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de Vries ME, Carpinelli MR, Fuller JN, Sutton Y, Partridge DD, Auden A, Anderson PJ, Jane SM, Dworkin S. Grainyhead-like 2 interacts with noggin to regulate tissue fusion in mouse. Development 2024; 151:dev202420. [PMID: 38300806 PMCID: PMC10946436 DOI: 10.1242/dev.202420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
Defective tissue fusion during mammalian embryogenesis results in congenital anomalies, such as exencephaly, spina bifida and cleft lip and/or palate. The highly conserved transcription factor grainyhead-like 2 (Grhl2) is a crucial regulator of tissue fusion, with mouse models lacking GRHL2 function presenting with a fully penetrant open cranial neural tube, facial and abdominal clefting (abdominoschisis), and an open posterior neuropore. Here, we show that GRHL2 interacts with the soluble morphogen protein and bone morphogenetic protein (BMP) inhibitor noggin (NOG) to impact tissue fusion during development. The maxillary prominence epithelium in embryos lacking Grhl2 shows substantial morphological abnormalities and significant upregulation of NOG expression, together with aberrantly distributed pSMAD5-positive cells within the neural crest cell-derived maxillary prominence mesenchyme, indicative of disrupted BMP signalling. Reducing this elevated NOG expression (by generating Grhl2-/-;Nog+/- embryos) results in delayed embryonic lethality, partial tissue fusion rescue, and restoration of tissue form within the craniofacial epithelia. These data suggest that aberrant epithelial maintenance, partially regulated by noggin-mediated regulation of BMP-SMAD pathways, may underpin tissue fusion defects in Grhl2-/- mice.
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Affiliation(s)
- Michael E. de Vries
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria 3004, Australia
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Marina R. Carpinelli
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria 3004, Australia
| | - Jarrad N. Fuller
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Yindi Sutton
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria 3004, Australia
| | - Darren D. Partridge
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria 3004, Australia
| | - Alana Auden
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria 3004, Australia
| | - Peter J. Anderson
- Australian Craniofacial Unit, Women and Children's Hospital, Adelaide, SA 5005, Australia
- Faculty of Health Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, People's Republic of China
| | - Stephen M. Jane
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria 3004, Australia
| | - Sebastian Dworkin
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia
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2
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Pattaroni C, Begka C, Cardwell B, Jaffar J, Macowan M, Harris NL, Westall GP, Marsland BJ. Multi-omics integration reveals a nonlinear signature that precedes progression of lung fibrosis. Clin Transl Immunology 2024; 13:e1485. [PMID: 38269243 PMCID: PMC10807351 DOI: 10.1002/cti2.1485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/11/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
Objectives Idiopathic pulmonary fibrosis (IPF) is a devastating progressive interstitial lung disease with poor outcomes. While decades of research have shed light on pathophysiological mechanisms associated with the disease, our understanding of the early molecular events driving IPF and its progression is limited. With this study, we aimed to model the leading edge of fibrosis using a data-driven approach. Methods Multiple omics modalities (transcriptomics, metabolomics and lipidomics) of healthy and IPF lung explants representing different stages of fibrosis were combined using an unbiased approach. Multi-Omics Factor Analysis of datasets revealed latent factors specifically linked with established fibrotic disease (Factor1) and disease progression (Factor2). Results Features characterising Factor1 comprised well-established hallmarks of fibrotic disease such as defects in surfactant, epithelial-mesenchymal transition, extracellular matrix deposition, mitochondrial dysfunction and purine metabolism. Comparatively, Factor2 identified a signature revealing a nonlinear trajectory towards disease progression. Molecular features characterising Factor2 included genes related to transcriptional regulation of cell differentiation, ciliogenesis and a subset of lipids from the endocannabinoid class. Machine learning models, trained upon the top transcriptomics features of each factor, accurately predicted disease status and progression when tested on two independent datasets. Conclusion This multi-omics integrative approach has revealed a unique signature which may represent the inflection point in disease progression, representing a promising avenue for the identification of therapeutic targets aimed at addressing the progressive nature of the disease.
