1
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Renz PF, Ghoshdastider U, Baghai Sain S, Valdivia-Francia F, Khandekar A, Ormiston M, Bernasconi M, Duré C, Kretz JA, Lee M, Hyams K, Forny M, Pohly M, Ficht X, Ellis SJ, Moor AE, Sendoel A. In vivo single-cell CRISPR uncovers distinct TNF programmes in tumour evolution. Nature 2024:10.1038/s41586-024-07663-y. [PMID: 39020166 DOI: 10.1038/s41586-024-07663-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/04/2024] [Indexed: 07/19/2024]
Abstract
The tumour evolution model posits that malignant transformation is preceded by randomly distributed driver mutations in cancer genes, which cause clonal expansions in phenotypically normal tissues. Although clonal expansions can remodel entire tissues1-3, the mechanisms that result in only a small number of clones transforming into malignant tumours remain unknown. Here we develop an in vivo single-cell CRISPR strategy to systematically investigate tissue-wide clonal dynamics of the 150 most frequently mutated squamous cell carcinoma genes. We couple ultrasound-guided in utero lentiviral microinjections, single-cell RNA sequencing and guide capture to longitudinally monitor clonal expansions and document their underlying gene programmes at single-cell transcriptomic resolution. We uncover a tumour necrosis factor (TNF) signalling module, which is dependent on TNF receptor 1 and involving macrophages, that acts as a generalizable driver of clonal expansions in epithelial tissues. Conversely, during tumorigenesis, the TNF signalling module is downregulated. Instead, we identify a subpopulation of invasive cancer cells that switch to an autocrine TNF gene programme associated with epithelial-mesenchymal transition. Finally, we provide in vivo evidence that the autocrine TNF gene programme is sufficient to mediate invasive properties and show that the TNF signature correlates with shorter overall survival of patients with squamous cell carcinoma. Collectively, our study demonstrates the power of applying in vivo single-cell CRISPR screening to mammalian tissues, unveils distinct TNF programmes in tumour evolution and highlights the importance of understanding the relationship between clonal expansions in epithelia and tumorigenesis.
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Affiliation(s)
- Peter F Renz
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Umesh Ghoshdastider
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Simona Baghai Sain
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Fabiola Valdivia-Francia
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Ameya Khandekar
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Mark Ormiston
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Martino Bernasconi
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Clara Duré
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jonas A Kretz
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Minkyoung Lee
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Katie Hyams
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Merima Forny
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Marcel Pohly
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Xenia Ficht
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Stephanie J Ellis
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Ataman Sendoel
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland.
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2
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Luan J, Truong C, Vuchkovska A, Guo W, Good J, Liu B, Gang A, Infarinato N, Stewart K, Polak L, Pasolli HA, Andretta E, Rudensky AY, Fuchs E, Miao Y. CD80 on skin stem cells promotes local expansion of regulatory T cells upon injury to orchestrate repair within an inflammatory environment. Immunity 2024; 57:1071-1086.e7. [PMID: 38677291 PMCID: PMC11265648 DOI: 10.1016/j.immuni.2024.04.003] [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: 12/12/2022] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 04/29/2024]
Abstract
Following tissue damage, epithelial stem cells (SCs) are mobilized to enter the wound, where they confront harsh inflammatory environments that can impede their ability to repair the injury. Here, we investigated the mechanisms that protect skin SCs within this inflammatory environment. Characterization of gene expression profiles of hair follicle SCs (HFSCs) that migrated into the wound site revealed activation of an immune-modulatory program, including expression of CD80, major histocompatibility complex class II (MHCII), and CXC motif chemokine ligand 5 (CXCL5). Deletion of CD80 in HFSCs impaired re-epithelialization, reduced accumulation of peripherally generated Treg (pTreg) cells, and increased infiltration of neutrophils in wounded skin. Importantly, similar wound healing defects were also observed in mice lacking pTreg cells. Our findings suggest that upon skin injury, HFSCs establish a temporary protective network by promoting local expansion of Treg cells, thereby enabling re-epithelialization while still kindling inflammation outside this niche until the barrier is restored.
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Affiliation(s)
- Jingyun Luan
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60615, USA
| | - Cynthia Truong
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Aleksandra Vuchkovska
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60615, USA
| | - Weijie Guo
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60615, USA
| | - Jennifer Good
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60615, USA
| | - Bijun Liu
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60615, USA
| | - Audrey Gang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60615, USA
| | - Nicole Infarinato
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Katherine Stewart
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Lisa Polak
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Hilda Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Emma Andretta
- Howard Hughes Medical Institute, Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute, Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Yuxuan Miao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60615, USA.
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3
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Moreno JA, Dudchenko O, Feigin CY, Mereby SA, Chen Z, Ramos R, Almet AA, Sen H, Brack BJ, Johnson MR, Li S, Wang W, Gaska JM, Ploss A, Weisz D, Omer AD, Yao W, Colaric Z, Kaur P, Leger JS, Nie Q, Mena A, Flanagan JP, Keller G, Sanger T, Ostrow B, Plikus MV, Kvon EZ, Aiden EL, Mallarino R. Emx2 underlies the development and evolution of marsupial gliding membranes. Nature 2024; 629:127-135. [PMID: 38658750 PMCID: PMC11062917 DOI: 10.1038/s41586-024-07305-3] [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: 03/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
Phenotypic variation among species is a product of evolutionary changes to developmental programs1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium-an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2 is a critical upstream regulator of patagium development. Moreover, we identify different cis-regulatory elements that may be responsible for driving increased Emx2 expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2 expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty.
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Affiliation(s)
- Jorge A Moreno
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Charles Y Feigin
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Environment and Genetics, La Trobe University, Bundoora, Victoria, Australia
| | - Sarah A Mereby
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Zhuoxin Chen
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Raul Ramos
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Harsha Sen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Benjamin J Brack
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew R Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sha Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wei Wang
- Lewis Sigler Center for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Jenna M Gaska
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weijie Yao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Parwinder Kaur
- The University of Western Australia, Crawley, Western Australia, Australia
| | - Judy St Leger
- Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Qing Nie
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | | | | | - Greta Keller
- Department of Biology, Loyola University, Chicago, IL, USA
| | - Thomas Sanger
- Department of Biology, Loyola University, Chicago, IL, USA
| | - Bruce Ostrow
- Department of Biology, Grand Valley State University, Allendale, MI, USA
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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4
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Grit JL, McGee LE, Tovar EA, Essenburg CJ, Wolfrum E, Beddows I, Williams K, Sheridan RTC, Schipper JL, Adams M, Arumugam M, Vander Woude T, Gurunathan S, Field JM, Wulfkuhle J, Petricoin EF, Graveel CR, Steensma MR. p53 modulates kinase inhibitor resistance and lineage plasticity in NF1-related MPNSTs. Oncogene 2024; 43:1411-1430. [PMID: 38480916 PMCID: PMC11068581 DOI: 10.1038/s41388-024-03000-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 05/05/2024]
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are chemotherapy resistant sarcomas that are a leading cause of death in neurofibromatosis type 1 (NF1). Although NF1-related MPNSTs derive from neural crest cell origin, they also exhibit intratumoral heterogeneity. TP53 mutations are associated with significantly decreased survival in MPNSTs, however the mechanisms underlying TP53-mediated therapy responses are unclear in the context of NF1-deficiency. We evaluated the role of two commonly altered genes, MET and TP53, in kinome reprograming and cellular differentiation in preclinical MPNST mouse models. We previously showed that MET amplification occurs early in human MPNST progression and that Trp53 loss abrogated MET-addiction resulting in MET inhibitor resistance. Here we demonstrate a novel mechanism of therapy resistance whereby p53 alters MET stability, localization, and downstream signaling leading to kinome reprogramming and lineage plasticity. Trp53 loss also resulted in a shift from RAS/ERK to AKT signaling and enhanced sensitivity to MEK and mTOR inhibition. In response to MET, MEK and mTOR inhibition, we observed broad and heterogeneous activation of key differentiation genes in Trp53-deficient lines suggesting Trp53 loss also impacts lineage plasticity in MPNSTs. These results demonstrate the mechanisms by which p53 loss alters MET dependency and therapy resistance in MPNSTS through kinome reprogramming and phenotypic flexibility.
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Affiliation(s)
- Jamie L Grit
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Lauren E McGee
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Elizabeth A Tovar
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Curt J Essenburg
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Emily Wolfrum
- Bioinformatics & Biostatistics Core, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Ian Beddows
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Kaitlin Williams
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | | | - Joshua L Schipper
- Flow Cytometry Core, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Marie Adams
- Genomics Core, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Menusha Arumugam
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Thomas Vander Woude
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Sharavana Gurunathan
- Department of Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Jeffrey M Field
- Department of Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Julia Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 20110, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 20110, USA
| | - Carrie R Graveel
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Matthew R Steensma
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.
- Helen DeVos Children's Hospital, Corewell Health System, Grand Rapids, MI, 49503, USA.
- Michigan State University College of Human Medicine, Grand Rapids, MI, 49503, USA.
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5
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Goupil E, Lacroix L, Brière J, Guga S, Saba-El-Leil MK, Meloche S, Labbé JC. OSGN-1 is a conserved flavin-containing monooxygenase required to stabilize the intercellular bridge in late cytokinesis. Proc Natl Acad Sci U S A 2024; 121:e2308570121. [PMID: 38442170 PMCID: PMC10945809 DOI: 10.1073/pnas.2308570121] [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: 05/22/2023] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
Cytokinesis is the last step of cell division and is regulated by the small GTPase RhoA. RhoA activity is required for all steps of cytokinesis, including prior to abscission when daughter cells are ultimately physically separated. Like germ cells in all animals, the Caenorhabditis elegans embryonic germline founder cell initiates cytokinesis but does not complete abscission, leaving a stable intercellular bridge between the two daughter cells. Here, we identify and characterize C. elegans OSGN-1 as a cytokinetic regulator that promotes RhoA activity during late cytokinesis. Sequence analyses and biochemical reconstitutions reveal that OSGN-1 is a flavin-containing monooxygenase (MO). Genetic analyses indicate that the MO activity of OSGN-1 is required to maintain active RhoA at the end of cytokinesis in the germline founder cell and to stabilize the intercellular bridge. Deletion of OSGIN1 in human cells results in an increase in binucleation as a result of cytokinetic furrow regression, and this phenotype can be rescued by expressing a catalytically active form of C. elegans OSGN-1, indicating that OSGN-1 and OSGIN1 are functional orthologs. We propose that OSGN-1 and OSGIN1 are conserved MO enzymes required to maintain RhoA activity at the intercellular bridge during late cytokinesis and thus favor its stability, enabling proper abscission in human cells and bridge stabilization in C. elegans germ cells.
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Affiliation(s)
- Eugénie Goupil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Léa Lacroix
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Jonathan Brière
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Sandra Guga
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Marc K. Saba-El-Leil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Sylvain Meloche
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
- Department of Pharmacology and Physiology, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Jean-Claude Labbé
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
- Department of Pathology and Cell Biology, Université de Montréal, Montréal, QCH3C 3J7, Canada
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6
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Tierney MT, Polak L, Yang Y, Abdusselamoglu MD, Baek I, Stewart KS, Fuchs E. Vitamin A resolves lineage plasticity to orchestrate stem cell lineage choices. Science 2024; 383:eadi7342. [PMID: 38452090 PMCID: PMC11177320 DOI: 10.1126/science.adi7342] [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: 05/15/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024]
Abstract
Lineage plasticity-a state of dual fate expression-is required to release stem cells from their niche constraints and redirect them to tissue compartments where they are most needed. In this work, we found that without resolving lineage plasticity, skin stem cells cannot effectively generate each lineage in vitro nor regrow hair and repair wounded epidermis in vivo. A small-molecule screen unearthed retinoic acid as a critical regulator. Combining high-throughput approaches, cell culture, and in vivo mouse genetics, we dissected its roles in tissue regeneration. We found that retinoic acid is made locally in hair follicle stem cell niches, where its levels determine identity and usage. Our findings have therapeutic implications for hair growth as well as chronic wounds and cancers, where lineage plasticity is unresolved.
