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Burkhalter MD, Stiff T, Maerz LD, Casar Tena T, Wiese H, Gerhards J, Sailer SA, Vu LAT, Duong Phu M, Donow C, Alupei M, Iben S, Groth M, Wiese S, Church JA, Jeggo PA, Philipp M. Cilia defects upon loss of WDR4 are linked to proteasomal hyperactivity and ubiquitin shortage. Cell Death Dis 2024; 15:660. [PMID: 39251572 PMCID: PMC11384789 DOI: 10.1038/s41419-024-07042-5] [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: 02/03/2024] [Revised: 08/07/2024] [Accepted: 08/29/2024] [Indexed: 09/11/2024]
Abstract
The WD repeat-containing protein 4 (WDR4) has repeatedly been associated with primary microcephaly, a condition of impaired brain and skull growth. Often, faulty centrosomes cause microcephaly, yet aberrant cilia may also be involved. Here, we show using a combination of approaches in human fibroblasts, zebrafish embryos and patient-derived cells that WDR4 facilitates cilium formation. Molecularly, we associated WDR4 loss-of-function with increased protein synthesis and concomitant upregulation of proteasomal activity, while ubiquitin precursor pools are reduced. Inhibition of proteasomal activity as well as supplementation with free ubiquitin restored normal ciliogenesis. Proteasome inhibition ameliorated microcephaly phenotypes. Thus, we propose that WDR4 loss-of-function impairs head growth and neurogenesis via aberrant cilia formation, initially caused by disturbed protein and ubiquitin homeostasis.
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Affiliation(s)
- Martin D Burkhalter
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, 72074, Tübingen, Germany
| | - Tom Stiff
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Lars D Maerz
- Institute for Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Teresa Casar Tena
- Institute for Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Heike Wiese
- Core Unit Mass Spectrometry and Proteomics, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Julian Gerhards
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, 72074, Tübingen, Germany
| | - Steffen A Sailer
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, 72074, Tübingen, Germany
| | - Linh Anna Trúc Vu
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, 72074, Tübingen, Germany
| | - Max Duong Phu
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, 72074, Tübingen, Germany
| | - Cornelia Donow
- Institute for Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Marius Alupei
- Department of Dermatology, Ulm University, 89081, Ulm, Germany
| | - Sebastian Iben
- Department of Dermatology, Ulm University, 89081, Ulm, Germany
| | - Marco Groth
- Core Facility Next Generation Sequencing, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745, Jena, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Joseph A Church
- Department of Pediatrics, Keck School of Medicine of University of Southern California, Children's Hospital Los Angeles, Los Angeles, CA, 90033, USA
| | - Penelope A Jeggo
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Melanie Philipp
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, 72074, Tübingen, Germany.
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Babu S, Takeuchi Y, Masai I. Banp regulates DNA damage response and chromosome segregation during the cell cycle in zebrafish retina. eLife 2022; 11:74611. [PMID: 35942692 PMCID: PMC9363121 DOI: 10.7554/elife.74611] [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: 10/11/2021] [Accepted: 07/05/2022] [Indexed: 11/25/2022] Open
Abstract
Btg3-associated nuclear protein (Banp) was originally identified as a nuclear matrix-associated region (MAR)-binding protein and it functions as a tumor suppressor. At the molecular level, Banp regulates transcription of metabolic genes via a CGCG-containing motif called the Banp motif. However, its physiological roles in embryonic development are unknown. Here, we report that Banp is indispensable for the DNA damage response and chromosome segregation during mitosis. Zebrafish banp mutants show mitotic cell accumulation and apoptosis in developing retina. We found that DNA replication stress and tp53-dependent DNA damage responses were activated to induce apoptosis in banp mutants, suggesting that Banp is required for regulation of DNA replication and DNA damage repair. Furthermore, consistent with mitotic cell accumulation, chromosome segregation was not smoothly processed from prometaphase to anaphase in banp morphants, leading to a prolonged M-phase. Our RNA- and ATAC-sequencing identified 31 candidates for direct Banp target genes that carry the Banp motif. Interestingly, a DNA replication fork regulator, wrnip1, and two chromosome segregation regulators, cenpt and ncapg, are included in this list. Thus, Banp directly regulates transcription of wrnip1 for recovery from DNA replication stress, and cenpt and ncapg for chromosome segregation during mitosis. Our findings provide the first in vivo evidence that Banp is required for cell-cycle progression and cell survival by regulating DNA damage responses and chromosome segregation during mitosis. In order for a cell to divide, it must progress through a series of carefully controlled steps known as the cell cycle. First, the cell replicates its DNA and both copies get segregated to opposite ends. The cell then splits into two and each new cell receives a copy of