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Affiliation(s)
- Céline Pattaroni
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Christina Begka
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Bailey Cardwell
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Jade Jaffar
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Matthew Macowan
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Nicola L Harris
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Glen P Westall
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
- Department of Respiratory MedicineAlfred HospitalMelbourneVICAustralia
| | - Benjamin J Marsland
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
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3
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Forrester-Gauntlett B, Peters L, Oback B. Grainyhead-like 2 is required for morphological integrity of mouse embryonic stem cells and orderly formation of inner ear-like organoids. Front Cell Dev Biol 2023; 11:1112069. [PMID: 37745294 PMCID: PMC10513505 DOI: 10.3389/fcell.2023.1112069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Mutations in the transcription factor gene grainyhead-like 2 (GRHL2) are associated with progressive non-syndromic sensorineural deafness autosomal dominant type 28 (DFNA28) in humans. Since complete loss of Grhl2 is lethal in mouse embryos, we studied its role during inner ear pathology and hearing loss in vitro. To this end, we generated different homozygous deletions to knockout Grhl2 in mouse embryonic stem cells (Grhl2-KO ESCs), including some mimicking naturally occurring truncations in the dimerisation domain related to human DFNA28. Under naïve culture conditions, Grhl2-KO cells in suspension were more heterogenous in size and larger than wild-type controls. Adherent Grhl2-KO cells were also larger, with a less uniform shape, flattened, less circular morphology, forming loose monolayer colonies with poorly defined edges. These changes correlated with lower expression of epithelial cadherin Cdh1 but no changes in tight junction markers (Ocln, Tjp2) or other Grhl isoforms (Grhl1, Grhl3). Clonogenicity from single cells, proliferation rates of cell populations and proliferation markers were reduced in Grhl2-KO ESCs. We next induced stepwise directed differentiation of Grhl2-KO ESCs along an otic pathway, giving rise to three-dimensional inner ear-like organoids (IELOs). Quantitative morphometry revealed that Grhl2-KO cells initially formed larger IELOs with a less compacted structure, more eccentric shape and increased surface area. These morphological changes persisted for up to one week. They were partially rescued by forced cell aggregation and fully restored by stably overexpressing exogenous Grhl2 in Grhl2-KO ESCs, indicating that Grhl2 alters cell-cell interactions. On day 8, aggregates were transferred into minimal maturation medium to allow self-guided organogenesis for another two weeks. During this period, Grhl2-KO cells and wild-type controls developed similarly, expressing neural, neuronal and sensory hair cell markers, while maintaining their initial differences in size and shape. In summary, Grhl2 is required for morphological maintenance of ESCs and orderly formation of IELOs, consistent with an essential role in organising epithelial integrity during inner ear development. Our findings validate quantitative morphometry as a useful, non-invasive screening method for molecular phenotyping of candidate mutations during organoid development.
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Affiliation(s)
- Blaise Forrester-Gauntlett
- Animal Biotech, AgResearch, Hamilton, New Zealand
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Linda Peters
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Björn Oback
- Animal Biotech, AgResearch, Hamilton, New Zealand
- School of Science, University of Waikato, Hamilton, New Zealand
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
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4
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Wen J, Qin G, Jiang Z, Lin Z, Zhou R, Dai H, Xu Z, Chen W, Song Q. E74‑like ETS transcription factor 5 facilitates cell proliferation through regulating the expression of adenomatous polyposis coli 2 in non‑small cell lung cancer. Int J Mol Med 2023; 52:75. [PMID: 37449511 PMCID: PMC10555483 DOI: 10.3892/ijmm.2023.5278] [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: 03/01/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023] Open
Abstract
E74‑like ETS transcription factor 5 (ELF5) is known to regulate the specification and differentiation of epithelial cells in the embryonic lung. However, the pathological function of ELF5 in lung cancer has yet to be fully elucidated. In the present study, the expression of ELF5 was found to be significantly higher in lung adenocarcinoma compared with that in corresponding adjacent normal tissues. Subsequently, cell and animal experiments were performed to investigate the role of ELF5 in lung adenocarcinoma cells. The results indicated that the overexpression of ELF5 increased the proliferation of lung adenocarcinoma cells, whereas, by contrast, a reduction in the expression of ELF5 led to a decrease in their proliferation. Mechanistically, the hypothesis is advanced that ELF5 can promote lung cancer cell proliferation through inhibiting adenomatous polyposis coli 2 and increasing the expression of cyclin D1, which is a critical downstream target of the Wnt pathway. Taken together, these findings support the notion that ELF5 exerts an essential role in the proliferation of lung adenocarcinoma cells and may be a therapeutic target for the treatment of lung adenocarcinoma.