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Affiliation(s)
- Matthew T Tierney
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University; New York, NY 10065, USA
| | - Lisa Polak
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University; New York, NY 10065, USA
| | | | - Merve Deniz Abdusselamoglu
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University; New York, NY 10065, USA
| | | | - Katherine S Stewart
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University; New York, NY 10065, USA
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University; New York, NY 10065, USA
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7
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Javary J, Goupil E, Soulez M, Kanshin E, Bouchard A, Seternes OM, Thibault P, Labbé JC, Meloche S. Phosphoproteomic analysis identifies supervillin as an ERK3 substrate regulating cytokinesis and cell ploidy. J Cell Physiol 2024; 239:e30938. [PMID: 36576983 DOI: 10.1002/jcp.30938] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/29/2022]
Abstract
Extracellular signal-regulated kinase 3 (ERK3) is a poorly characterized member of the mitogen-activated protein (MAP) kinase family. Functional analysis of the ERK3 signaling pathway has been hampered by a lack of knowledge about the substrates and downstream effectors of the kinase. Here, we used large-scale quantitative phosphoproteomics and targeted gene silencing to identify direct ERK3 substrates and gain insight into its cellular functions. Detailed validation of one candidate substrate identified the gelsolin/villin family member supervillin (SVIL) as a bona fide ERK3 substrate. We show that ERK3 phosphorylates SVIL on Ser245 to regulate myosin II activation and cytokinesis completion in dividing cells. Depletion of SVIL or ERK3 leads to increased cytokinesis failure and multinucleation, a phenotype rescued by wild type SVIL but not by the non-phosphorylatable S245A mutant. Our results unveil a new function of the atypical MAP kinase ERK3 in cell division and the regulation of cell ploidy.
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Affiliation(s)
- Joaquim Javary
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
| | - Eugénie Goupil
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
| | - Mathilde Soulez
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
| | - Evgeny Kanshin
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
- NYU Langone Health, New York City, New York, USA
| | - Antoine Bouchard
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
- Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada
| | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
- Department of Chemistry, Faculty of Arts and Sciences, Université de Montréal, Montreal, Quebec, Canada
| | - Jean-Claude Labbé
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Sylvain Meloche
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
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8
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Johnson MR, Li S, Guerrero-Juarez CF, Miller P, Brack BJ, Mereby SA, Moreno JA, Feigin CY, Gaska J, Rivera-Perez JA, Nie Q, Ploss A, Shvartsman SY, Mallarino R. A multifunctional Wnt regulator underlies the evolution of rodent stripe patterns. Nat Ecol Evol 2023; 7:2143-2159. [PMID: 37813945 PMCID: PMC10839778 DOI: 10.1038/s41559-023-02213-7] [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: 03/29/2023] [Accepted: 08/27/2023] [Indexed: 10/11/2023]
Abstract
Animal pigment patterns are excellent models to elucidate mechanisms of biological organization. Although theoretical simulations, such as Turing reaction-diffusion systems, recapitulate many animal patterns, they are insufficient to account for those showing a high degree of spatial organization and reproducibility. Here, we study the coat of the African striped mouse (Rhabdomys pumilio) to uncover how periodic stripes form. Combining transcriptomics, mathematical modelling and mouse transgenics, we show that the Wnt modulator Sfrp2 regulates the distribution of hair follicles and establishes an embryonic prepattern that foreshadows pigment stripes. Moreover, by developing in vivo gene editing in striped mice, we find that Sfrp2 knockout is sufficient to alter the stripe pattern. Strikingly, mutants exhibited changes in pigmentation, revealing that Sfrp2 also regulates hair colour. Lastly, through evolutionary analyses, we find that striped mice have evolved lineage-specific changes in regulatory elements surrounding Sfrp2, many of which may be implicated in modulating the expression of this gene. Altogether, our results show that a single factor controls coat pattern formation by acting both as an orienting signalling mechanism and a modulator of pigmentation. More broadly, our work provides insights into how spatial patterns are established in developing embryos and the mechanisms by which phenotypic novelty originates.
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Affiliation(s)
- Matthew R Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sha Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Christian F Guerrero-Juarez
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Department of Mathematics, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA, USA
| | - Pearson Miller
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Benjamin J Brack
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sarah A Mereby
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Jorge A Moreno
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Charles Y Feigin
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Jenna Gaska
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Qing Nie
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Department of Mathematics, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Stanislav Y Shvartsman
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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9
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Vikhe Patil K, Meijer M, Mak KHM, Yang W, Falcão AM, Castelo-Branco G, Genander M. Co-expression of PADI isoforms during progenitor differentiation enables functional diversity. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220451. [PMID: 37778375 PMCID: PMC10542451 DOI: 10.1098/rstb.2022.0451] [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: 02/28/2023] [Accepted: 05/02/2023] [Indexed: 10/03/2023] Open
Abstract
Protein isoforms, generated through alternative splicing or promoter usage, contribute to tissue function. Here, we characterize the expression of predicted Padi3α and Padi3β isoforms in hair follicles and describe expression of Padi2β, a hitherto unknown PADI2 isoform, in the oligodendrocyte lineage. Padi2β transcription is initiated from a downstream intronic promoter, generating an N-terminally truncated, unstable, PADI2β. By contrast to the established role of the canonical PADI2 (PADI2α) (Falcao et al. 2019 Cell Rep. 27, 1090-1102.e10. (doi:10.1016/j.celrep.2019.03.108)), PADI2β inhibits oligodendrocyte differentiation, suggesting that PADI2 isoforms exert opposing effects on oligodendrocyte lineage progression. We localize Padi3α and Padi3β to developing hair follicles and find that both transcripts are expressed at low levels in progenitor cells, only to increase in expression concomitant with differentiation. When expressed in vitro, PADI3α and PADI3β are enriched in the cytoplasm and precipitate together. Whereas PADI3β protein stability is low and PADI3β fails to induce protein citrullination, we find that the enzymatic activity and protein stability of PADI3α is reduced in the presence of PADI3β. We propose that PADI3β modulates PADI3α activity by direct binding and heterodimer formation. Here, we establish expression and function of Padi2 and Padi3 isoforms, expanding on the mechanisms in place to regulate citrullination in complex tissues. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- Kim Vikhe Patil
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Mandy Meijer
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kylie Hin-Man Mak
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Wei Yang
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ana Mendanha Falcão
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's Associate Laboratory, PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Center for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden
| | - Maria Genander
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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10
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Palmiero M, Cantarosso I, di Blasio L, Monica V, Peracino B, Primo L, Puliafito A. Collective directional migration drives the formation of heteroclonal cancer cell clusters. Mol Oncol 2023; 17:1699-1725. [PMID: 36587372 PMCID: PMC10483614 DOI: 10.1002/1878-0261.13369] [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: 08/09/2022] [Revised: 11/11/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023] Open
Abstract
Metastasisation occurs through the acquisition of invasive and survival capabilities that allow tumour cells to colonise distant sites. While the role of multicellular aggregates in cancer dissemination is acknowledged, the mechanisms that drive the formation of multiclonal cell aggregates are not fully elucidated. Here, we show that cancer cells of different tissue of origins can perform collective directional migration and can actively form heteroclonal aggregates in 3D, through a proliferation-independent mechanism. Coalescence of distant cell clusters is mediated by subcellular actin-rich protrusions and multicellular outgrowths that extend towards neighbouring aggregates. Coherently, perturbation of cytoskeletal dynamics impairs collective migration while myosin II activation is necessary for multicellular movements. We put forward the hypothesis that cluster attraction is mediated by secreted soluble factors. Such a hypothesis is consistent with the abrogation of aggregation by inhibition of PI3K/AKT/mTOR and MEK/ERK, the chemoattracting activity of conditioned culture media and with a wide screening of secreted proteins. Our results present a novel collective migration model and shed light on the mechanisms of formation of heteroclonal aggregates in cancer.
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Affiliation(s)
- Miriam Palmiero
- Candiolo Cancer Institute, FPO – IRCCSCandioloItaly
- Department of OncologyUniversity of TurinCandioloItaly
| | - Isabel Cantarosso
- Candiolo Cancer Institute, FPO – IRCCSCandioloItaly
- Department of OncologyUniversity of TurinCandioloItaly
| | - Laura di Blasio
- Candiolo Cancer Institute, FPO – IRCCSCandioloItaly
- Department of OncologyUniversity of TurinCandioloItaly
| | - Valentina Monica
- Candiolo Cancer Institute, FPO – IRCCSCandioloItaly
- Department of OncologyUniversity of TurinCandioloItaly
| | - Barbara Peracino
- Department of Clinical and Biological SciencesSan Luigi Hospital, University of TurinOrbassanoItaly
| | - Luca Primo
- Candiolo Cancer Institute, FPO – IRCCSCandioloItaly
- Department of OncologyUniversity of TurinCandioloItaly
| | - Alberto Puliafito
- Candiolo Cancer Institute, FPO – IRCCSCandioloItaly
- Department of OncologyUniversity of TurinCandioloItaly
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11
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Monteiro P, Yeon B, Wallis SS, Godinho SA. Centrosome amplification fine tunes tubulin acetylation to differentially control intracellular organization. EMBO J 2023; 42:e112812. [PMID: 37403793 PMCID: PMC10425843 DOI: 10.15252/embj.2022112812] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/05/2023] [Accepted: 06/14/2023] [Indexed: 07/06/2023] Open
Abstract
Intracellular organelle organization is conserved in eukaryotic cells and is primarily achieved through active transport by motor proteins along the microtubule cytoskeleton. Microtubule post-translational modifications (PTMs) can contribute to microtubule diversity and differentially regulate motor-mediated transport. Here, we show that centrosome amplification, commonly observed in cancer and shown to promote aneuploidy and invasion, induces a global change in organelle positioning towards the cell periphery and facilitates nuclear migration through confined spaces. This reorganization requires kinesin-1 and is analogous to the loss of dynein. Cells with amplified centrosomes display increased levels of acetylated tubulin, a PTM that could enhance kinesin-1-mediated transport. Depletion of α-tubulin acetyltransferase 1 (αTAT1) to block tubulin acetylation rescues the displacement of centrosomes, mitochondria, and vimentin but not Golgi or endosomes. Analyses of the distribution of total and acetylated microtubules indicate that the polarized distribution of modified microtubules, rather than levels alone, plays an important role in the positioning of specific organelles, such as the centrosome. We propose that increased tubulin acetylation differentially impacts kinesin-1-mediated organelle displacement to regulate intracellular organization.
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Affiliation(s)
- Pedro Monteiro
- Centre for Cancer Cell and Molecular Biology, Barts Cancer InstituteQueen Mary University of LondonLondonUK
- Institut Curie, Paris Sciences and Lettres Research UniversityCentre National de la Recherche Scientifique, UMR144ParisFrance
| | - Bongwhan Yeon
- Centre for Cancer Cell and Molecular Biology, Barts Cancer InstituteQueen Mary University of LondonLondonUK
| | - Samuel S Wallis
- Centre for Cancer Cell and Molecular Biology, Barts Cancer InstituteQueen Mary University of LondonLondonUK
| | - Susana A Godinho
- Centre for Cancer Cell and Molecular Biology, Barts Cancer InstituteQueen Mary University of LondonLondonUK
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12
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Yang Y, Gomez N, Infarinato N, Adam RC, Sribour M, Baek I, Laurin M, Fuchs E. The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates. Nat Cell Biol 2023; 25:1185-1195. [PMID: 37488435 PMCID: PMC10415178 DOI: 10.1038/s41556-023-01184-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/08/2023] [Indexed: 07/26/2023]
Abstract
During development, progenitors simultaneously activate one lineage while silencing another, a feature highly regulated in adult stem cells but derailed in cancers. Equipped to bind cognate motifs in closed chromatin, pioneer factors operate at these crossroads, but how they perform fate switching remains elusive. Here we tackle this question with SOX9, a master regulator that diverts embryonic epidermal stem cells (EpdSCs) into becoming hair follicle stem cells. By engineering mice to re-activate SOX9 in adult EpdSCs, we trigger fate switching. Combining epigenetic, proteomic and functional analyses, we interrogate the ensuing chromatin and transcriptional dynamics, slowed temporally by the mature EpdSC niche microenvironment. We show that as SOX9 binds and opens key hair follicle enhancers de novo in EpdSCs, it simultaneously recruits co-factors away from epidermal enhancers, which are silenced. Unhinged from its normal regulation, sustained SOX9 subsequently activates oncogenic transcriptional regulators that chart the path to cancers typified by constitutive SOX9 expression.