the duplicated genetic material. If any of the stages in the cell cycle become disrupted or mis-regulated this can lead to uncontrolled divisions that may result in cancer. Researchers have often used a structure within the eye known as the retina to study the cell cycle in zebrafish and other animals as cells in the retina rapidly divide in a highly controlled manner. A protein called Banp is known to help stop tumors from growing in humans and mice, but its normal role in the body, particularly the cell cycle, has remained unclear. To investigate, Babu et al. studied the retina of mutant zebrafish that were unable to make the Banp protein. The experiments revealed that two stress responses indicating DNA damage or defects in copying DNA were active in the retinal cells of the mutant zebrafish. This suggested that Banp allows cell to progress through the cell cycle by repairing any DNA damage that may arise during replication. Banp does this by activating the gene for another protein called Wrnip1. Babu et al. also found that Banp helps segregate the two copies of DNA during cell division by promoting the activation of two other proteins called Cenpt and Ncapg. Further experiments identified 31 genes that were directly regulated by Banp. These findings demonstrate that Banp is required for zebrafish cells to be able to accurately copy their DNA and divide in to two new cells. In the future, the work of Babu et al. will provide a useful resource to investigate how tumors grow and spread around the body, and may contribute to the development of new treatments for cancer.
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Affiliation(s)
- Swathy Babu
- Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Yuki Takeuchi
- Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Ichiro Masai
- Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
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Tingler M, Philipp M, Burkhalter MD. DNA Replication proteins in primary microcephaly syndromes. Biol Cell 2022; 114:143-159. [PMID: 35182397 DOI: 10.1111/boc.202100061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 11/30/2022]
Abstract
SCOPE Improper expansion of neural stem and progenitor cells during brain development manifests in primary microcephaly. It is characterized by a reduced head circumference, which correlates with a reduction in brain size. This often corresponds to a general underdevelopment of the brain and entails cognitive, behavioral and motoric retardation. In the past decade significant research efforts have been undertaken to identify genes and the molecular mechanisms underlying microcephaly. One such gene set encompasses factors required for DNA replication. Intriguingly, a growing body of evidence indicates that a substantial number of these genes mediate faithful centrosome and cilium function in addition to their canonical function in genome duplication. Here, we summarize, which DNA replication factors are associated with microcephaly syndromes and to which extent they impact on centrosomes and cilia. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Melanie Tingler
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, Tübingen, 72074, Germany
| | - Melanie Philipp
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, Tübingen, 72074, Germany
| | - Martin D Burkhalter
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, Tübingen, 72074, Germany
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Gupta S, Ozimek-Kulik JE, Phillips JK. Nephronophthisis-Pathobiology and Molecular Pathogenesis of a Rare Kidney Genetic Disease. Genes (Basel) 2021; 12:genes12111762. [PMID: 34828368 PMCID: PMC8623546 DOI: 10.3390/genes12111762] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
The exponential rise in our understanding of the aetiology and pathophysiology of genetic cystic kidney diseases can be attributed to the identification of cystogenic genes over the last three decades. The foundation of this was laid by positional cloning strategies which gradually shifted towards next-generation sequencing (NGS) based screenings. This shift has enabled the discovery of novel cystogenic genes at an accelerated pace unlike ever before and, most notably, the past decade has seen the largest increase in identification of the genes which cause nephronophthisis (NPHP). NPHP is a monogenic autosomal recessive cystic kidney disease caused by mutations in a diverse clade of over 26 identified genes and is the most common genetic cause of renal failure in children. NPHP gene types present with some common pathophysiological features alongside a diverse range of extra-renal phenotypes associated with specific syndromic presentations. This review provides a timely update on our knowledge of this disease, including epidemiology, pathophysiology, anatomical and molecular features. We delve into the diversity of the NPHP causing genes and discuss known molecular mechanisms and biochemical pathways that may have possible points of intersection with polycystic kidney disease (the most studied renal cystic pathology). We delineate the pathologies arising from extra-renal complications and co-morbidities and their impact on quality of life. Finally, we discuss the current diagnostic and therapeutic modalities available for disease management, outlining possible avenues of research to improve the prognosis for NPHP patients.
