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Kim SE, Kim HY, Wlodarczyk BJ, Finnell RH. The novel linkage between Fuz and Gpr161 genes regulates sonic hedgehog signaling during mouse embryonic development. bioRxiv 2024:2024.01.11.575263. [PMID: 38260275 PMCID: PMC10802560 DOI: 10.1101/2024.01.11.575263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Sonic hedgehog (Shh) signaling regulates embryonic morphogenesis utilizing primary cilia, the cell antenna acting as a signaling hub. Fuz, an effector of planar cell polarity (PCP) signaling, involves Shh signaling via cilia formation, while the G protein-coupled receptor 161 (Gpr161) is a negative regulator of Shh signaling. The range of phenotypic malformations observed in mice bearing mutations in either of these two genes is similar; however, their functional relations have not been previously explored. This study identified the genetic and biochemical link between Fuz and Gpr161 in mouse embryonic development. Fuz was genetically epistatic to Gpr161 via Shh signaling during mouse embryonic development. The FUZ biochemically interacted with GPR161, and Fuz regulated Gpr161 ciliary trafficking via β-arrestin2. Our study suggested the novel Gpr161-Fuz axis that regulates Shh signaling during mouse embryonic development.
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Affiliation(s)
- Sung-Eun Kim
- Department of Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin/Dell Medical School, Austin, TX, 78723, USA
| | | | - Bogdan J. Wlodarczyk
- Departments of Molecular and Cellular Biology, Molecular and Human Genetics, and Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard H. Finnell
- Department of Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin/Dell Medical School, Austin, TX, 78723, USA
- Departments of Molecular and Cellular Biology, Molecular and Human Genetics, and Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
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Kim J, Rothová MM, Madan E, Rhee S, Weng G, Palma AM, Liao L, David E, Amit I, Hajkarim MC, Vudatha V, Gutiérrez-García A, Moreno E, Winn R, Trevino J, Fisher PB, Brickman JM, Gogna R, Won KJ. Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development. Proc Natl Acad Sci U S A 2023; 120:e2205371120. [PMID: 36595695 PMCID: PMC9926237 DOI: 10.1073/pnas.2205371120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/16/2022] [Indexed: 01/05/2023] Open
Abstract
Development of multicellular organisms is orchestrated by persistent cell-cell communication between neighboring partners. Direct interaction between different cell types can induce molecular signals that dictate lineage specification and cell fate decisions. Current single-cell RNA-seq technology cannot adequately analyze cell-cell contact-dependent gene expression, mainly due to the loss of spatial information. To overcome this obstacle and resolve cell-cell contact-specific gene expression during embryogenesis, we performed RNA sequencing of physically interacting cells (PIC-seq) and assessed them alongside similar single-cell transcriptomes derived from developing mouse embryos between embryonic day (E) 7.5 and E9.5. Analysis of the PIC-seq data identified gene expression signatures that were dependent on the presence of specific neighboring cell types. Our computational predictions, validated experimentally, demonstrated that neural progenitor (NP) cells upregulate Lhx5 and Nkx2-1 genes, when exclusively interacting with definitive endoderm (DE) cells. Moreover, there was a reciprocal impact on the transcriptome of DE cells, as they tend to upregulate Rax and Gsc when in contact with NP cells. Using individual cell transcriptome data, we formulated a means of computationally predicting the impact of one cell type on the transcriptome of its neighboring cell types. We have further developed a distinctive spatial-t-distributed stochastic neighboring embedding to display the pseudospatial distribution of cells in a 2-dimensional space. In summary, we describe an innovative approach to study contact-specific gene regulation during embryogenesis.