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Affiliation(s)
- Yihao Yang
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Nicholas Gomez
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Allen Institute for Cell Sciences, Seattle, WA, USA
| | - Nicole Infarinato
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- PRECISIONscientia, Yardley, PA, USA
| | - Rene C Adam
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Megan Sribour
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Inwha Baek
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Kyung Hee University, Seoul, South Korea
| | - Mélanie Laurin
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
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13
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Gallini S, Annusver K, Rahman NT, Gonzalez DG, Yun S, Matte-Martone C, Xin T, Lathrop E, Suozzi KC, Kasper M, Greco V. Injury prevents Ras mutant cell expansion in mosaic skin. Nature 2023; 619:167-175. [PMID: 37344586 PMCID: PMC10322723 DOI: 10.1038/s41586-023-06198-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/11/2023] [Indexed: 06/23/2023]
Abstract
Healthy skin is a mosaic of wild-type and mutant clones1,2. Although injury can cooperate with mutated Ras family proteins to promote tumorigenesis3-12, the consequences in genetically mosaic skin are unknown. Here we show that after injury, wild-type cells suppress aberrant growth induced by oncogenic Ras. HrasG12V/+ and KrasG12D/+ cells outcompete wild-type cells in uninjured, mosaic tissue but their expansion is prevented after injury owing to an increase in the fraction of proliferating wild-type cells. Mechanistically, we show that, unlike HrasG12V/+ cells, wild-type cells respond to autocrine and paracrine secretion of EGFR ligands, and this differential activation of the EGFR pathway explains the competitive switch during injury repair. Inhibition of EGFR signalling via drug or genetic approaches diminishes the proportion of dividing wild-type cells after injury, leading to the expansion of HrasG12V/+ cells. Increased proliferation of wild-type cells via constitutive loss of the cell cycle inhibitor p21 counteracts the expansion of HrasG12V/+ cells even in the absence of injury. Thus, injury has a role in switching the competitive balance between oncogenic and wild-type cells in genetically mosaic skin.
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Affiliation(s)
- Sara Gallini
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Karl Annusver
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Nur-Taz Rahman
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale School of Medicine, New Haven, CT, USA
| | - David G Gonzalez
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Sangwon Yun
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Tianchi Xin
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | | | - Maria Kasper
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Valentina Greco
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Departments of Cell Biology and Dermatology, Yale Stem Cell Center, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
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14
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Dervovic D, Malik AA, Chen ELY, Narimatsu M, Adler N, Afiuni-Zadeh S, Krenbek D, Martinez S, Tsai R, Boucher J, Berman JM, Teng K, Ayyaz A, Lü Y, Mbamalu G, Loganathan SK, Lee J, Zhang L, Guidos C, Wrana J, Valipour A, Roux PP, Reimand J, Jackson HW, Schramek D. In vivo CRISPR screens reveal Serpinb9 and Adam2 as regulators of immune therapy response in lung cancer. Nat Commun 2023; 14:3150. [PMID: 37258521 PMCID: PMC10232477 DOI: 10.1038/s41467-023-38841-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/18/2023] [Indexed: 06/02/2023] Open
Abstract
How the genetic landscape governs a tumor's response to immunotherapy remains poorly understood. To assess the immune-modulatory capabilities of 573 genes associated with altered cytotoxicity in human cancers, here we perform CRISPR/Cas9 screens directly in mouse lung cancer models. We recover the known immune evasion factors Stat1 and Serpinb9 and identify the cancer testis antigen Adam2 as an immune modulator, whose expression is induced by KrasG12D and further elevated by immunotherapy. Using loss- and gain-of-function experiments, we show that ADAM2 functions as an oncogene by restraining interferon and TNF cytokine signaling causing reduced presentation of tumor-associated antigens. ADAM2 also restricts expression of the immune checkpoint inhibitors PDL1, LAG3, TIGIT and TIM3 in the tumor microenvironment, which might explain why ex vivo expanded and adoptively transferred cytotoxic T-cells show enhanced cytotoxic efficacy in ADAM2 overexpressing tumors. Together, direct in vivo CRISPR/Cas9 screens can uncover genetic alterations that control responses to immunotherapies.
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Affiliation(s)
- Dzana Dervovic
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ahmad A Malik
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Edward L Y Chen
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Masahiro Narimatsu
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Nina Adler
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Somaieh Afiuni-Zadeh
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Dagmar Krenbek
- Department of Pathology and Bacteriology, Klinik Floridsdorf, Vienna, Austria
| | - Sebastien Martinez
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ricky Tsai
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Jonathan Boucher
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Jacob M Berman
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Katie Teng
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Arshad Ayyaz
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - YiQing Lü
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Geraldine Mbamalu
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Sampath K Loganathan
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Otolaryngology, Head and Neck Surgery, McGill University, Montreal, QC, Canada
| | - Jongbok Lee
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Li Zhang
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Departments of Laboratory Medicine and Pathobiology, Immunology, University of Toronto, Toronto, ON, Canada
| | - Cynthia Guidos
- SickKids Research Institute, University Health Network, Toronto, ON, Canada
| | - Jeffrey Wrana
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Arschang Valipour
- Karl-Landsteiner-Institute for Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
| | - Philippe P Roux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Jüri Reimand
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Hartland W Jackson
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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15
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Garcia-Diaz C, Pöysti A, Mereu E, Clements MP, Brooks LJ, Galvez-Cancino F, Castillo SP, Tang W, Beattie G, Courtot L, Ruiz S, Roncaroli F, Yuan Y, Marguerat S, Quezada SA, Heyn H, Parrinello S. Glioblastoma cell fate is differentially regulated by the microenvironments of the tumor bulk and infiltrative margin. Cell Rep 2023; 42:112472. [PMID: 37149862 DOI: 10.1016/j.celrep.2023.112472] [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: 06/25/2022] [Revised: 03/14/2023] [Accepted: 04/19/2023] [Indexed: 05/09/2023] Open
Abstract
Glioblastoma (GBM) recurrence originates from invasive margin cells that escape surgical debulking, but to what extent these cells resemble their bulk counterparts remains unclear. Here, we generated three immunocompetent somatic GBM mouse models, driven by subtype-associated mutations, to compare matched bulk and margin cells. We find that, regardless of mutations, tumors converge on common sets of neural-like cellular states. However, bulk and margin have distinct biology. Injury-like programs associated with immune infiltration dominate in the bulk, leading to the generation of lowly proliferative injured neural progenitor-like cells (iNPCs). iNPCs account for a significant proportion of dormant GBM cells and are induced by interferon signaling within T cell niches. In contrast, developmental-like trajectories are favored within the immune-cold margin microenvironment resulting in differentiation toward invasive astrocyte-like cells. These findings suggest that the regional tumor microenvironment dominantly controls GBM cell fate and biological vulnerabilities identified in the bulk may not extend to the margin residuum.
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Affiliation(s)
- Claudia Garcia-Diaz
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Anni Pöysti
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Elisabetta Mereu
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Melanie P Clements
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Lucy J Brooks
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Felipe Galvez-Cancino
- Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK
| | - Simon P Castillo
- Division of Molecular Pathology & Centre for Evolution and Cancer, The Institute of Cancer Research, London SM2 5NG, UK
| | - Wenhao Tang
- Department of Mathematics, Imperial College London, London, UK
| | - Gordon Beattie
- CRUK City of London Centre Single Cell Genomics Facility, UCL Cancer Institute, University College London, London, UK; Genomics Translational Technology Platform, UCL Cancer Institute, University College London, London, UK
| | - Lilas Courtot
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Sara Ruiz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Federico Roncaroli
- Geoffrey Jefferson Brain Research Centre, Division of Neuroscience, School of Biological Sciences, Faculty of Brain and Mental Health, University of Manchester, Manchester, UK
| | - Yinyin Yuan
- Division of Molecular Pathology & Centre for Evolution and Cancer, The Institute of Cancer Research, London SM2 5NG, UK
| | - Samuel Marguerat
- Genomics Translational Technology Platform, UCL Cancer Institute, University College London, London, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
| | - Simona Parrinello
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK.
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16
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Stewart KS, Gonzales KAU, Yuan S, Tierney MT, Bonny AR, Yang Y, Infarinato NR, Cowley CJ, Levorse JM, Pasolli HA, Ghosh S, Rothlin CV, Fuchs E. Stem cells tightly regulate dead cell clearance to maintain tissue fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541773. [PMID: 37293114 PMCID: PMC10245816 DOI: 10.1101/2023.05.22.541773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Macrophages and dendritic cells have long been appreciated for their ability to migrate to and engulf dying cells and debris, including some of the billions of cells that are naturally eliminated from our body daily. However, a substantial number of these dying cells are cleared by 'non-professional phagocytes', local epithelial cells that are critical to organismal fitness. How non-professional phagocytes sense and digest nearby apoptotic corpses while still performing their normal tissue functions is unclear. Here, we explore the molecular mechanisms underlying their multifunctionality. Exploiting the cyclical bouts of tissue regeneration and degeneration during the hair cycle, we show that stem cells can transiently become non-professional phagocytes when confronted with dying cells. Adoption of this phagocytic state requires both local lipids produced by apoptotic corpses to activate RXRα, and tissue-specific retinoids for RARγ activation. This dual factor dependency enables tight regulation of the genes requisite to activate phagocytic apoptotic clearance. The tunable phagocytic program we describe here offers an effective mechanism to offset phagocytic duties against the primary stem cell function of replenishing differentiated cells to preserve tissue integrity during homeostasis. Our findings have broad implications for other non-motile stem or progenitor cells which experience cell death in an immune-privileged niche.
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Affiliation(s)
- Katherine S Stewart
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Kevin AU Gonzales
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Shaopeng Yuan
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Matthew T Tierney
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Alain R Bonny
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Yihao Yang
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Nicole R Infarinato
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Christopher J Cowley
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - John M Levorse
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Hilda Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
| | - Sourav Ghosh
- Departments of Neurology and Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Carla V Rothlin
- Departments of Immunobiology and Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
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17
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Kondratyev M, Pesic A, Ketela T, Stickle N, Beswick C, Shalev Z, Marastoni S, Samadian S, Dvorkin-Gheva A, Sayad A, Bashkurov M, Boasquevisque P, Datti A, Pugh TJ, Virtanen C, Moffat J, Grénman RA, Koritzinsky M, Wouters BG. Identification of acquired Notch3 dependency in metastatic Head and Neck Cancer. Commun Biol 2023; 6:538. [PMID: 37202533 DOI: 10.1038/s42003-023-04828-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 04/11/2023] [Indexed: 05/20/2023] Open
Abstract
During cancer development, tumor cells acquire changes that enable them to invade surrounding tissues and seed metastasis at distant sites. These changes contribute to the aggressiveness of metastatic cancer and interfere with success of therapy. Our comprehensive analysis of "matched" pairs of HNSCC lines derived from primary tumors and corresponding metastatic sites identified several components of Notch3 signaling that are differentially expressed and/or altered in metastatic lines and confer a dependency on this pathway. These components were also shown to be differentially expressed between early and late stages of tumors in a TMA constructed from over 200 HNSCC patients. Finally, we show that suppression of Notch3 improves survival in mice in both subcutaneous and orthotopic models of metastatic HNSCC. Novel treatments targeting components of this pathway may prove effective in targeting metastatic HNSCC cells alone or in combination with conventional therapies.