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Affiliation(s)
- Jing Wen
- Department of Radiology, Nanfang Hospital, Southern Medical University
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515
| | - Genggeng Qin
- Department of Radiology, Nanfang Hospital, Southern Medical University
| | - Zhaojing Jiang
- Department of Radiation Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280
| | - Zixun Lin
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515
| | - Ruixin Zhou
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515
| | - Hui Dai
- Hospital Office, Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou, Jiangxi 341000
| | - Zhanfa Xu
- Department of Radiology, Nanfang Hospital, Southern Medical University
| | - Weiguo Chen
- Department of Radiology, Nanfang Hospital, Southern Medical University
| | - Qiancheng Song
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515
- Department of Neurosurgery, Institute of Brain Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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5
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Crane-Smith Z, De Castro SCP, Nikolopoulou E, Wolujewicz P, Smedley D, Lei Y, Mather E, Santos C, Hopkinson M, Pitsillides AA, Finnell RH, Ross ME, Copp AJ, Greene NDE. A non-coding insertional mutation of Grhl2 causes gene over-expression and multiple structural anomalies including cleft palate, spina bifida and encephalocele. Hum Mol Genet 2023; 32:2681-2692. [PMID: 37364051 PMCID: PMC10460492 DOI: 10.1093/hmg/ddad094] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/19/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Orofacial clefts, including cleft lip and palate (CL/P) and neural tube defects (NTDs) are among the most common congenital anomalies, but knowledge of the genetic basis of these conditions remains incomplete. The extent to which genetic risk factors are shared between CL/P, NTDs and related anomalies is also unclear. While identification of causative genes has largely focused on coding and loss of function mutations, it is hypothesized that regulatory mutations account for a portion of the unidentified heritability. We found that excess expression of Grainyhead-like 2 (Grhl2) causes not only spinal NTDs in Axial defects (Axd) mice but also multiple additional defects affecting the cranial region. These include orofacial clefts comprising midline cleft lip and palate and abnormalities of the craniofacial bones and frontal and/or basal encephalocele, in which brain tissue herniates through the cranium or into the nasal cavity. To investigate the causative mutation in the Grhl2Axd strain, whole genome sequencing identified an approximately 4 kb LTR retrotransposon insertion that disrupts the non-coding regulatory region, lying approximately 300 base pairs upstream of the 5' UTR. This insertion also lies within a predicted long non-coding RNA, oriented on the reverse strand, which like Grhl2 is over-expressed in Axd (Grhl2Axd) homozygous mutant embryos. Initial analysis of the GRHL2 upstream region in individuals with NTDs or cleft palate revealed rare or novel variants in a small number of cases. We hypothesize that mutations affecting the regulation of GRHL2 may contribute to craniofacial anomalies and NTDs in humans.
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Affiliation(s)
- Zoe Crane-Smith
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Sandra C P De Castro
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Evanthia Nikolopoulou
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Paul Wolujewicz
- Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
| | - Damian Smedley
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Emma Mather
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Chloe Santos
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Mark Hopkinson
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London NW1 0TU, UK
| | - Andrew A Pitsillides
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London NW1 0TU, UK
| | | | - Richard H Finnell
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - M Elisabeth Ross
- Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
| | - Andrew J Copp
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Nicholas D E Greene
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
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6
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Willis TL, Lodge EJ, Andoniadou CL, Yianni V. Cellular interactions in the pituitary stem cell niche. Cell Mol Life Sci 2022; 79:612. [PMID: 36451046 PMCID: PMC9712314 DOI: 10.1007/s00018-022-04612-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 09/27/2022] [Accepted: 10/25/2022] [Indexed: 12/03/2022]
Abstract
Stem cells in the anterior pituitary gland can give rise to all resident endocrine cells and are integral components for the appropriate development and subsequent maintenance of the organ. Located in discreet niches within the gland, stem cells are involved in bi-directional signalling with their surrounding neighbours, interactions which underpin pituitary gland homeostasis and response to organ challenge or physiological demand. In this review we highlight core signalling pathways that steer pituitary progenitors towards specific endocrine fate decisions throughout development. We further elaborate on those which are conserved in the stem cell niche postnatally, including WNT, YAP/TAZ and Notch signalling. Furthermore, we have collated a directory of single cell RNA sequencing studies carried out on pituitaries across multiple organisms, which have the potential to provide a vast database to study stem cell niche components in an unbiased manner. Reviewing published data, we highlight that stem cells are one of the main signalling hubs within the anterior pituitary. In future, coupling single cell sequencing approaches with genetic manipulation tools in vivo, will enable elucidation of how previously understudied signalling pathways function within the anterior pituitary stem cell niche.
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Affiliation(s)
- Thea L Willis
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Emily J Lodge
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Cynthia L Andoniadou
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK.
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
| | - Val Yianni
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK.
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7
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Gasperoni JG, Fuller JN, Darido C, Wilanowski T, Dworkin S. Grainyhead-like (Grhl) Target Genes in Development and Cancer. Int J Mol Sci 2022; 23:ijms23052735. [PMID: 35269877 PMCID: PMC8911041 DOI: 10.3390/ijms23052735] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 12/12/2022] Open
Abstract
Grainyhead-like (GRHL) factors are essential, highly conserved transcription factors (TFs) that regulate processes common to both natural cellular behaviours during embryogenesis, and de-regulation of growth and survival pathways in cancer. Serving to drive the transcription, and therefore activation of multiple co-ordinating pathways, the three GRHL family members (GRHL1-3) are a critical conduit for modulating the molecular landscape that guides cellular decision-making processes during proliferation, epithelial-mesenchymal transition (EMT) and migration. Animal models and in vitro approaches harbouring GRHL loss or gain-of-function are key research tools to understanding gene function, which gives confidence that resultant phenotypes and cellular behaviours may be translatable to humans. Critically, identifying and characterising the target genes to which these factors bind is also essential, as they allow us to discover and understand novel genetic pathways that could ultimately be used as targets for disease diagnosis, drug discovery and therapeutic strategies. GRHL1-3 and their transcriptional targets have been shown to drive comparable cellular processes in Drosophila, C. elegans, zebrafish and mice, and have recently also been implicated in the aetiology and/or progression of a number of human congenital disorders and cancers of epithelial origin. In this review, we will summarise the state of knowledge pertaining to the role of the GRHL family target genes in both development and cancer, primarily through understanding the genetic pathways transcriptionally regulated by these factors across disparate disease contexts.