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Affiliation(s)
- Shabarni Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
- Correspondence:
| | - Justyna E. Ozimek-Kulik
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
- School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia
- Department of Paediatric Nephrology, Sydney Children’s Hospital Network, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Jacqueline Kathleen Phillips
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
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Kobar K, Collett K, Prykhozhij SV, Berman JN. Zebrafish Cancer Predisposition Models. Front Cell Dev Biol 2021; 9:660069. [PMID: 33987182 PMCID: PMC8112447 DOI: 10.3389/fcell.2021.660069] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
Cancer predisposition syndromes are rare, typically monogenic disorders that result from germline mutations that increase the likelihood of developing cancer. Although these disorders are individually rare, resulting cancers collectively represent 5-10% of all malignancies. In addition to a greater incidence of cancer, affected individuals have an earlier tumor onset and are frequently subjected to long-term multi-modal cancer screening protocols for earlier detection and initiation of treatment. In vivo models are needed to better understand tumor-driving mechanisms, tailor patient screening approaches and develop targeted therapies to improve patient care and disease prognosis. The zebrafish (Danio rerio) has emerged as a robust model for cancer research due to its high fecundity, time- and cost-efficient genetic manipulation and real-time high-resolution imaging. Tumors developing in zebrafish cancer models are histologically and molecularly similar to their human counterparts, confirming the validity of these models. The zebrafish platform supports both large-scale random mutagenesis screens to identify potential candidate/modifier genes and recently optimized genome editing strategies. These techniques have greatly increased our ability to investigate the impact of certain mutations and how these lesions impact tumorigenesis and disease phenotype. These unique characteristics position the zebrafish as a powerful in vivo tool to model cancer predisposition syndromes and as such, several have already been created, including those recapitulating Li-Fraumeni syndrome, familial adenomatous polyposis, RASopathies, inherited bone marrow failure syndromes, and several other pathogenic mutations in cancer predisposition genes. In addition, the zebrafish platform supports medium- to high-throughput preclinical drug screening to identify compounds that may represent novel treatment paradigms or even prevent cancer evolution. This review will highlight and synthesize the findings from zebrafish cancer predisposition models created to date. We will discuss emerging trends in how these zebrafish cancer models can improve our understanding of the genetic mechanisms driving cancer predisposition and their potential to discover therapeutic and/or preventative compounds that change the natural history of disease for these vulnerable children, youth and adults.
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Affiliation(s)
- Kim Kobar
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Keon Collett
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | | | - Jason N. Berman
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Pediatrics, University of Ottawa, Ottawa, ON, Canada
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6
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Primary cilia and the DNA damage response: linking a cellular antenna and nuclear signals. Biochem Soc Trans 2021; 49:829-841. [PMID: 33843966 DOI: 10.1042/bst20200751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 11/17/2022]
Abstract
The maintenance of genome stability involves integrated biochemical activities that detect DNA damage or incomplete replication, delay the cell cycle, and direct DNA repair activities on the affected chromatin. These processes, collectively termed the DNA damage response (DDR), are crucial for cell survival and to avoid disease, particularly cancer. Recent work has highlighted links between the DDR and the primary cilium, an antenna-like, microtubule-based signalling structure that extends from a centriole docked at the cell surface. Ciliary dysfunction gives rise to a range of complex human developmental disorders termed the ciliopathies. Mutations in ciliopathy genes have been shown to impact on several functions that relate to centrosome integrity, DNA damage signalling, responses to problems in DNA replication and the control of gene expression. This review covers recent findings that link cilia and the DDR and explores the various roles played by key genes in these two contexts. It outlines how proteins encoded by ciliary genes impact checkpoint signalling, DNA replication and repair, gene expression and chromatin remodelling. It discusses how these diverse activities may integrate nuclear responses with those that affect a structure of the cell periphery. Additional directions for exploration of the interplay between these pathways are highlighted, with a focus on new ciliary gene candidates that alter genome stability.