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Affiliation(s)
- Maria Kondratyev
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada.
| | - Aleksandra Pesic
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Troy Ketela
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Natalie Stickle
- Princess Margaret Cancer Center, Bioinformatics and HPC Core, Toronto, ON, Canada
| | - Christine Beswick
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Zvi Shalev
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Stefano Marastoni
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Soroush Samadian
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Anna Dvorkin-Gheva
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Azin Sayad
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Mikhail Bashkurov
- SMART High-Content Screening facility at Network Biology Collaborative Centre, Toronto, ON, Canada
| | - Pedro Boasquevisque
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Alessandro Datti
- SMART High-Content Screening facility at Network Biology Collaborative Centre, Toronto, ON, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Carl Virtanen
- Princess Margaret Cancer Center, Bioinformatics and HPC Core, Toronto, ON, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | | | - Bradly G Wouters
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada.
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18
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Liu S, Hur YH, Cai X, Cong Q, Yang Y, Xu C, Bilate AM, Gonzales KAU, Parigi SM, Cowley CJ, Hurwitz B, Luo JD, Tseng T, Gur-Cohen S, Sribour M, Omelchenko T, Levorse J, Pasolli HA, Thompson CB, Mucida D, Fuchs E. A tissue injury sensing and repair pathway distinct from host pathogen defense. Cell 2023; 186:2127-2143.e22. [PMID: 37098344 PMCID: PMC10321318 DOI: 10.1016/j.cell.2023.03.031] [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: 09/29/2022] [Revised: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 04/27/2023]
Abstract
Pathogen infection and tissue injury are universal insults that disrupt homeostasis. Innate immunity senses microbial infections and induces cytokines/chemokines to activate resistance mechanisms. Here, we show that, in contrast to most pathogen-induced cytokines, interleukin-24 (IL-24) is predominately induced by barrier epithelial progenitors after tissue injury and is independent of microbiome or adaptive immunity. Moreover, Il24 ablation in mice impedes not only epidermal proliferation and re-epithelialization but also capillary and fibroblast regeneration within the dermal wound bed. Conversely, ectopic IL-24 induction in the homeostatic epidermis triggers global epithelial-mesenchymal tissue repair responses. Mechanistically, Il24 expression depends upon both epithelial IL24-receptor/STAT3 signaling and hypoxia-stabilized HIF1α, which converge following injury to trigger autocrine and paracrine signaling involving IL-24-mediated receptor signaling and metabolic regulation. Thus, parallel to innate immune sensing of pathogens to resolve infections, epithelial stem cells sense injury signals to orchestrate IL-24-mediated tissue repair.
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Affiliation(s)
- Siqi Liu
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Yun Ha Hur
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Xin Cai
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Qian Cong
- McDermott Center for Human Growth and Development, Department of Biophysics, and Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yihao Yang
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Chiwei Xu
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Angelina M Bilate
- Laboratory of Mucosal Immunology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Kevin Andrew Uy Gonzales
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - S Martina Parigi
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Christopher J Cowley
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Brian Hurwitz
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Tiffany Tseng
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Shiri Gur-Cohen
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Megan Sribour
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Tatiana Omelchenko
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - John Levorse
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Hilda Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Elaine Fuchs
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
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19
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Azevedo-Pereira RL, Manley NC, Dong C, Zhang Y, Lee AG, Zatulovskaia Y, Gupta V, Vu J, Han S, Berry JE, Bliss TM, Steinberg GK. Decoding the molecular crosstalk between grafted stem cells and the stroke-injured brain. Cell Rep 2023; 42:112353. [PMID: 37043353 PMCID: PMC10562513 DOI: 10.1016/j.celrep.2023.112353] [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: 08/12/2021] [Revised: 01/25/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023] Open
Abstract
Stem cell therapy shows promise for multiple disorders; however, the molecular crosstalk between grafted cells and host tissue is largely unknown. Here, we take a step toward addressing this question. Using translating ribosome affinity purification (TRAP) with sequencing tools, we simultaneously decode the transcriptomes of graft and host for human neural stem cells (hNSCs) transplanted into the stroke-injured rat brain. Employing pathway analysis tools, we investigate the interactions between the two transcriptomes to predict molecular pathways linking host and graft genes; as proof of concept, we predict host-secreted factors that signal to the graft and the downstream molecular cascades they trigger in the graft. We identify a potential host-graft crosstalk pathway where BMP6 from the stroke-injured brain induces graft secretion of noggin, a known brain repair factor. Decoding the molecular interplay between graft and host is a critical step toward deciphering the molecular mechanisms of stem cell action.
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Affiliation(s)
| | - Nathan C Manley
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Chen Dong
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Yue Zhang
- Stanford Genetics Bioinformatics Service Center, Stanford University, Stanford, CA 94305, USA
| | - Alex G Lee
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Yulia Zatulovskaia
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Varun Gupta
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Jennifer Vu
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Summer Han
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Jack E Berry
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Tonya M Bliss
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA.
| | - Gary K Steinberg
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA.
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20
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von Berlin L, Westholm JO, Ratz M, Frisén J. Early fate bias in neuroepithelial progenitors of hippocampal neurogenesis. Hippocampus 2023; 33:391-401. [PMID: 36468233 DOI: 10.1002/hipo.23482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/17/2022] [Accepted: 11/19/2022] [Indexed: 12/12/2022]
Abstract
Hippocampal adult neural stem cells emerge from progeny of the neuroepithelial lineage during murine brain development. Hippocampus development is increasingly well understood. However, the clonal relationships between early neuroepithelial stem cells and postnatal neurogenic cells remain unclear, especially at the single-cell level. Here we report fate bias and gene expression programs in thousands of clonally related cells in the juvenile hippocampus based on single-cell RNA-seq of barcoded clones. We find evidence for early fate restriction of neuroepithelial stem cells to either neurogenic progenitor cells of the dentate gyrus region or oligodendrogenic, non-neurogenic fate supplying cells for other hippocampal regions including gray matter areas and the Cornu ammonis region 1/3. Our study provides new insights into the phenomenon of early fate restriction guiding the development of postnatal hippocampal neurogenesis.
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Affiliation(s)
- Leonie von Berlin
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Jakub Orzechowski Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- KTH Royal Institute of Technology, Department of Gene Technology, Stockholm, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
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21
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Aldea D, Kokalari B, Atsuta Y, Dingwall HL, Zheng Y, Nace A, Cotsarelis G, Kamberov YG. Differential modularity of the mammalian Engrailed 1 enhancer network directs sweat gland development. PLoS Genet 2023; 19:e1010614. [PMID: 36745673 PMCID: PMC9934363 DOI: 10.1371/journal.pgen.1010614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/16/2023] [Accepted: 01/13/2023] [Indexed: 02/07/2023] Open
Abstract
Enhancers are context-specific regulators of expression that drive biological complexity and variation through the redeployment of conserved genes. An example of this is the enhancer-mediated control of Engrailed 1 (EN1), a pleiotropic gene whose expression is required for the formation of mammalian eccrine sweat glands. We previously identified the En1 candidate enhancer (ECE) 18 cis-regulatory element that has been highly and repeatedly derived on the human lineage to potentiate ectodermal EN1 and induce our species' uniquely high eccrine gland density. Intriguingly, ECE18 quantitative activity is negligible outside of primates and ECE18 is not required for En1 regulation and eccrine gland formation in mice, raising the possibility that distinct enhancers have evolved to modulate the same trait. Here we report the identification of the ECE20 enhancer and show it has conserved functionality in mouse and human developing skin ectoderm. Unlike ECE18, knock-out of ECE20 in mice reduces ectodermal En1 and eccrine gland number. Notably, we find ECE20, but not ECE18, is also required for En1 expression in the embryonic mouse brain, demonstrating that ECE20 is a pleiotropic En1 enhancer. Finally, that ECE18 deletion does not potentiate the eccrine phenotype of ECE20 knock-out mice supports the secondary incorporation of ECE18 into the regulation of this trait in primates. Our findings reveal that the mammalian En1 regulatory machinery diversified to incorporate both shared and lineage-restricted enhancers to regulate the same phenotype, and also have implications for understanding the forces that shape the robustness and evolvability of developmental traits.
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Affiliation(s)
- Daniel Aldea
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Blerina Kokalari
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Yuji Atsuta
- Genetics Department, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Heather L. Dingwall
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Ying Zheng
- Department of Dermatology, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Arben Nace
- Department of Dermatology, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - George Cotsarelis
- Department of Dermatology, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Yana G. Kamberov
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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22
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The NOTCH-RIPK4-IRF6-ELOVL4 Axis Suppresses Squamous Cell Carcinoma. Cancers (Basel) 2023; 15:cancers15030737. [PMID: 36765696 PMCID: PMC9913669 DOI: 10.3390/cancers15030737] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/03/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
Receptor-interacting serine/threonine protein kinase 4 (RIPK4) and its kinase substrate the transcription factor interferon regulatory factor 6 (IRF6) play critical roles in the development and maintenance of the epidermis. In addition, ourselves and others have previously shown that RIPK4 is a NOTCH target gene that suppresses the development of cutaneous and head and neck squamous cell carcinomas (HNSCCs). In this study, we used autochthonous mouse models, where the expression of Pik3caH1047R oncogene predisposes the skin and oral cavity to tumor development, and show that not only loss of Ripk4, but also loss of its kinase substrate Irf6, triggers rapid SCC development. In vivo rescue experiments using Ripk4 or a kinase-dead Ripk4 mutant showed that the tumor suppressive function of Ripk4 is dependent on its kinase activity. To elucidate critical mediators of this tumor suppressive pathway, we performed transcriptional profiling of Ripk4-deficient epidermal cells followed by multiplexed in vivo CRISPR screening to identify genes with tumor suppressive capabilities. We show that Elovl4 is a critical Notch-Ripk4-Irf6 downstream target gene, and that Elovl4 loss itself triggers SCC development. Importantly, overexpression of Elovl4 suppressed tumor growth of Ripk4-deficient keratinocytes. Altogether, our work identifies a potent Notch1-Ripk4-Irf6-Elovl4 tumor suppressor axis.
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23
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Garside GB, Sandoval M, Beronja S, Rudolph KL. Lentiviral in situ targeting of stem cells in unperturbed intestinal epithelium. BMC Biol 2023; 21:6. [PMID: 36627630 PMCID: PMC9832770 DOI: 10.1186/s12915-022-01466-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/16/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Methods for the long-term in situ transduction of the unperturbed murine intestinal epithelium have not been developed in past research. Such a method could speed up functional studies and screens to identify genetic factors influencing intestinal epithelium biology. Here, we developed an efficient method achieving this long-sought goal. RESULTS We used ultrasound-guided microinjections to transduce the embryonic endoderm at day 8 (E8.0) in utero. The injection procedure can be completed in 20 min and had a 100% survival rate. By injecting a small volume (0.1-0.2 μl) of concentrated virus, single shRNA constructs as well as lentiviral libraries can successfully be transduced. The new method stably and reproducibly targets adult intestinal epithelium, as well as other endoderm-derived organs such as the lungs, pancreas, liver, stomach, and bladder. Postnatal analysis of young adult mice indicates that single transduced cells at E8.0 gave rise to crypt fields that were comprised of 20-30 neighbouring crypts per crypt-field at 90 days after birth. Lentiviral targeting of ApcMin/+ mutant and wildtype mice revealed that heterozygous loss of Apc function suppresses the developmental normal growth pattern of intestinal crypt fields. This suppression of crypt field sizes did not involve a reduction of the crypt number per field, indicating that heterozygous Apc loss impaired the growth of individual crypts within the fields. Lentiviral-mediated shRNA knockdown of p53 led to an approximately 20% increase of individual crypts per field in both Apc+/+ and ApcMin/+ mice, associating with an increase in crypt size in ApcMin/+ mice but a slight reduction in crypt size in Apc+/+ mice. Overall, p53 knockdown rescued the reduction in crypt field size in Apc-mutant mice but had no effect on crypt field size in wildtype mice. CONCLUSIONS This study develops a novel technique enabling robust and reproducible in vivo targeting of intestinal stem cells in situ in the unperturbed intestinal epithelium across different regions of the intestine. In vivo somatic gene editing and genetic screening of lentiviral libraries has the potential to speed up discoveries and mechanistic understanding of genetic pathways controlling the biology of the intestinal epithelium during development and postnatal life. The here developed method enables such approaches.