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Affiliation(s)
- Jemma G. Gasperoni
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (J.G.G.); (J.N.F.)
| | - Jarrad N. Fuller
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (J.G.G.); (J.N.F.)
| | - Charbel Darido
- The Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia;
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tomasz Wilanowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland;
| | - Sebastian Dworkin
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (J.G.G.); (J.N.F.)
- Correspondence:
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8
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Khattar D, Fernandes S, Snowball J, Guo M, Gillen MC, Jain SS, Sinner D, Zacharias W, Swarr DT. PI3K signaling specifies proximal-distal fate by driving a developmental gene regulatory network in SOX9+ mouse lung progenitors. eLife 2022; 11:67954. [PMID: 35976093 PMCID: PMC9427112 DOI: 10.7554/elife.67954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
The tips of the developing respiratory buds are home to important progenitor cells marked by the expression of SOX9 and ID2. Early in embryonic development (prior to E13.5), SOX9+progenitors are multipotent, generating both airway and alveolar epithelium, but are selective progenitors of alveolar epithelial cells later in development. Transcription factors, including Sox9, Etv5, Irx, Mycn, and Foxp1/2 interact in complex gene regulatory networks to control proliferation and differentiation of SOX9+progenitors. Molecular mechanisms by which these transcription factors and other signaling pathways control chromatin state to establish and maintain cell-type identity are not well-defined. Herein, we analyze paired gene expression (RNA-Seq) and chromatin accessibility (ATAC-Seq) data from SOX9+ epithelial progenitor cells (EPCs) during embryonic development in Mus musculus. Widespread changes in chromatin accessibility were observed between E11.5 and E16.5, particularly at distal cis-regulatory elements (e.g. enhancers). Gene regulatory network (GRN) inference identified a common SOX9+ progenitor GRN, implicating phosphoinositide 3-kinase (PI3K) signaling in the developmental regulation of SOX9+ progenitor cells. Consistent with this model, conditional ablation of PI3K signaling in the developing lung epithelium in mouse resulted in an expansion of the SOX9+ EPC population and impaired airway epithelial cell differentiation. These data demonstrate that PI3K signaling is required for epithelial patterning during lung organogenesis, and emphasize the combinatorial power of paired RNA and ATAC seq in defining regulatory networks in development.
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Affiliation(s)
- Divya Khattar
- Department of Pediatrics, University of CincinnatiCincinnatiUnited States
| | - Sharlene Fernandes
- Perinatal Institute, Cincinnati Children's Hospital Medical CenterCincinnatiUnited States,Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical CenterWinston-SalemUnited States
| | - John Snowball
- Perinatal Institute, Cincinnati Children's Hospital Medical CenterCincinnatiUnited States,Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical CenterWinston-SalemUnited States
| | - Minzhe Guo
- Perinatal Institute, Cincinnati Children's Hospital Medical CenterCincinnatiUnited States,Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical CenterWinston-SalemUnited States
| | - Matthew C Gillen
- Department of Pediatrics, University of CincinnatiCincinnatiUnited States
| | - Suchi Singh Jain
- Perinatal Institute, Cincinnati Children's Hospital Medical CenterCincinnatiUnited States,Wake Forest UniversityWinston-SalemUnited States
| | - Debora Sinner
- Perinatal Institute, Cincinnati Children's Hospital Medical CenterCincinnatiUnited States,Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical CenterWinston-SalemUnited States,Department of Pediatrics, University of CincinnatiCincinnatiUnited States
| | - William Zacharias
- Perinatal Institute, Cincinnati Children's Hospital Medical CenterCincinnatiUnited States,Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical CenterWinston-SalemUnited States,Department of Medicine, University of CincinnatiCincinnatiUnited States
| | - Daniel T Swarr
- Department of Pediatrics, University of CincinnatiCincinnatiUnited States,Perinatal Institute, Cincinnati Children's Hospital Medical CenterCincinnatiUnited States,Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical CenterWinston-SalemUnited States,Department of Pediatrics, University of CincinnatiCincinnatiUnited States
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9
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Quintanal-Villalonga A, Taniguchi H, Zhan YA, Hasan MM, Chavan SS, Meng F, Uddin F, Allaj V, Manoj P, Shah NS, Chan JM, Ciampricotti M, Chow A, Offin M, Ray-Kirton J, Egger JD, Bhanot UK, Linkov I, Asher M, Roehrl MH, Ventura K, Qiu J, de Stanchina E, Chang JC, Rekhtman N, Houck-Loomis B, Koche RP, Yu HA, Sen T, Rudin CM. Comprehensive molecular characterization of lung tumors implicates AKT and MYC signaling in adenocarcinoma to squamous cell transdifferentiation. J Hematol Oncol 2021; 14:170. [PMID: 34656143 PMCID: PMC8520275 DOI: 10.1186/s13045-021-01186-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/04/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Lineage plasticity, the ability to transdifferentiate among distinct phenotypic identities, facilitates therapeutic resistance in cancer. In lung adenocarcinomas (LUADs), this phenomenon includes small cell and squamous cell (LUSC) histologic transformation in the context of acquired resistance to targeted inhibition of driver mutations. LUAD-to-LUSC transdifferentiation, occurring in up to 9% of EGFR-mutant patients relapsed on osimertinib, is associated with notably poor prognosis. We hypothesized