. Herein we focused on morphological abnormalities of the sperm flagellum (MMAF), a phenotype also termed "short tails," which constitutes one of the most severe sperm morphological defects resulting in asthenozoospermia. In previous work based on whole-exome sequencing of a cohort of 167 MMAF-affected individuals, we identified bi-allelic loss-of-function mutations in more than 30% of the tested subjects. In this study, we further analyzed this cohort and identified five individuals with homozygous truncating variants in TTC29, a gene preferentially and highly expressed in the testis, and encoding a tetratricopeptide repeat-containing protein related to the intraflagellar transport (IFT). One individual carried a frameshift variant, another one carried a homozygous stop-gain variant, and three carried the same splicing variant affecting a consensus donor site. The deleterious effect of this last variant was confirmed on the corresponding transcript and protein product. In addition, we produced and analyzed TTC29 loss-of-function models in the flagellated protist T. brucei and in M. musculus. Both models confirmed the importance of TTC29 for flagellar beating. We showed that in T. brucei the TPR structural motifs, highly conserved between the studied orthologs, are critical for TTC29 axonemal localization and flagellar beating. Overall our work demonstrates that TTC29 is a conserved axonemal protein required for flagellar structure and beating and that TTC29 mutations are a cause of male sterility due to MMAF.
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Affiliation(s)
- Patrick Lorès
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Denis Dacheux
- Université de Bordeaux, Microbiologie Fondamentale et Pathogénicité, CNRS UMR 5234, Bordeaux, France; Institut Polytechnique de Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR-CNRS 5234, 33000 Bordeaux, France
| | - Zine-Eddine Kherraf
- INSERM U1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; CHU de Grenoble, UM GI-DPI, Grenoble 38000, France
| | - Jean-Fabrice Nsota Mbango
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Charles Coutton
- INSERM U1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; CHU Grenoble Alpes, UM de Génétique Chromosomique, Grenoble, France
| | - Laurence Stouvenel
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Come Ialy-Radio
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Amir Amiri-Yekta
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Marjorie Whitfield
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Alain Schmitt
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Caroline Cazin
- INSERM U1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Maëlle Givelet
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Lucile Ferreux
- Laboratoire d'Histologie Embryologie - Biologie de la Reproduction - CECOS Groupe Hospitalier Universitaire Paris Centre, Assistance Publique-Hôpitaux de Paris, Paris 75014, France
| | - Selima Fourati Ben Mustapha
- Histologie Embryologie et Biologie de la Reproduction, Centre de Promotion des Sciences de la Reproduction, Polyclinique les Jasmins, Centre Urbain Nord, 1003 Tunis, Tunisia
| | - Lazhar Halouani
- Histologie Embryologie et Biologie de la Reproduction, Centre de Promotion des Sciences de la Reproduction, Polyclinique les Jasmins, Centre Urbain Nord, 1003 Tunis, Tunisia
| | - Ouafi Marrakchi
- Histologie Embryologie et Biologie de la Reproduction, Centre de Promotion des Sciences de la Reproduction, Polyclinique les Jasmins, Centre Urbain Nord, 1003 Tunis, Tunisia
| | - Abbas Daneshipour
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Elma El Khouri
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Marcio Do Cruzeiro
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Maryline Favier
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - François Guillonneau
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Marhaba Chaudhry
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Zeinab Sakheli
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Jean-Philippe Wolf
- INSERM U1016, Institut Cochin, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France; Laboratoire d'Histologie Embryologie - Biologie de la Reproduction - CECOS Groupe Hospitalier Universitaire Paris Centre, Assistance Publique-Hôpitaux de Paris, Paris 75014, France
| | - Catherine Patrat
- INSERM U1016, Institut Cochin, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France; Laboratoire d'Histologie Embryologie - Biologie de la Reproduction - CECOS Groupe Hospitalier Universitaire Paris Centre, Assistance Publique-Hôpitaux de Paris, Paris 75014, France
| | - Gérard Gacon
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Sergey N Savinov
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Seyedeh Hanieh Hosseini
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institutefor Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Derrick R Robinson
- Université de Bordeaux, Microbiologie Fondamentale et Pathogénicité, CNRS UMR 5234, Bordeaux, France
| | - Raoudha Zouari
- Histologie Embryologie et Biologie de la Reproduction, Centre de Promotion des Sciences de la Reproduction, Polyclinique les Jasmins, Centre Urbain Nord, 1003 Tunis, Tunisia
| | - Ahmed Ziyyat
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France; Laboratoire d'Histologie Embryologie - Biologie de la Reproduction - CECOS Groupe Hospitalier Universitaire Paris Centre, Assistance Publique-Hôpitaux de Paris, Paris 75014, France
| | - Christophe Arnoult
- INSERM U1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Emmanuel Dulioust
- INSERM U1016, Institut Cochin, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France; Laboratoire d'Histologie Embryologie - Biologie de la Reproduction - CECOS Groupe Hospitalier Universitaire Paris Centre, Assistance Publique-Hôpitaux de Paris, Paris 75014, France
| | - Mélanie Bonhivers
- Université de Bordeaux, Microbiologie Fondamentale et Pathogénicité, CNRS UMR 5234, Bordeaux, France
| | - Pierre F Ray
- INSERM U1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; CHU de Grenoble, UM GI-DPI, Grenoble 38000, France
| | - Aminata Touré
- INSERM U1016, Institut Cochin, Paris 75014, France; Centre National de la Recherche Scientifique UMR8104, Paris 75014, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France.