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Affiliation(s)
- George B. Garside
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
- National Center for Tumor Diseases, 01307 Dresden, Germany
| | - Madeline Sandoval
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA
| | - Slobodan Beronja
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA
| | - K. Lenhard Rudolph
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
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24
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Langille E, Al-Zahrani KN, Ma Z, Liang M, Uuskula-Reimand L, Espin R, Teng K, Malik A, Bergholtz H, El Ghamrasni S, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lü Y, Oh RH, Kozma KJ, Trcka D, Narimatsu M, Liu JC, Nguyen T, Barutcu S, Loganathan SK, Bremner R, Bader GD, Egan SE, Cescon DW, Sørlie T, Wrana JL, Jackson HW, Wilson MD, Witkiewicz AK, Knudsen ES, Pujana MA, Wahl GM, Schramek D. Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer. Cancer Discov 2022; 12:2930-2953. [PMID: 36108220 PMCID: PMC9812400 DOI: 10.1158/2159-8290.cd-21-0865] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/15/2022] [Accepted: 09/13/2022] [Indexed: 01/21/2023]
Abstract
Systematically investigating the scores of genes mutated in cancer and discerning disease drivers from inconsequential bystanders is a prerequisite for precision medicine but remains challenging. Here, we developed a somatic CRISPR/Cas9 mutagenesis screen to study 215 recurrent "long-tail" breast cancer genes, which revealed epigenetic regulation as a major tumor-suppressive mechanism. We report that components of the BAP1 and COMPASS-like complexes, including KMT2C/D, KDM6A, BAP1, and ASXL1/2 ("EpiDrivers"), cooperate with PIK3CAH1047R to transform mouse and human breast epithelial cells. Mechanistically, we find that activation of PIK3CAH1047R and concomitant EpiDriver loss triggered an alveolar-like lineage conversion of basal mammary epithelial cells and accelerated formation of luminal-like tumors, suggesting a basal origin for luminal tumors. EpiDriver mutations are found in ∼39% of human breast cancers, and ∼50% of ductal carcinoma in situ express casein, suggesting that lineage infidelity and alveogenic mimicry may significantly contribute to early steps of breast cancer etiology. SIGNIFICANCE Infrequently mutated genes comprise most of the mutational burden in breast tumors but are poorly understood. In vivo CRISPR screening identified functional tumor suppressors that converged on epigenetic regulation. Loss of epigenetic regulators accelerated tumorigenesis and revealed lineage infidelity and aberrant expression of alveogenesis genes as potential early events in tumorigenesis. This article is highlighted in the In This Issue feature, p. 2711.
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Affiliation(s)
- Ellen Langille
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Khalid N. Al-Zahrani
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Zhibo Ma
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Minggao Liang
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | | | - Roderic Espin
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Spain
| | - Katie Teng
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ahmad Malik
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Helga Bergholtz
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
| | - Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Somaieh Afiuni-Zadeh
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ricky Tsai
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sana Alvi
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Andrew Elia
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - YiQing Lü
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Robin H. Oh
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Katelyn J. Kozma
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Daniel Trcka
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Masahiro Narimatsu
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jeff C. Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Thomas Nguyen
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Seda Barutcu
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sampath K. Loganathan
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Rod Bremner
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gary D. Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sean E. Egan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - David W. Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway
| | - Jeffrey L. Wrana
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hartland W. Jackson
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Michael D. Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | | | - Erik S. Knudsen
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York
| | - Miguel Angel Pujana
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Spain
| | - Geoffrey M. Wahl
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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25
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Kantzer CG, Yang W, Grommisch D, Patil KV, Mak KHM, Shirokova V, Genander M. ID1 and CEBPA coordinate epidermal progenitor cell differentiation. Development 2022; 149:282464. [PMID: 36330928 PMCID: PMC9845743 DOI: 10.1242/dev.201262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
The regulatory circuits that coordinate epidermal differentiation during development are still not fully understood. Here, we report that the transcriptional regulator ID1 is enriched in mouse basal epidermal progenitor cells and find ID1 expression to be diminished upon differentiation. In utero silencing of Id1 impairs progenitor cell proliferation, leads to precocious delamination of targeted progenitor cells and enables differentiated keratinocytes to retain progenitor markers and characteristics. Transcriptional profiling suggests that ID1 acts by mediating adhesion to the basement membrane while inhibiting spinous layer differentiation. Co-immunoprecipitation reveals ID1 binding to transcriptional regulators of the class I bHLH family. We localize bHLH Tcf3, Tcf4 and Tcf12 to epidermal progenitor cells during epidermal stratification and establish TCF3 as a downstream effector of ID1-mediated epidermal proliferation. Finally, we identify crosstalk between CEBPA, a known mediator of epidermal differentiation, and Id1, and demonstrate that CEBPA antagonizes BMP-induced activation of Id1. Our work establishes ID1 as a key coordinator of epidermal development, acting to balance progenitor proliferation with differentiation and unveils how functional crosstalk between CEBPA and Id1 orchestrates epidermal lineage progression.
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Affiliation(s)
| | - Wei Yang
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - David Grommisch
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Kim Vikhe Patil
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Kylie Hin-Man Mak
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Vera Shirokova
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Maria Genander
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden,Author for correspondence ()
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26
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Scott-Solomon E, Hsu YC. Neurobiology, Stem Cell Biology, and Immunology: An Emerging Triad for Understanding Tissue Homeostasis and Repair. Annu Rev Cell Dev Biol 2022; 38:419-446. [PMID: 36201298 PMCID: PMC10085582 DOI: 10.1146/annurev-cellbio-120320-032429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The peripheral nervous system (PNS) endows animals with the remarkable ability to sense and respond to a dynamic world. Emerging evidence shows the PNS also participates in tissue homeostasis and repair by integrating local changes with organismal and environmental changes. Here, we provide an in-depth summary of findings delineating the diverse roles of peripheral nerves in modulating stem cell behaviors and immune responses under steady-state conditions and in response to injury and duress, with a specific focus on the skin and the hematopoietic system. These examples showcase how elucidating neuro-stem cell and neuro-immune cell interactions provides a conceptual framework that connects tissue biology and local immunity with systemic bodily changes to meet varying demands. They also demonstrate how changes in these interactions can manifest in stress, aging, cancer, and inflammation, as well as how these findings can be harnessed to guide the development of new therapeutics.
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Affiliation(s)
- Emily Scott-Solomon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA; ,
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Ya-Chieh Hsu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA; ,
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
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27
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Soffer A, Mahly A, Padmanabhan K, Cohen J, Adir O, Loushi E, Fuchs Y, Williams SE, Luxenburg C. Apoptosis and tissue thinning contribute to symmetric cell division in the developing mouse epidermis in a nonautonomous way. PLoS Biol 2022; 20:e3001756. [PMID: 35969606 PMCID: PMC9410552 DOI: 10.1371/journal.pbio.3001756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 08/25/2022] [Accepted: 07/13/2022] [Indexed: 11/18/2022] Open
Abstract
Mitotic spindle orientation (SO) is a conserved mechanism that governs cell fate and tissue morphogenesis. In the developing epidermis, a balance between self-renewing symmetric divisions and differentiative asymmetric divisions is necessary for normal development. While the cellular machinery that executes SO is well characterized, the extrinsic cues that guide it are poorly understood. Here, we identified the basal cell adhesion molecule (BCAM), a β1 integrin coreceptor, as a novel regulator of epidermal morphogenesis. In utero RNAi-mediated depletion of Bcam in the mouse embryo did not hinder β1 integrin distribution or cell adhesion and polarity. However, Bcam depletion promoted apoptosis, thinning of the epidermis, and symmetric cell division, and the defects were reversed by concomitant overexpression of the apoptosis inhibitor Xiap. Moreover, in mosaic epidermis, depletion of Bcam or Xiap induced symmetric divisions in neighboring wild-type cells. These results identify apoptosis and epidermal architecture as extrinsic cues that guide SO in the developing epidermis.
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Affiliation(s)
- Arad Soffer
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adnan Mahly
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Krishnanand Padmanabhan
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jonathan Cohen
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orit Adir
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eidan Loushi
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yaron Fuchs
- Department of Biology, Technion—Israel Institute of Technology, Haifa, Israel
| | - Scott E. Williams
- Departments of Pathology & Laboratory Medicine and Biology, Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Chen Luxenburg
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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28
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THY1-mediated mechanisms converge to drive YAP activation in skin homeostasis and repair. Nat Cell Biol 2022; 24:1049-1063. [PMID: 35798842 DOI: 10.1038/s41556-022-00944-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 05/18/2022] [Indexed: 12/24/2022]
Abstract
Anchored cells of the basal epidermis constantly undergo proliferation in an overcrowded environment. An important regulator of epidermal proliferation is YAP, which can be controlled by both cell-matrix and cell-cell interactions. Here, we report that THY1, a GPI-anchored protein, inhibits epidermal YAP activity through converging molecular mechanisms. THY1 deficiency leads to increased adhesion by activating the integrin-β1-SRC module. Notably, regardless of high cellular densities, the absence of THY1 leads to the dissociation of an adherens junction complex that enables the release and translocation of YAP. Due to increased YAP-dependent proliferation, Thy1-/- mice display enhanced wound repair and hair follicle regeneration. Taken together, our work reveals THY1 as a crucial regulator of cell-matrix and cell-cell interactions that controls YAP activity in skin homeostasis and regeneration.
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29
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Anillin governs mitotic rounding during early epidermal development. BMC Biol 2022; 20:145. [PMID: 35710398 PMCID: PMC9205045 DOI: 10.1186/s12915-022-01345-9] [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: 03/14/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
Background The establishment of tissue architecture requires coordination between distinct processes including basement membrane assembly, cell adhesion, and polarity; however, the underlying mechanisms remain poorly understood. The actin cytoskeleton is ideally situated to orchestrate tissue morphogenesis due to its roles in mechanical, structural, and regulatory processes. However, the function of many pivotal actin-binding proteins in mammalian development is poorly understood. Results Here, we identify a crucial role for anillin (ANLN), an actin-binding protein, in orchestrating epidermal morphogenesis. In utero RNAi-mediated silencing of Anln in mouse embryos disrupted epidermal architecture marked by adhesion, polarity, and basement membrane defects. Unexpectedly, these defects cannot explain the profoundly perturbed epidermis of Anln-depleted embryos. Indeed, even before these defects emerge, Anln-depleted epidermis exhibits abnormalities in mitotic rounding and its associated processes: chromosome segregation, spindle orientation, and mitotic progression, though not in cytokinesis that was disrupted only in Anln-depleted cultured keratinocytes. We further show that ANLN localizes to the cell cortex during mitotic rounding, where it regulates the distribution of active RhoA and the levels, activity, and structural organization of the cortical actomyosin proteins. Conclusions Our results demonstrate that ANLN is a major regulator of epidermal morphogenesis and identify a novel role for ANLN in mitotic rounding, a near-universal process that governs cell shape, fate, and tissue morphogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01345-9.
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Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics. Nat Neurosci 2022; 25:285-294. [PMID: 35210624 PMCID: PMC8904259 DOI: 10.1038/s41593-022-01011-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 01/11/2022] [Indexed: 01/02/2023]
Abstract
The mammalian brain contains many specialized cells that develop from a thin sheet of neuroepithelial progenitor cells. Single-cell transcriptomics revealed hundreds of molecularly diverse cell types in the nervous system, but the lineage relationships between mature cell types and progenitor cells are not well understood. Here we show in vivo barcoding of early progenitors to simultaneously profile cell phenotypes and clonal relations in the mouse brain using single-cell and spatial transcriptomics. By reconstructing thousands of clones, we discovered fate-restricted progenitor cells in the mouse hippocampal neuroepithelium and show that microglia are derived from few primitive myeloid precursors that massively expand to generate widely dispersed progeny. We combined spatial transcriptomics with clonal barcoding and disentangled migration patterns of clonally related cells in densely labeled tissue sections. Our approach enables high-throughput dense reconstruction of cell phenotypes and clonal relations at the single-cell and tissue level in individual animals and provides an integrated approach for understanding tissue architecture. Ratz et al. present an easy-to-use method to barcode progenitor cells, enabling profiling of cell phenotypes and clonal relations using single-cell and spatial transcriptomics, providing an integrated approach for understanding brain architecture.