that multi-parameter profiling of the components of mixed histology (LUAD/LUSC) tumors could provide insight into factors licensing lineage plasticity between these histologies. METHODS We performed genomic, epigenomics, transcriptomics and protein analyses of microdissected LUAD and LUSC components from mixed histology tumors, pre-/post-transformation tumors and reference non-transformed LUAD and LUSC samples. We validated our findings through genetic manipulation of preclinical models in vitro and in vivo and performed patient-derived xenograft (PDX) treatments to validate potential therapeutic targets in a LUAD PDX model acquiring LUSC features after osimertinib treatment. RESULTS Our data suggest that LUSC transdifferentiation is primarily driven by transcriptional reprogramming rather than mutational events. We observed consistent relative upregulation of PI3K/AKT, MYC and PRC2 pathway genes. Concurrent activation of PI3K/AKT and MYC induced squamous features in EGFR-mutant LUAD preclinical models. Pharmacologic inhibition of EZH1/2 in combination with osimertinib prevented relapse with squamous-features in an EGFR-mutant patient-derived xenograft model, and inhibition of EZH1/2 or PI3K/AKT signaling re-sensitized resistant squamous-like tumors to osimertinib. CONCLUSIONS Our findings provide the first comprehensive molecular characterization of LUSC transdifferentiation, suggesting putative drivers and potential therapeutic targets to constrain or prevent lineage plasticity.
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Affiliation(s)
- Alvaro Quintanal-Villalonga
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA.
| | - Hirokazu Taniguchi
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Yingqian A Zhan
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Maysun M Hasan
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta S Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fanli Meng
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fathema Uddin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Viola Allaj
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Parvathy Manoj
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Nisargbhai S Shah
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Joseph M Chan
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Metamia Ciampricotti
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Andrew Chow
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Michael Offin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Jordana Ray-Kirton
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacklynn D Egger
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Umesh K Bhanot
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Linkov
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marina Asher
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael H Roehrl
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katia Ventura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan Qiu
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jason C Chang
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natasha Rekhtman
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian Houck-Loomis
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Helena A Yu
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
- Weill Cornell Medical College, 1275 York Avenue, New York, NY, 10065, USA
| | - Triparna Sen
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA.
- Weill Cornell Medical College, 1275 York Avenue, New York, NY, 10065, USA.
| | - Charles M Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA.
- Weill Cornell Medical College, 1275 York Avenue, New York, NY, 10065, USA.
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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10
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Deng Z, Cangkrama M, Butt T, Jane SM, Carpinelli MR. Grainyhead-like transcription factors: guardians of the skin barrier. Vet Dermatol 2021; 32:553-e152. [PMID: 33843098 DOI: 10.1111/vde.12956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/24/2020] [Accepted: 12/14/2020] [Indexed: 01/02/2023]
Abstract
There has been selective pressure to maintain a skin barrier since terrestrial animals evolved 360 million years ago. These animals acquired an unique integumentary system with a keratinized, stratified, squamous epithelium surface barrier. The barrier protects against dehydration and entry of microbes and toxins. The skin barrier centres on the stratum corneum layer of the epidermis and consists of cornified envelopes cemented by the intercorneocyte lipid matrix. Multiple components of the barrier undergo cross-linking by transglutaminase (TGM) enzymes, while keratins provide additional mechanical strength. Cellular tight junctions also are crucial for barrier integrity. The grainyhead-like (GRHL) transcription factors regulate the formation and maintenance of the integument in diverse species. GRHL3 is essential for formation of the skin barrier during embryonic development, whereas GRHL1 maintains the skin barrier postnatally. This is achieved by transactivation of Tgm1 and Tgm5, respectively. In addition to its barrier function, GRHL3 plays key roles in wound repair and as an epidermal tumour suppressor. In its former role, GRHL3 activates the planar cell polarity signalling pathway to mediate wound healing by providing directional migration cues. In squamous epithelium, GRHL3 regulates the balance between proliferation and differentiation, and its loss induces squamous cell carcinoma (SCC). In the skin, this is mediated through increased expression of MIR21, which reduces the expression levels of GRHL3 and its direct target, PTEN, leading to activation of the PI3K-AKT signalling pathway. These data position the GRHL family as master regulators of epidermal homeostasis across a vast gulf of evolutionary history.