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Affiliation(s)
- Junil Kim
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N2200, Denmark
- School of Systems Biomedical Science, Soongsil University, Dongjak-Gu, Seoul06978, Republic of Korea
| | - Michaela Mrugala Rothová
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen2200, Denmark
| | - Esha Madan
- Champalimaud Centre for the Unknown, Lisbon1400-038, Portugal
| | - Siyeon Rhee
- Department of Biology, Stanford University, Stanford, CA94305
| | - Guangzheng Weng
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N2200, Denmark
| | | | - Linbu Liao
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N2200, Denmark
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot7610001, Israel
| | | | - Vignesh Vudatha
- Department of Surgery, Virginia Commonwealth University, Richmond, VA23298-0033
| | | | - Eduardo Moreno
- Champalimaud Centre for the Unknown, Lisbon1400-038, Portugal
| | - Robert Winn
- School of Medicine, Virginia Commonwealth University Massey Cancer Center, Virginia Commonwealth University, Richmond, VA23298-0033
| | - Jose Trevino
- Department of Surgery, Virginia Commonwealth University, Richmond, VA23298-0033
| | - Paul B. Fisher
- School of Medicine, Virginia Commonwealth University Massey Cancer Center, Virginia Commonwealth University, Richmond, VA23298-0033
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA23298-0033
- School of Medicine, VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, VA23298-0033
| | - Joshua M. Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen2200, Denmark
| | - Rajan Gogna
- School of Medicine, Virginia Commonwealth University Massey Cancer Center, Virginia Commonwealth University, Richmond, VA23298-0033
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA23298-0033
- School of Medicine, VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, VA23298-0033
| | - Kyoung Jae Won
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N2200, Denmark
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA90069
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Ichikawa T, Zhang HT, Panavaite L, Erzberger A, Fabrèges D, Snajder R, Wolny A, Korotkevich E, Tsuchida-Straeten N, Hufnagel L, Kreshuk A, Hiiragi T. An ex vivo system to study cellular dynamics underlying mouse peri-implantation development. Dev Cell 2022; 57:373-386.e9. [PMID: 35063082 PMCID: PMC8826647 DOI: 10.1016/j.devcel.2021.12.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 08/23/2021] [Accepted: 12/23/2021] [Indexed: 01/09/2023]
Abstract
Upon implantation, mammalian embryos undergo major morphogenesis and key developmental processes such as body axis specification and gastrulation. However, limited accessibility obscures the study of these crucial processes. Here, we develop an ex vivo Matrigel-collagen-based culture to recapitulate mouse development from E4.5 to E6.0. Our system not only recapitulates embryonic growth, axis initiation, and overall 3D architecture in 49% of the cases, but its compatibility with light-sheet microscopy also enables the study of cellular dynamics through automatic cell segmentation. We find that, upon implantation, release of the increasing tension in the polar trophectoderm is necessary for its constriction and invagination. The resulting extra-embryonic ectoderm plays a key role in growth, morphogenesis, and patterning of the neighboring epiblast, which subsequently gives rise to all embryonic tissues. This 3D ex vivo system thus offers unprecedented access to peri-implantation development for in toto monitoring, measurement, and spatiotemporally controlled perturbation, revealing a mechano-chemical interplay between extra-embryonic and embryonic tissues.
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Affiliation(s)
- Takafumi Ichikawa
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Hui Ting Zhang
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Collaboration for PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Laura Panavaite
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Collaboration for PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Anna Erzberger
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
| | - Dimitri Fabrèges
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Rene Snajder
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Adrian Wolny
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | | | | | - Lars Hufnagel
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Anna Kreshuk
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Takashi Hiiragi
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, 606-8501 Kyoto, Japan.
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Mark M, Teletin M, Wendling O, Vonesch JL, Féret B, Hérault Y, Ghyselinck NB. Pathogenesis of Anorectal Malformations in Retinoic Acid Receptor Knockout Mice Studied by HREM. Biomedicines 2021; 9:742. [PMID: 34203310 PMCID: PMC8301324 DOI: 10.3390/biomedicines9070742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022] Open
Abstract
Anorectal malformations (ARMs) are relatively common congenital abnormalities, but their pathogenesis is poorly understood. Previous gene knockout studies indicated that the signalling pathway mediated by the retinoic acid receptors (RAR) is instrumental to the formation of the anorectal canal and of various urogenital structures. Here, we show that simultaneous ablation of the three RARs in the mouse embryo results in a spectrum of malformations of the pelvic organs in which anorectal and urinary bladder ageneses are consistently associated. We found that these ageneses could be accounted for by defects in the processes of growth and migration of the cloaca, the embryonic structure from which the anorectal canal and urinary bladder originate. We further show that these defects are preceded by a failure of the lateral shift of the umbilical arteries and propose vascular abnormalities as a possible cause of ARM. Through the comparisons of these phenotypes with those of other mutant mice and of human patients, we would like to suggest that morphological data may provide a solid base to test molecular as well as clinical hypotheses.