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31
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Di Meo D, Ravindran P, Sadhanasatish T, Dhumale P, Püschel AW. The balance of mitochondrial fission and fusion in cortical axons depends on the kinases SadA and SadB. Cell Rep 2021; 37:110141. [PMID: 34936879 DOI: 10.1016/j.celrep.2021.110141] [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: 04/09/2021] [Revised: 10/17/2021] [Accepted: 11/29/2021] [Indexed: 01/21/2023] Open
Abstract
Neurons are highly polarized cells that display characteristic differences in the organization of their organelles in axons and dendrites. The kinases SadA and SadB (SadA/B) promote the formation of distinct axonal and dendritic extensions during the development of cortical and hippocampal neurons. Here, we show that SadA/B are required for the specific dynamics of axonal mitochondria. Ankyrin B (AnkB) stimulates the activity of SadA/B that function as regulators of mitochondrial dynamics through the phosphorylation of tau. Suppression of SadA/B or AnkB in cortical neurons induces the elongation of mitochondria by disrupting the balance of fission and fusion. SadA/B-deficient neurons show an accumulation of hyper-fused mitochondria and activation of the integrated stress response (ISR). The normal dynamics of axonal mitochondria could be restored by mild actin destabilization. Thus, the elongation after loss of SadA/B results from an excessive stabilization of actin filaments and reduction of Drp1 recruitment to mitochondria.
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Affiliation(s)
- Danila Di Meo
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, Schloßplatz 5, 48149 Münster, Germany; Cells-in-Motion Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Priyadarshini Ravindran
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, Schloßplatz 5, 48149 Münster, Germany
| | - Tanmay Sadhanasatish
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, Schloßplatz 5, 48149 Münster, Germany; Cells-in-Motion Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Pratibha Dhumale
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, Schloßplatz 5, 48149 Münster, Germany; Cells-in-Motion Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Andreas W Püschel
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, Schloßplatz 5, 48149 Münster, Germany; Cells-in-Motion Interfaculty Center, University of Münster, 48149 Münster, Germany.
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32
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Taniguchi S, Tanaka Y, Elhance A, Oshimori N. A mechanistic basis for the malignant progression of salivary gland tumors. iScience 2021; 24:103508. [PMID: 34934927 PMCID: PMC8661530 DOI: 10.1016/j.isci.2021.103508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/25/2021] [Accepted: 11/22/2021] [Indexed: 11/19/2022] Open
Abstract
Salivary gland tumors are diverse neoplasms, likely reflecting differences in the tissue- and cell-of-origin. 80%-90% of tumors arising in the sublingual gland (SLG) are malignant, whereas the other major glands often form benign tumors. Owing to the lack of experimental models to explore the etiology of salivary gland tumors, the cellular and molecular bases of malignancy remain unknown. Here, we generated a murine model of HRASG12V-driven salivary gland tumors amenable to examine tumor onset and malignant progression. We found that HMGA2 marks the tumor onset, and transformed-SOX2+ stem/progenitor cells expand exclusively in SLG tumors. Lineage tracing experiments showed that SLG tumor cells undergo an extensive epithelial-mesenchymal transition (EMT) and TGF-β-responding tumor cells are a source of mesenchymal tumor cells invading the surrounding stroma. This study advances our understanding of the mechanistic basis of salivary gland malignancy and may help combat this highly heterogeneous cancer.
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Affiliation(s)
- Sachiko Taniguchi
- Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Yuya Tanaka
- Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Ajit Elhance
- Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Naoki Oshimori
- Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR 97239, USA
- Department of Dermatology, Oregon Health and Science University, Portland, OR 97239, USA
- Department of Otolaryngology, Head & Neck Surgery, Oregon Health and Science University, Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA
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33
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Gonzales KAU, Polak L, Matos I, Tierney MT, Gola A, Wong E, Infarinato NR, Nikolova M, Luo S, Liu S, Novak JSS, Lay K, Pasolli HA, Fuchs E. Stem cells expand potency and alter tissue fitness by accumulating diverse epigenetic memories. Science 2021; 374:eabh2444. [PMID: 34822296 DOI: 10.1126/science.abh2444] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Kevin Andrew Uy Gonzales
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Lisa Polak
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Irina Matos
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.,Immunology Discovery, Genentech Inc., South San Francisco, CA 94080, USA
| | - Matthew T Tierney
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Anita Gola
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Ellen Wong
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Nicole R Infarinato
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Maria Nikolova
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Shijing Luo
- Jones Day Intellectual Property Law Firm, New York, NY 10281, USA
| | - Siqi Liu
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Jesse S S Novak
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Kenneth Lay
- Laboratory of Human Genetics and Therapeutics, Institute of Medical Biology, A∗STAR, Singapore 138648, Singapore
| | - Hilda Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Elaine Fuchs
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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34
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Mout L, van Royen ME, de Ridder C, Stuurman D, van de Geer WS, Marques R, Buck SAJ, French PJ, van de Werken HJG, Mathijssen RHJ, de Wit R, Lolkema MP, van Weerden WM. Continued Androgen Signalling Inhibition improves Cabazitaxel Efficacy in Prostate Cancer. EBioMedicine 2021; 73:103681. [PMID: 34749299 PMCID: PMC8586743 DOI: 10.1016/j.ebiom.2021.103681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND The androgen receptor (AR) pathway is a key driver of neoplastic behaviour in the different stages of metastatic prostate cancer (mPCa). Targeting the AR therefore remains the cornerstone for mPCa treatment. We have previously reported that activation of AR signalling affects taxane chemo-sensitivity in preclinical models of castration resistant PCa (CRPC). Here, we explored the anti-tumour efficacy of the AR targeted inhibitor enzalutamide combined with cabazitaxel. METHODS We used the AR positive CRPC model PC346C-DCC-K to assess the in vitro and in vivo activity of combining enzalutamide with cabazitaxel. Subsequent validation studies were performed using an enzalutamide resistant VCaP model. To investigate the impact of AR signalling on cabazitaxel activity we used quantitative live-cell imaging of tubulin stabilization and apoptosis related nuclear fragmentation. FINDINGS Enzalutamide strongly amplified cabazitaxel anti-tumour activity in the patient-derived xenograft models PC346C-DCC-K (median time to humane endpoint 77 versus 48 days, P<0.0001) and VCaP-Enza-B (median time to humane endpoint 80 versus 53 days, P<0.001). Although enzalutamide treatment by itself was ineffective in reducing tumour growth, it significantly suppressed AR signalling in PC346C-DCC-K tumours as shown by AR target gene expression. The addition of enzalutamide enhanced cabazitaxel induced apoptosis as shown by live-cell imaging (P<0.001). INTERPRETATION Our study demonstrates that cabazitaxel efficacy can be improved by simultaneous blocking of AR signalling by enzalutamide, even if AR targeted treatment no longer affects tumour growth. These findings support clinical studies that combine AR targeted inhibitors with cabazitaxel in CRPC.
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Affiliation(s)
- Lisanne Mout
- Department of Medical Oncology Erasmus MC Cancer Institute, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Martin E van Royen
- Department of Pathology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Cancer Treatment Screening Facility Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Corrina de Ridder
- Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Debra Stuurman
- Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Wesley S van de Geer
- Department of Medical Oncology Erasmus MC Cancer Institute, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Cancer Computational Biology Center Erasmus MC Cancer Institute, University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Rute Marques
- Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Stefan A J Buck
- Department of Medical Oncology Erasmus MC Cancer Institute, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Pim J French
- Cancer Treatment Screening Facility Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Department of Neurology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Harmen J G van de Werken
- Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Cancer Computational Biology Center Erasmus MC Cancer Institute, University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Ron H J Mathijssen
- Department of Medical Oncology Erasmus MC Cancer Institute, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Department of Pathology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Cancer Treatment Screening Facility Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Department of Neurology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Cancer Computational Biology Center Erasmus MC Cancer Institute, University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Ronald de Wit
- Department of Medical Oncology Erasmus MC Cancer Institute, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Martijn P Lolkema
- Department of Medical Oncology Erasmus MC Cancer Institute, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Wytske M van Weerden
- Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands.
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35
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Larsen SB, Cowley CJ, Sajjath SM, Barrows D, Yang Y, Carroll TS, Fuchs E. Establishment, maintenance, and recall of inflammatory memory. Cell Stem Cell 2021; 28:1758-1774.e8. [PMID: 34320411 PMCID: PMC8500942 DOI: 10.1016/j.stem.2021.07.001] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/21/2021] [Accepted: 07/01/2021] [Indexed: 01/12/2023]
Abstract
Known for nearly a century but through mechanisms that remain elusive, cells retain a memory of inflammation that equips them to react quickly and broadly to diverse secondary stimuli. Using murine epidermal stem cells as a model, we elucidate how cells establish, maintain, and recall inflammatory memory. Specifically, we landscape and functionally interrogate temporal, dynamic changes to chromatin accessibility, histone modifications, and transcription factor binding that occur during inflammation, post-resolution, and in memory recall following injury. We unearth an essential, unifying role for the general stress-responsive transcription factor FOS, which partners with JUN and cooperates with stimulus-specific STAT3 to establish memory; JUN then remains with other homeostatic factors on memory domains, facilitating rapid FOS re-recruitment and gene re-activation upon diverse secondary challenges. Extending our findings, we offer a comprehensive, potentially universal mechanism behind inflammatory memory and less discriminate recall phenomena with profound implications for tissue fitness in health and disease.
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Affiliation(s)
- Samantha B. Larsen
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA,New York University School of Medicine, Neuroscience Institute, New York, NY 10016, USA
| | - Christopher J. Cowley
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Sairaj M. Sajjath
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Douglas Barrows
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Yihao Yang
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Thomas S. Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Elaine Fuchs
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA,Lead Contact to whom correspondence should be addressed during the review process:
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36
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Yu Y, Zhang X, Liu F, Zhu P, Zhang L, Peng Y, Yan X, Li Y, Hua P, Liu C, Li Q, Zhang L. A stress-induced miR-31-CLOCK-ERK pathway is a key driver and therapeutic target for skin aging. NATURE AGING 2021; 1:795-809. [PMID: 37117623 DOI: 10.1038/s43587-021-00094-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/30/2021] [Indexed: 04/30/2023]
Abstract
Regressive changes in epithelial stem cells underlie mammalian skin aging, but the driving mechanisms are not well understood. Here, we report that mouse skin hair follicle stem cell (HFSC) aging is initiated by their intrinsic upregulation of miR-31, a microRNA that can be induced by physical injury or genotoxic stress and is also strongly upregulated in aged human skin epithelium. Using transgenic and conditional knockout mouse models plus a lineage-tracing technique, we show that miR-31 acts as a key driver of HFSC aging by directly targeting Clock, a core circadian clock gene whose deregulation activates a MAPK/ERK cascade to induce HFSC depletion via transepidermal elimination. Notably, blocking this pathway by either conditional miR-31 ablation or clinically approved MAPK/ERK inhibitors provides safe and effective protection against skin aging, enlightening a promising therapeutic avenue for treating skin aging and other genotoxic stress-induced skin conditions such as radiodermatitis.