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Affiliation(s)
- Zihao Deng
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Michael Cangkrama
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Tariq Butt
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Stephen M Jane
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Marina R Carpinelli
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
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11
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de Vries M, Owens HG, Carpinelli MR, Partridge D, Kersbergen A, Sutherland KD, Auden A, Anderson PJ, Jane SM, Dworkin S. Delineating the roles of Grhl2 in craniofacial development through tissue-specific conditional deletion and epistasis approaches in mouse. Dev Dyn 2021; 250:1191-1209. [PMID: 33638290 DOI: 10.1002/dvdy.322] [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: 12/15/2020] [Revised: 01/31/2021] [Accepted: 02/20/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The highly conserved Grainyhead-like (Grhl) family of transcription factors play critical roles in the development of the neural tube and craniofacial skeleton. In particular, deletion of family member Grainyhead-like 2 (Grhl2) leads to mid-gestational embryonic lethality, maxillary clefting, abdominoschisis, and both cranial and caudal neural tube closure defects. These highly pleiotropic and systemic defects suggest that Grhl2 plays numerous critical developmental roles to ensure correct morphogenesis and patterning. RESULTS Here, using four separate Cre-lox conditional deletion models, as well as one genetic epistasis approach (Grhl2+/- ;Edn1+/- double heterozygous mice) we have investigated tissue-specific roles of Grhl2 in embryonic development, with a particular focus on the craniofacial skeleton. We find that loss of Grhl2 in the pharyngeal epithelium (using the ShhCre driver) leads to low-penetrance micrognathia, whereas deletion of Grhl2 within the ectoderm of the pharynx (NestinCre ) leads to small, albeit significant, differences in the proximal-distal elongation of both the maxilla and mandible. Loss of Grhl2 in endoderm (Sox17-2aiCre ) resulted in noticeable lung defects and a single instance of secondary palatal clefting, although formation of other endoderm-derived organs such as the stomach, bladder and intestines was not affected. Lastly, deletion of Grhl2 in cells of the neural crest (Wnt1Cre ) did not lead to any discernible defects in craniofacial development, and similarly, our epistasis approach did not detect any phenotypic consequences of loss of a single allele of both Grhl2 and Edn1. CONCLUSION Taken together, our study identifies a pharyngeal-epithelium intrinsic, non-cell-autonomous role for Grhl2 in the patterning and formation of the craniofacial skeleton, as well as an endoderm-specific role for Grhl2 in the formation and establishment of the mammalian lung.
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Affiliation(s)
- Michael de Vries
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, Australia.,Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Harley G Owens
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, Australia
| | - Marina R Carpinelli
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, Australia
| | - Darren Partridge
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, Australia
| | - Ariena Kersbergen
- ACRF Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kate D Sutherland
- ACRF Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Alana Auden
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, Australia
| | - Peter J Anderson
- Australian Craniofacial Unit, Women and Children's Hospital, Adelaide, South Australia, Australia.,Faculty of Health Sciences, University of Adelaide, South Australia, Australia.,Nanjing Medical University, Nanjing, China
| | - Stephen M Jane
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, Australia
| | - Sebastian Dworkin
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
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12
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Sundararajan V, Pang QY, Choolani M, Huang RYJ. Spotlight on the Granules (Grainyhead-Like Proteins) - From an Evolutionary Conserved Controller of Epithelial Trait to Pioneering the Chromatin Landscape. Front Mol Biosci 2020; 7:213. [PMID: 32974388 PMCID: PMC7471608 DOI: 10.3389/fmolb.2020.00213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/03/2020] [Indexed: 12/12/2022] Open
Abstract
Among the transcription factors that are conserved across phylogeny, the grainyhead family holds vital roles in driving the epithelial cell fate. In Drosophila, the function of grainyhead (grh) gene is essential during developmental processes such as epithelial differentiation, tracheal tube formation, maintenance of wing and hair polarity, and epidermal barrier wound repair. Three main mammalian orthologs of grh: Grainyhead-like 1-3 (GRHL1, GRHL2, and GRHL3) are highly conserved in terms of their gene structures and functions. GRHL proteins are essentially associated with the development and maintenance of the epithelial phenotype across diverse physiological conditions such as epidermal differentiation and craniofacial development as well as pathological functions including hearing impairment and neural tube defects. More importantly, through direct chromatin binding and induction of epigenetic alterations, GRHL factors function as potent suppressors of oncogenic cellular dedifferentiation program – epithelial-mesenchymal transition and its associated tumor-promoting phenotypes such as tumor cell migration and invasion. On the contrary, GRHL factors also induce pro-tumorigenic effects such as increased migration and anchorage-independent growth in certain tumor types. Furthermore, investigations focusing on the epithelial-specific activation of grh and GRHL factors have revealed that these factors potentially act as a pioneer factor in establishing a cell-type/cell-state specific accessible chromatin landscape that is exclusive for epithelial gene transcription. In this review, we highlight the essential roles of grh and GRHL factors during embryogenesis and pathogenesis, with a special focus on its emerging pioneering function.