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49
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Liu C, He X, Liu W, Yang S, Wang L, Li W, Wu H, Tang S, Ni X, Wang J, Gao Y, Tian S, Zhang L, Cong J, Zhang Z, Tan Q, Zhang J, Li H, Zhong Y, Lv M, Li J, Jin L, Cao Y, Zhang F. Bi-allelic Mutations in TTC29 Cause Male Subfertility with Asthenoteratospermia in Humans and Mice. Am J Hum Genet 2019; 105:1168-1181. [PMID: 31735294 DOI: 10.1016/j.ajhg.2019.10.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022] Open
Abstract
As a type of severe asthenoteratospermia, multiple morphological abnormalities of the flagella (MMAF) are characterized by the presence of immotile spermatozoa with severe flagellar malformations. MMAF is a genetically heterogeneous disorder, and the known MMAF-associated genes can only account for approximately 60% of human MMAF cases. Here we conducted whole-exome sequencing and identified bi-allelic truncating mutations of the TTC29 (tetratricopeptide repeat domain 29) gene in three (3.8%) unrelated cases from a cohort of 80 MMAF-affected Han Chinese men. TTC29 is preferentially expressed in the testis, and TTC29 protein contains the tetratricopeptide repeat domains that play an important role in cilia- and flagella-associated functions. All of the men harboring TTC29 mutations presented a typical MMAF phenotype and dramatic disorganization in axonemal and/or other peri-axonemal structures. Immunofluorescence assays of spermatozoa from men harboring TTC29 mutations showed deficiency of TTC29 and remarkably reduced staining of intraflagellar-transport-complex-B-associated proteins (TTC30A and IFT52). We also generated a Ttc29-mutated mouse model through the use of CRISPR-Cas9 technology. Remarkably, Ttc29-mutated male mice also presented reduced sperm motility, abnormal flagellar ultrastructure, and male subfertility. Furthermore, intracytoplasmic sperm injections performed for Ttc29-mutated mice and men harboring TTC29 mutations consistently acquired satisfactory outcomes. Collectively, our experimental observations in humans and mice suggest that bi-allelic mutations in TTC29, as an important genetic pathogeny, can induce MMAF-related asthenoteratospermia. Our study also provided effective guidance for clinical diagnosis and assisted reproduction treatments.
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Duclos GE, Teixeira VH, Autissier P, Gesthalter YB, Reinders-Luinge MA, Terrano R, Dumas YM, Liu G, Mazzilli SA, Brandsma CA, van den Berge M, Janes SM, Timens W, Lenburg ME, Spira A, Campbell JD, Beane J. Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution. SCIENCE ADVANCES 2019; 5:eaaw3413. [PMID: 31844660 PMCID: PMC6905872 DOI: 10.1126/sciadv.aaw3413] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
The human bronchial epithelium is composed of multiple distinct cell types that cooperate to defend against environmental insults. While studies have shown that smoking alters bronchial epithelial function and morphology, its precise effects on specific cell types and overall tissue composition are unclear. We used single-cell RNA sequencing to profile bronchial epithelial cells from six never and six current smokers. Unsupervised analyses led to the characterization of a set of toxin metabolism genes that localized to smoker ciliated cells, tissue remodeling associated with a loss of club cells and extensive goblet cell hyperplasia, and a previously unidentified peri-goblet epithelial subpopulation in smokers who expressed a marker of bronchial premalignant lesions. Our data demonstrate that smoke exposure drives a complex landscape of cellular alterations that may prime the human bronchial epithelium for disease.
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Affiliation(s)
- Grant E. Duclos
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Vitor H. Teixeira
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Patrick Autissier
- Boston University Flow Cytometry Core Facility, Boston University School of Medicine, Boston, MA, USA
| | - Yaron B. Gesthalter
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Marjan A. Reinders-Luinge
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
| | - Robert Terrano
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Yves M. Dumas
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Gang Liu
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Sarah A. Mazzilli
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, Netherlands
| | - Sam M. Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
- Department of Thoracic Medicine, University College London Hospital, London, UK
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
| | - Marc E. Lenburg
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Avrum Spira
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Johnson & Johnson Innovation, Cambridge, MA, USA
| | - Joshua D. Campbell
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jennifer Beane
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
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