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Affiliation(s)
- Yao Yu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xia Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fengzhen Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Peiying Zhu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liping Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - You Peng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinyu Yan
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yin Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Peng Hua
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Caiyue Liu
- Department of Plastic & Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Qingfeng Li
- Department of Plastic & Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Liang Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
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Mangold K, Mašek J, He J, Lendahl U, Fuchs E, Andersson ER. Highly efficient manipulation of nervous system gene expression with NEPTUNE. CELL REPORTS METHODS 2021; 1:100043. [PMID: 34557863 PMCID: PMC8457050 DOI: 10.1016/j.crmeth.2021.100043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/07/2021] [Accepted: 06/11/2021] [Indexed: 11/03/2022]
Abstract
Genetic loss and gain of function in mice have typically been studied by using knockout or knockin mice that take months to years to generate. To address this problem for the nervous system, we developed NEPTUNE (NEural Plate Targeting by in Utero NanoinjEction) to rapidly and flexibly transduce the neural plate with virus prior to neurulation, and thus manipulate the future nervous system. Stable integration in >95% of cells in the brain enabled long-term overexpression, and conditional expression was achieved by using cell-type-specific MiniPromoters. Knockdown of Olig2 by using NEPTUNE recapitulated the phenotype of Olig2 -/- embryos. We used NEPTUNE to investigate Sptbn2, mutations in which cause spinocerebellar ataxia type 5. Sptbn2 knockdown induced dose-dependent defects in the neural tube, embryonic turning, and abdominal wall closure, previously unreported functions for Sptbn2. NEPTUNE thus offers a rapid and cost-effective technique to test gene function in the nervous system and can reveal phenotypes incompatible with life.
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Affiliation(s)
- Katrin Mangold
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Jan Mašek
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14183, Sweden
| | - Jingyan He
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Urban Lendahl
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Elaine Fuchs
- Laboratory of Mammalian Cell Biology and Development, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Emma R. Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 17177, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14183, Sweden
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Maru Y, Tanaka N, Tatsumi Y, Nakamura Y, Itami M, Hippo Y. Kras activation in endometrial organoids drives cellular transformation and epithelial-mesenchymal transition. Oncogenesis 2021; 10:46. [PMID: 34172714 PMCID: PMC8233399 DOI: 10.1038/s41389-021-00337-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/04/2021] [Accepted: 06/10/2021] [Indexed: 01/06/2023] Open
Abstract
KRAS, an oncogene, is frequently activated by mutations in many cancers. Kras-driven adenocarcinoma development in the lung, pancreas, and biliary tract has been extensively studied using gene targeting in mice. By taking the organoid- and allograft-based genetic approach to these organs, essentially the same results as in vivo models were obtained in terms of tumor development. To verify the applicability of this approach to other organs, we investigated whether the combination of Kras activation and Pten inactivation, which gives rise to endometrial tumors in mice, could transform murine endometrial organoids in the subcutis of immunodeficient mice. We found that in KrasG12D-expressing endometrial organoids, Pten knockdown did not confer tumorigenicity, but Cdkn2a knockdown or Trp53 deletion led to the development of carcinosarcoma (CS), a rare, aggressive tumor comprising both carcinoma and sarcoma. Although they originated from epithelial cells, some CS cells expressed both epithelial and mesenchymal markers. Upon inoculation in immunodeficient mice, tumor-derived round organoids developed carcinoma or CS, whereas spindle-shaped organoids formed monophasic sarcoma only, suggesting an irreversible epithelial-mesenchymal transition during the transformation of endometrial cells and progression. As commonly observed in mutant Kras-driven tumors, the deletion of the wild-type Kras allele was identified in most induced tumors, whereas some epithelial cells in CS-derived organoids were unexpectedly negative for KrasG12D. Collectively, we showed that the oncogenic potential of KrasG12D and the histological features of derived tumors are context-dependent and varies according to the organ type and experimental settings. Our findings provide novel insights into the mechanisms underlying tissue-specific Kras-driven tumorigenesis.
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Affiliation(s)
- Yoshiaki Maru
- Department of Molecular Carcinogenesis, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Naotake Tanaka
- Department of Gynecology, Chiba Cancer Center, Chiba, Japan
| | - Yasutoshi Tatsumi
- Division of Oncogenomics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Yuki Nakamura
- Division of Oncogenomics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Makiko Itami
- Division of Surgical Pathology, Chiba Cancer Center, Chiba, Japan
| | - Yoshitaka Hippo
- Department of Molecular Carcinogenesis, Chiba Cancer Center Research Institute, Chiba, Japan.
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Liu F, Zhang X, Peng Y, Zhang L, Yu Y, Hua P, Zhu P, Yan X, Li Y, Zhang L. miR-24 controls the regenerative competence of hair follicle progenitors by targeting Plk3. Cell Rep 2021; 35:109225. [PMID: 34107258 DOI: 10.1016/j.celrep.2021.109225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/17/2021] [Accepted: 05/13/2021] [Indexed: 01/04/2023] Open
Abstract
Maintaining a suitable level of sensitivity to environmental cues is crucial for proper function of adult stem cells. Here, we explore how the intrinsic sensitivity of skin hair follicle (HF) progenitors to growth stimuli is dynamically regulated. We discover miR-24 is an miRNA whose expression in HF progenitors inversely correlates with their growth potency in vivo. We show that its upregulation in adult skin epithelium leads to blunted responses of HF progenitors to growth cues and retards hair regeneration, while its conditional ablation leads to hyper-sensitized growth responsiveness of HF progenitors and precocious hair regeneration. Mechanistically, we find that miR-24 limits the intrinsic growth competence of HF progenitor by directly targeting Plk3, whose downregulation leads to reduced expression of CCNE1, a key cyclin for cell-cycle entry. These findings reveal an miRNA-mediated dynamic and cell-intrinsic mechanism used by HF progenitors to adapt their regenerative competence for different physiological conditions.
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Affiliation(s)
- Fengzhen Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xia Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - You Peng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liping Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yao Yu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Peng Hua
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Peiying Zhu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyu Yan
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yin Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liang Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China; Department of Plastic & Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China.
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40
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Kameneva P, Artemov AV, Kastriti ME, Faure L, Olsen TK, Otte J, Erickson A, Semsch B, Andersson ER, Ratz M, Frisén J, Tischler AS, de Krijger RR, Bouderlique T, Akkuratova N, Vorontsova M, Gusev O, Fried K, Sundström E, Mei S, Kogner P, Baryawno N, Kharchenko PV, Adameyko I. Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin. Nat Genet 2021; 53:694-706. [PMID: 33833454 PMCID: PMC7610777 DOI: 10.1038/s41588-021-00818-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 02/16/2021] [Indexed: 02/01/2023]
Abstract
Characterization of the progression of cellular states during human embryogenesis can provide insights into the origin of pediatric diseases. We examined the transcriptional states of neural crest- and mesoderm-derived lineages differentiating into adrenal glands, kidneys, endothelium and hematopoietic tissue between post-conception weeks 6 and 14 of human development. Our results reveal transitions connecting the intermediate mesoderm and progenitors of organ primordia, the hematopoietic system and endothelial subtypes. Unexpectedly, by using a combination of single-cell transcriptomics and lineage tracing, we found that intra-adrenal sympathoblasts at that stage are directly derived from nerve-associated Schwann cell precursors, similarly to local chromaffin cells, whereas the majority of extra-adrenal sympathoblasts arise from the migratory neural crest. In humans, this process persists during several weeks of development within the large intra-adrenal ganglia-like structures, which may also serve as reservoirs of originating cells in neuroblastoma.
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Affiliation(s)
- Polina Kameneva
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
| | - Artem V Artemov
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Maria Eleni Kastriti
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Department of Molecular Neurosciences, Medical University of Vienna, Vienna, Austria
| | - Louis Faure
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Thale K Olsen
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Jörg Otte
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Alek Erickson
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
| | - Bettina Semsch
- Department of Comparative Medicine, Karolinska Institutet, Solna, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Emma R Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Arthur S Tischler
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology CS, Utrecht, the Netherlands
- Deptartment of Pathology, University Medical Center Utrecht CX, Utrecht, the Netherlands
| | - Thibault Bouderlique
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Natalia Akkuratova
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
- Institute of Translational Biomedicine, St. Petersburg University, St. Petersburg, Russia
| | - Maria Vorontsova
- Endocrinology Research Centre, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russian Federation
- Institute for Regenerative Medicine, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Oleg Gusev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
- RIKEN Innovation Center, RIKEN, Yokohama, Japan
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - Kaj Fried
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Erik Sundström
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | - Shenglin Mei
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Per Kogner
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Ninib Baryawno
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden.
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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Tomizawa RR, Tabin CJ, Atsuta Y. In ovo electroporation of chicken limb bud ectoderm: Electroporation to chick limb ectoderm. Dev Dyn 2021; 251:1628-1638. [PMID: 33899315 DOI: 10.1002/dvdy.352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Deciphering how ectodermal tissues form, and how they maintain their integrity, is crucial for understanding epidermal development and pathogenesis. However, lack of simple and rapid gene manipulation techniques limits genetic studies to elucidate mechanisms underlying these events. RESULTS Here we describe an easy method for electroporation of chick limb bud ectoderm enabling gene manipulation during ectoderm development and wound healing. Taking advantage of a small parafilm well that constrains DNA plasmids locally and the fact that the limb ectoderm arises from a defined site, we target the limb ectoderm forming region by in ovo electroporation. This approach results in focal and efficient transgenesis of the limb ectodermal cells. Further, using a previously described Msx2 promoter, gene manipulation can be specifically targeted to the apical ectodermal ridge (AER), a signaling center regulating limb development. Using the electroporation technique to deliver a fluorescent marker into the embryonic limb ectoderm, we show its utility in performing time-lapse imaging during wound healing. This analysis revealed previously unrecognized dynamic remodeling of the actin cytoskeleton and lamellipodia formation at the edges of the wound. We find that the lamellipodia formation requires activity of Rac1 GTPase, suggesting its necessity for wound closure. CONCLUSION Our method is simple and easy. Thus, it would permit high throughput tests for gene function during limb ectodermal development and wound healing.
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Affiliation(s)
| | | | - Yuji Atsuta
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
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42
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Repeated mutation of a developmental enhancer contributed to human thermoregulatory evolution. Proc Natl Acad Sci U S A 2021; 118:2021722118. [PMID: 33850016 PMCID: PMC8072367 DOI: 10.1073/pnas.2021722118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Humans sweat to cool their bodies and have by far the highest eccrine sweat gland density among primates. Humans' high eccrine gland density has long been recognized as a hallmark human evolutionary adaptation, but its genetic basis has been unknown. In humans, expression of the Engrailed 1 (EN1) transcription factor correlates with the onset of eccrine gland formation. In mice, regulation of ectodermal En1 expression is a major determinant of natural variation in eccrine gland density between strains, and increased En1 expression promotes the specification of more eccrine glands. Here, we show that regulation of EN1 has evolved specifically on the human lineage to promote eccrine gland formation. Using comparative genomics and validation of ectodermal enhancer activity in mice, we identified a human EN1 skin enhancer, hECE18. We showed that multiple epistatically interacting derived substitutions in the human ECE18 enhancer increased its activity compared with nonhuman ape orthologs in cultured keratinocytes. Repression of hECE18 in human cultured keratinocytes specifically attenuated EN1 expression, indicating this element positively regulates EN1 in this context. In a humanized enhancer knock-in mouse, hECE18 increased developmental En1 expression in the skin to induce the formation of more eccrine glands. Our study uncovers a genetic basis contributing to the evolution of one of the most singular human adaptations and implicates multiple interacting mutations in a single enhancer as a mechanism for human evolutionary change.
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43
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Ex utero mouse embryogenesis from pre-gastrulation to late organogenesis. Nature 2021; 593:119-124. [PMID: 33731940 DOI: 10.1038/s41586-021-03416-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 03/04/2021] [Indexed: 12/25/2022]
Abstract
The mammalian body plan is established shortly after the embryo implants into the maternal uterus, and our understanding of post-implantation developmental processes remains limited. Although pre- and peri-implantation mouse embryos are routinely cultured in vitro1,2, approaches for the robust culture of post-implantation embryos from egg cylinder stages until advanced organogenesis remain to be established. Here we present highly effective platforms for the ex utero culture of post-implantation mouse embryos, which enable the appropriate development of embryos from before gastrulation (embryonic day (E) 5.5) until the hindlimb formation stage (E11). Late gastrulating embryos (E7.5) are grown in three-dimensional rotating bottles, whereas extended culture from pre-gastrulation stages (E5.5 or E6.5) requires a combination of static and rotating bottle culture platforms. Histological, molecular and single-cell RNA sequencing analyses confirm that the ex utero cultured embryos recapitulate in utero development precisely. This culture system is amenable to the introduction of a variety of embryonic perturbations and micro-manipulations, the results of which can be followed ex utero for up to six days. The establishment of a system for robustly growing normal mouse embryos ex utero from pre-gastrulation to advanced organogenesis represents a valuable tool for investigating embryogenesis, as it eliminates the uterine barrier and allows researchers to mechanistically interrogate post-implantation morphogenesis and artificial embryogenesis in mammals.