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Affiliation(s)
- Vignesh Sundararajan
- Center for Translational Medicine, Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Qing You Pang
- Center for Translational Medicine, Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Obstetrics and Gynaecology, National University of Singapore, Singapore, Singapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, National University of Singapore, Singapore, Singapore
| | - Ruby Yun-Ju Huang
- Department of Obstetrics and Gynaecology, National University of Singapore, Singapore, Singapore.,School of Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
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13
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Carpinelli MR, de Vries ME, Auden A, Butt T, Deng Z, Partridge DD, Miles LB, Georgy SR, Haigh JJ, Darido C, Brabletz S, Brabletz T, Stemmler MP, Dworkin S, Jane SM. Inactivation of Zeb1 in GRHL2-deficient mouse embryos rescues mid-gestation viability and secondary palate closure. Dis Model Mech 2020; 13:dmm.042218. [PMID: 32005677 PMCID: PMC7104862 DOI: 10.1242/dmm.042218] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 01/13/2020] [Indexed: 12/12/2022] Open
Abstract
Cleft lip and palate are common birth defects resulting from failure of the facial processes to fuse during development. The mammalian grainyhead-like (Grhl1-3) genes play key roles in a number of tissue fusion processes including neurulation, epidermal wound healing and eyelid fusion. One family member, Grhl2, is expressed in the epithelial lining of the first pharyngeal arch in mice at embryonic day (E)10.5, prompting analysis of the role of this factor in palatogenesis. Grhl2-null mice die at E11.5 with neural tube defects and a cleft face phenotype, precluding analysis of palatal fusion at a later stage of development. However, in the first pharyngeal arch of Grhl2-null embryos, dysregulation of transcription factors that drive epithelial-mesenchymal transition (EMT) occurs. The aberrant expression of these genes is associated with a shift in RNA-splicing patterns that favours the generation of mesenchymal isoforms of numerous regulators. Driving the EMT perturbation is loss of expression of the EMT-suppressing transcription factors Ovol1 and Ovol2, which are direct GRHL2 targets. The expression of the miR-200 family of microRNAs, also GRHL2 targets, is similarly reduced, resulting in a 56-fold upregulation of Zeb1 expression, a major driver of mesenchymal cellular identity. The critical role of GRHL2 in mediating cleft palate in Zeb1−/− mice is evident, with rescue of both palatal and facial fusion seen in Grhl2−/−;Zeb1−/− embryos. These findings highlight the delicate balance between GRHL2/ZEB1 and epithelial/mesenchymal cellular identity that is essential for normal closure of the palate and face. Perturbation of this pathway may underlie cleft palate in some patients. Summary: Epithelial transcription factor GRHL2 is required for face closure while mesenchymal transcription factor ZEB1 is required for palate closure. Surprisingly, animals lacking both factors close their face and secondary palate.
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Affiliation(s)
- Marina R Carpinelli
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Michael E de Vries
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Alana Auden
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Tariq Butt
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Zihao Deng
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Darren D Partridge
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Lee B Miles
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Smitha R Georgy
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Jody J Haigh
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Charbel Darido
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Simone Brabletz
- Department of Experimental Medicine I, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Thomas Brabletz
- Department of Experimental Medicine I, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Marc P Stemmler
- Department of Experimental Medicine I, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Sebastian Dworkin
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Stephen M Jane
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
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14
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de Vries M, Carpinelli M, Rutland E, Hatzipantelis A, Partridge D, Auden A, Anderson PJ, De Groef B, Wu H, Osterwalder M, Visel A, Jane SM, Dworkin S. Interrogating the Grainyhead-like 2 (Grhl2) genomic locus identifies an enhancer element that regulates palatogenesis in mouse. Dev Biol 2020; 459:194-203. [PMID: 31782997 DOI: 10.1016/j.ydbio.2019.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 10/25/2022]
Abstract
The highly-conserved Grainyhead-like (Grhl) transcription factors are critical regulators of embryogenesis that regulate cellular survival, proliferation, migration and epithelial integrity, especially during the formation of the craniofacial skeleton. Family member Grhl2 is expressed throughout epithelial tissues during development, and loss of Grhl2 function leads to significant defects in neurulation, abdominal wall closure, formation of the face and fusion of the maxilla/palate. Whereas numerous downstream target genes of Grhl2 have been identified, very little is known about how this crucial developmental transcription factor itself is regulated. Here, using in silico and in utero expression analyses and functional deletion in mice, we have identified a novel 2.4 kb enhancer element (mm1286) that drives reporter gene expression in a pattern that strongly recapitulates endogenous Grhl2 in the craniofacial primordia, modulates Grhl2 expression in these tissues, and augments Grhl2-mediated closure of the secondary palate. Deletion of this genomic element, in the context of inactivation of one allele of Grhl2 (through generation of double heterozygous Grhl2+/-;mm1286+/- mice), results in a significant predisposition to palatal clefting at birth. Moreover, we found that a highly conserved 325 bp region of mm1286 is both necessary and sufficient for mediating the craniofacial-specific enhancer activity of this region, and that an extremely well-conserved 12-bp sequence within this element (CTGTCAAACAGGT) substantially determines full enhancer function. Together, these data provide valuable new insights into the upstream genomic regulatory landscape responsible for transcriptional control of Grhl2 during palatal closure.