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Affiliation(s)
- Manuel Mark
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
- Service de Biologie de la Reproduction, Hôpitaux Universitaires de Strasbourg (HUS), 67300 Schiltigheim, France
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Marius Teletin
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
- Service de Biologie de la Reproduction, Hôpitaux Universitaires de Strasbourg (HUS), 67300 Schiltigheim, France
| | - Olivia Wendling
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Jean-Luc Vonesch
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
| | - Betty Féret
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
| | - Yann Hérault
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Norbert B. Ghyselinck
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
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Domenech C, Maillard L, Rousseau A, Guidez F, Petit L, Pla M, Clay D, Guimiot F, Sanfilippo S, Jacques S, de la Grange P, Robil N, Soulier J, Souyri M. Studies in an Early Development Window Unveils a Severe HSC Defect in both Murine and Human Fanconi Anemia. Stem Cell Reports 2018; 11:1075-1091. [PMID: 30449320 PMCID: PMC6234961 DOI: 10.1016/j.stemcr.2018.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 01/05/2023] Open
Abstract
Fanconi anemia (FA) causes bone marrow failure early during childhood, and recent studies indicate that a hematopoietic defect could begin in utero. We performed a unique kinetics study of hematopoiesis in Fancg-/- mouse embryos, between the early embryonic day 11.5 (E11.5) to E12.5 developmental window (when the highest level of hematopoietic stem cells [HSC] amplification takes place) and E14.5. This study reveals a deep HSC defect with exhaustion of proliferative and self-renewal capacities very early during development, together with severe FA clinical and biological manifestations, which are mitigated at E14.5 due to compensatory mechanisms that help to ensure survival of Fancg-/- embryos. It also reports that a deep HSC defect is also observed during human FA development, and that human FA fetal liver (FL) HSCs present a transcriptome profile similar to that of mouse E12.5 Fancg-/- FL HSCs. Altogether, our results highlight that early mouse FL could represent a good alternative model for studying Fanconi pathology.
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Affiliation(s)
- Carine Domenech
- CNRS UMR7622/IBPS, Paris, France; Université Pierre et Marie Curie, Sorbonne Universités, Paris, France; INSERM UMR_S1131, Hôpital Saint Louis, Paris, France; IUH, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Loïc Maillard
- CNRS UMR7622/IBPS, Paris, France; Université Pierre et Marie Curie, Sorbonne Universités, Paris, France; INSERM UMR_S1131, Hôpital Saint Louis, Paris, France; IUH, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Alix Rousseau
- IUH, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; INSERM U944/CNRS UMR7212, Hôpital Saint Louis, Paris, France
| | - Fabien Guidez
- INSERM UMR_S1131, Hôpital Saint Louis, Paris, France; IUH, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Laurence Petit
- CNRS UMR7622/IBPS, Paris, France; Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | - Marika Pla
- INSERM UMR_S1131, Hôpital Saint Louis, Paris, France; IUH, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Denis Clay
- INSERM U972, Hôpital Paul Brousse, Villejuif, France; Plateforme de cytométrie, UMS33, Université Paris Sud, Villejuif, France
| | - Fabien Guimiot
- Service de Foetopathologie, Hôpital Robert Debré, Paris, France
| | - Sandra Sanfilippo
- CNRS UMR7622/IBPS, Paris, France; Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | | | | | | | - Jean Soulier
- IUH, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; INSERM U944/CNRS UMR7212, Hôpital Saint Louis, Paris, France
| | - Michèle Souyri
- CNRS UMR7622/IBPS, Paris, France; Université Pierre et Marie Curie, Sorbonne Universités, Paris, France; INSERM UMR_S1131, Hôpital Saint Louis, Paris, France; IUH, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
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Abstract
Histone H3.3 is a highly conserved histone H3 replacement variant in metazoans and has been implicated in many important biological processes, including cell differentiation and reprogramming. Germline and somatic mutations in H3.3 genomic incorporation pathway components or in H3.3 encoding genes have been associated with human congenital diseases and cancers, respectively. However, the role of H3.3 in mammalian development remains unclear. To address this question, we generated H3.3-null mouse models through classical genetic approaches. We found that H3.3 plays an essential role in mouse development. Complete depletion of H3.3 leads to developmental retardation and early embryonic lethality. At the cellular level, H3.3 loss triggers cell cycle suppression and cell death. Surprisingly, H3.3 depletion does not dramatically disrupt gene regulation in the developing embryo. Instead, H3.3 depletion causes dysfunction of heterochromatin structures at telomeres, centromeres, and pericentromeric regions of chromosomes, leading to mitotic defects. The resulting karyotypical abnormalities and DNA damage lead to p53 pathway activation. In summary, our results reveal that an important function of H3.3 is to support chromosomal heterochromatic structures, thus maintaining genome integrity during mammalian development.
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Affiliation(s)
- Chuan-Wei Jang
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Yoichiro Shibata
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Joshua Starmer
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Della Yee
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Terry Magnuson
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
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