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Sandoval M, Ying Z, Beronja S. Interplay of opposing fate choices stalls oncogenic growth in murine skin epithelium. eLife 2021; 10:54618. [PMID: 33393458 PMCID: PMC7817173 DOI: 10.7554/elife.54618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 12/31/2020] [Indexed: 12/18/2022] Open
Abstract
Skin epithelium can accumulate a high burden of oncogenic mutations without morphological or functional consequences. To investigate the mechanism of oncogenic tolerance, we induced HrasG12V in single murine epidermal cells and followed them long term. We observed that HrasG12V promotes an early and transient clonal expansion driven by increased progenitor renewal that is replaced with an increase in progenitor differentiation leading to reduced growth. We attribute this dynamic effect to emergence of two populations within oncogenic clones: renewing progenitors along the edge and differentiating ones within the central core. As clone expansion is accompanied by progressive enlargement of the core and diminishment of the edge compartment, the intraclonal competition between the two populations results in stabilized oncogenic growth. To identify the molecular mechanism of HrasG12V-driven differentiation, we screened known Ras-effector in vivo and identified Rassf5 as a novel regulator of progenitor fate choice that is necessary and sufficient for oncogene-specific differentiation.
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Affiliation(s)
- Madeline Sandoval
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, United States
| | - Zhe Ying
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Slobodan Beronja
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
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Padmanabhan K, Grobe H, Cohen J, Soffer A, Mahly A, Adir O, Zaidel-Bar R, Luxenburg C. Thymosin β4 is essential for adherens junction stability and epidermal planar cell polarity. Development 2020; 147:dev.193425. [PMID: 33310787 PMCID: PMC7758630 DOI: 10.1242/dev.193425] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/27/2020] [Indexed: 01/19/2023]
Abstract
Planar cell polarity (PCP) is essential for tissue morphogenesis and homeostasis; however, the mechanisms that orchestrate the cell shape and packing dynamics required to establish PCP are poorly understood. Here, we identified a major role for the globular (G)-actin-binding protein thymosin-β4 (TMSB4X) in PCP establishment and cell adhesion in the developing epidermis. Depletion of Tmsb4x in mouse embryos hindered eyelid closure and hair-follicle angling owing to PCP defects. Tmsb4x depletion did not preclude epidermal cell adhesion in vivo or in vitro; however, it resulted in abnormal structural organization and stability of adherens junction (AJ) due to defects in filamentous (F)-actin and G-actin distribution. In cultured keratinocytes, TMSB4X depletion increased the perijunctional G/F-actin ratio and decreased G-actin incorporation into junctional actin networks, but it did not change the overall actin expression level or cellular F-actin content. A pharmacological treatment that increased the G/F-actin ratio and decreased actin polymerization mimicked the effects of Tmsb4x depletion on both AJs and PCP. Our results provide insights into the regulation of the actin pool and its involvement in AJ function and PCP establishment. Highlighted Article: By regulating actin pool distribution and incorporation into junctional actin networks, thymosin β4 regulates cell–cell adhesion, planar cell polarity and epidermal morphogenesis.
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Affiliation(s)
- Krishnanand Padmanabhan
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Hanna Grobe
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Jonathan Cohen
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Arad Soffer
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Adnan Mahly
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Orit Adir
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Ronen Zaidel-Bar
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Chen Luxenburg
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
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Functional Screening Techniques to Identify Long Non-Coding RNAs as Therapeutic Targets in Cancer. Cancers (Basel) 2020; 12:cancers12123695. [PMID: 33317042 PMCID: PMC7763270 DOI: 10.3390/cancers12123695] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Long non-coding RNAs (lncRNAs) are a recently discovered class of molecules in the cell, with potential to be utilized as therapeutic targets in cancer. A number of lncRNAs have been described to play important roles in tumor progression and drive molecular processes involved in cell proliferation, apoptosis or invasion. However, the vast majority of lncRNAs have not been studied in the context of cancer thus far. With the advent of CRISPR/Cas genome editing, high-throughput functional screening approaches to identify lncRNAs that impact cancer growth are becoming more accessible. Here, we review currently available methods to study hundreds to thousands of lncRNAs in parallel to elucidate their role in tumorigenesis and cancer progression. Abstract Recent technological advancements such as CRISPR/Cas-based systems enable multiplexed, high-throughput screening for new therapeutic targets in cancer. While numerous functional screens have been performed on protein-coding genes to date, long non-coding RNAs (lncRNAs) represent an emerging class of potential oncogenes and tumor suppressors, with only a handful of large-scale screens performed thus far. Here, we review in detail currently available screening approaches to identify new lncRNA drivers of tumorigenesis and tumor progression. We discuss the various approaches of genomic and transcriptional targeting using CRISPR/Cas9, as well as methods to post-transcriptionally target lncRNAs via RNA interference (RNAi), antisense oligonucleotides (ASOs) and CRISPR/Cas13. We discuss potential advantages, caveats and future applications of each method to provide an overview and guide on investigating lncRNAs as new therapeutic targets in cancer.
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Sundara Rajan S, Ludwig KR, Hall KL, Jones TL, Caplen NJ. Cancer biology functional genomics: From small RNAs to big dreams. Mol Carcinog 2020; 59:1343-1361. [PMID: 33043516 PMCID: PMC7702050 DOI: 10.1002/mc.23260] [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: 08/20/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
The year 2021 marks the 20th anniversary of the first publications reporting the discovery of the gene silencing mechanism, RNA interference (RNAi) in mammalian cells. Along with the many studies that delineated the proteins and substrates that form the RNAi pathway, this finding changed our understanding of the posttranscriptional regulation of mammalian gene expression. Furthermore, the development of methods that exploited the RNAi pathway began the technological revolution that eventually enabled the interrogation of mammalian gene function-from a single gene to the whole genome-in only a few days. The needs of the cancer research community have driven much of this progress. In this perspective, we highlight milestones in the development and application of RNAi-based methods to study carcinogenesis. We discuss how RNAi-based functional genetic analysis of exemplar tumor suppressors and oncogenes furthered our understanding of cancer initiation and progression and explore how such studies formed the basis of genome-wide scale efforts to identify cancer or cancer-type specific vulnerabilities, including studies conducted in vivo. Furthermore, we examine how RNAi technologies have revealed new cancer-relevant molecular targets and the implications for cancer of the first RNAi-based drugs. Finally, we discuss the future of functional genetic analysis, highlighting the increasing availability of complementary approaches to analyze cancer gene function.
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Affiliation(s)
- Soumya Sundara Rajan
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Katherine L. Hall
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
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48
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Fiore VF, Krajnc M, Quiroz FG, Levorse J, Pasolli HA, Shvartsman SY, Fuchs E. Mechanics of a multilayer epithelium instruct tumour architecture and function. Nature 2020; 585:433-439. [PMID: 32879493 DOI: 10.1038/s41586-020-2695-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 07/22/2020] [Indexed: 01/24/2023]
Abstract
Loss of normal tissue architecture is a hallmark of oncogenic transformation1. In developing organisms, tissues architectures are sculpted by mechanical forces during morphogenesis2. However, the origins and consequences of tissue architecture during tumorigenesis remain elusive. In skin, premalignant basal cell carcinomas form 'buds', while invasive squamous cell carcinomas initiate as 'folds'. Here, using computational modelling, genetic manipulations and biophysical measurements, we identify the biophysical underpinnings and biological consequences of these tumour architectures. Cell proliferation and actomyosin contractility dominate tissue architectures in monolayer, but not multilayer, epithelia. In stratified epidermis, meanwhile, softening and enhanced remodelling of the basement membrane promote tumour budding, while stiffening of the basement membrane promotes folding. Additional key forces stem from the stratification and differentiation of progenitor cells. Tumour-specific suprabasal stiffness gradients are generated as oncogenic lesions progress towards malignancy, which we computationally predict will alter extensile tensions on the tumour basement membrane. The pathophysiologic ramifications of this prediction are profound. Genetically decreasing the stiffness of basement membranes increases membrane tensions in silico and potentiates the progression of invasive squamous cell carcinomas in vivo. Our findings suggest that mechanical forces-exerted from above and below progenitors of multilayered epithelia-function to shape premalignant tumour architectures and influence tumour progression.
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Affiliation(s)
- Vincent F Fiore
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Matej Krajnc
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.,Jozef Stefan Institute, Ljubljana, Slovenia
| | - Felipe Garcia Quiroz
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - John Levorse
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - H Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
| | - Stanislav Y Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
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49
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Wnt/β-catenin Signaling in Tissue Self-Organization. Genes (Basel) 2020; 11:genes11080939. [PMID: 32823838 PMCID: PMC7464740 DOI: 10.3390/genes11080939] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Across metazoans, animal body structures and tissues exist in robust patterns that arise seemingly out of stochasticity of a few early cells in the embryo. These patterns ensure proper tissue form and function during early embryogenesis, development, homeostasis, and regeneration. Fundamental questions are how these patterns are generated and maintained during tissue homeostasis and regeneration. Though fascinating scientists for generations, these ideas remain poorly understood. Today, it is apparent that the Wnt/β-catenin pathway plays a central role in tissue patterning. Wnt proteins are small diffusible morphogens which are essential for cell type specification and patterning of tissues. In this review, we highlight several mechanisms described where the spatial properties of Wnt/β-catenin signaling are controlled, allowing them to work in combination with other diffusible molecules to control tissue patterning. We discuss examples of this self-patterning behavior during development and adult tissues' maintenance. The combination of new physiological culture systems, mathematical approaches, and synthetic biology will continue to fuel discoveries about how tissues are patterned. These insights are critical for understanding the intricate interplay of core patterning signals and how they become disrupted in disease.
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50
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Cai EY, Kufeld MN, Schuster S, Arora S, Larkin M, Germanos AA, Hsieh AC, Beronja S. Selective Translation of Cell Fate Regulators Mediates Tolerance to Broad Oncogenic Stress. Cell Stem Cell 2020; 27:270-283.e7. [PMID: 32516567 PMCID: PMC7993921 DOI: 10.1016/j.stem.2020.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 03/13/2020] [Accepted: 05/13/2020] [Indexed: 12/23/2022]
Abstract
Human skin tolerates a surprisingly high burden of oncogenic lesions. Although adult epidermis can suppress the expansion of individual mutant clones, the mechanisms behind tolerance to oncogene activation across broader regions of tissue are unclear. Here, we uncover a dynamic translational mechanism that coordinates oncogenic HRAS-induced hyperproliferation with loss of progenitor self-renewal to restrain aberrant growth and tumorigenesis. We identify translation initiator eIF2B5 as a central co-regulator of HRAS proliferation and cell fate choice. By coupling in vivo ribosome profiling with genetic screening, we provide direct evidence that oncogene-induced loss of progenitor self-renewal is driven by eIF2B5-mediated translation of ubiquitination genes. Ubiquitin ligase FBXO32 specifically inhibits epidermal renewal without affecting overall proliferation, thus restraining HRAS-driven tumorigenesis while maintaining normal tissue growth. Thus, oncogene-driven translation is not necessarily inherently tumor promoting but instead can manage widespread oncogenic stress by steering progenitor fate to prolong normal tissue growth.
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Affiliation(s)
- Elise Y Cai
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA
| | - Megan N Kufeld
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Samantha Schuster
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA
| | - Sonali Arora
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Madeline Larkin
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexandre A Germanos
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA
| | - Andrew C Hsieh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Slobodan Beronja
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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