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Affiliation(s)
- Michael de Vries
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, 3004, Australia; Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Marina Carpinelli
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, 3004, Australia
| | - Emilie Rutland
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, 3004, Australia
| | - Aaron Hatzipantelis
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, 3004, Australia
| | - Darren Partridge
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, 3004, Australia
| | - Alana Auden
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, 3004, Australia
| | - Peter J Anderson
- Australian Craniofacial Unit, Women and Children's Hospital, Adelaide, SA, 5005, Australia; Faculty of Health Sciences, University of Adelaide, SA, 5005, Australia; Nanjing Medical University, Nanjing, PR China
| | - Bert De Groef
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Han Wu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; School of Natural Sciences, University of California, Merced, CA, 95343, USA
| | - Stephen M Jane
- Department of Medicine, Monash University Central Clinical School, Prahran, Victoria, 3004, Australia
| | - Sebastian Dworkin
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, 3086, Australia.
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15
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Daniel E, Barlow HR, Sutton GI, Gu X, Htike Y, Cowdin MA, Cleaver O. Cyp26b1 is an essential regulator of distal airway epithelial differentiation during lung development. Development 2020; 147:dev181560. [PMID: 32001436 PMCID: PMC7044453 DOI: 10.1242/dev.181560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 01/23/2020] [Indexed: 12/16/2022]
Abstract
Proper organ development depends on coordinated communication between multiple cell types. Retinoic acid (RA) is an autocrine and paracrine signaling molecule essential for the development of most organs, including the lung. Despite extensive work detailing effects of RA deficiency in early lung morphogenesis, little is known about how RA regulates late gestational lung maturation. Here, we investigate the role of the RA catabolizing protein Cyp26b1 in the lung. Cyp26b1 is highly enriched in lung endothelial cells (ECs) throughout development. We find that loss of Cyp26b1 leads to reduction of alveolar type 1 cells, failure of alveolar inflation and early postnatal lethality in mouse. Furthermore, we observe expansion of distal epithelial progenitors, but no appreciable changes in proximal airways, ECs or stromal populations. Exogenous administration of RA during late gestation partially mimics these defects; however, transcriptional analyses comparing Cyp26b1-/- with RA-treated lungs reveal overlapping, but distinct, responses. These data suggest that defects observed in Cyp26b1-/- lungs are caused by both RA-dependent and RA-independent mechanisms. This work reports crucial cellular crosstalk during lung development involving Cyp26b1-expressing endothelium and identifies a novel RA modulator in lung development.
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Affiliation(s)
- Edward Daniel
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Haley R Barlow
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gabrielle I Sutton
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaowu Gu
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yadanar Htike
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mitzy A Cowdin
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ondine Cleaver
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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16
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Meta-Analysis of Grainyhead-Like Dependent Transcriptional Networks: A Roadmap for Identifying Novel Conserved Genetic Pathways. Genes (Basel) 2019; 10:genes10110876. [PMID: 31683705 PMCID: PMC6896185 DOI: 10.3390/genes10110876] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 12/17/2022] Open
Abstract
The Drosophila grainyhead (grh) and vertebrate Grainyhead-like (Grhl) transcription factors are among the most critical genes for epithelial development, maintenance and homeostasis, and are remarkably well conserved from fungi to humans. Mutations affecting grh/Grhl function lead to a myriad of developmental and adult onset epithelial disease, such as aberrant skin barrier formation, facial/palatal clefting, impaired neural tube closure, age-related hearing loss, ectodermal dysplasia, and importantly, cancers of epithelial origin. Recently, mutations in the family member GRHL3 have been shown to lead to both syndromic and non-syndromic facial and palatal clefting in humans, particularly the genetic disorder Van Der Woude Syndrome (VWS), as well as spina bifida, whereas mutations in mammalian Grhl2 lead to exencephaly and facial clefting. As transcription factors, Grhl proteins bind to and activate (or repress) a substantial number of target genes that regulate and drive a cascade of transcriptional networks. A multitude of large-scale datasets have been generated to explore the grh/Grhl-dependent transcriptome, following ablation or mis-regulation of grh/Grhl-function. Here, we have performed a meta-analysis of all 41 currently published grh and Grhl RNA-SEQ, and microarray datasets, in order to identify and characterise the transcriptional networks controlled by grh/Grhl genes across disparate biological contexts. Moreover, we have also cross-referenced our results with published ChIP and ChIP-SEQ datasets, in order to determine which of the critical effector genes are likely to be direct grh/Grhl targets, based on genomic occupancy by grh/Grhl genes. Lastly, to interrogate the predictive strength of our approach, we experimentally validated the expression of the top 10 candidate grhl target genes in epithelial development, in a zebrafish model lacking grhl3, and found that orthologues of seven of these (cldn23, ppl, prom2, ocln, slc6a19, aldh1a3, and sod3) were significantly down-regulated at 48 hours post-fertilisation. Therefore, our study provides a strong predictive resource for the identification of putative grh/grhl effector target genes.
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