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Matos-Rodrigues GE, Tan PB, Rocha-Martins M, Charlier CF, Gomes AL, Cabral-Miranda F, Grigaravicius P, Hofmann TG, Frappart PO, Martins RAP. Progenitor death drives retinal dysplasia and neuronal degeneration in a mouse model of ATRIP-Seckel syndrome. Dis Model Mech 2020; 13:dmm045807. [PMID: 32994318 PMCID: PMC7648607 DOI: 10.1242/dmm.045807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/27/2020] [Indexed: 01/03/2023] Open
Abstract
Seckel syndrome is a type of microcephalic primordial dwarfism (MPD) that is characterized by growth retardation and neurodevelopmental defects, including reports of retinopathy. Mutations in key mediators of the replication stress response, the mutually dependent partners ATR and ATRIP, are among the known causes of Seckel syndrome. However, it remains unclear how their deficiency disrupts the development and function of the central nervous system (CNS). Here, we investigated the cellular and molecular consequences of ATRIP deficiency in different cell populations of the developing murine neural retina. We discovered that conditional inactivation of Atrip in photoreceptor neurons did not affect their survival or function. In contrast, Atrip deficiency in retinal progenitor cells (RPCs) led to severe lamination defects followed by secondary photoreceptor degeneration and loss of vision. Furthermore, we showed that RPCs lacking functional ATRIP exhibited higher levels of replicative stress and accumulated endogenous DNA damage that was accompanied by stabilization of TRP53. Notably, inactivation of Trp53 prevented apoptosis of Atrip-deficient progenitor cells and was sufficient to rescue retinal dysplasia, neurodegeneration and loss of vision. Together, these results reveal an essential role of ATRIP-mediated replication stress response in CNS development and suggest that the TRP53-mediated apoptosis of progenitor cells might contribute to retinal malformations in Seckel syndrome and other MPD disorders.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Gabriel E Matos-Rodrigues
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Pedro B Tan
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Maurício Rocha-Martins
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Clara F Charlier
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Anielle L Gomes
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Felipe Cabral-Miranda
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | | | - Thomas G Hofmann
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, 55131 Germany
| | - Pierre-Olivier Frappart
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, 55131 Germany
| | - Rodrigo A P Martins
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
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Heigwer J, Kutzner J, Haeussler M, Burkhalter MD, Draebing T, Juergensen L, Katus HA, Philipp M, Westhoff JH, Hassel D. miR-103/107 regulates left-right asymmetry in zebrafish by modulating Kupffer's vesicle development and ciliogenesis. Biochem Biophys Res Commun 2020; 527:432-439. [PMID: 32334837 DOI: 10.1016/j.bbrc.2020.04.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/15/2020] [Indexed: 10/24/2022]
Abstract
In zebrafish, cilia movement within the Kupffer's vesicle (KV) generates a fluid flow responsible for accumulating nodal signals exclusively in the left lateral plate mesoderm, thereby initiating left-right patterning (LRP). Defects in LRP cause devastating congenital disorders including congenital heart malformations due to organ mis-positioning. We identified the miR-103/107 family to be involved in regulating LRP. Depletion of miR-103/107 in zebrafish embryos resulted in malpositioned and malformed visceral organs and hearts due to disturbed LRP gene expression, indicating early defects in LRP. Additionally, loss of miR-103/107 affected KV morphogenesis and cilia formation without disturbing endoderm development. Human fibroblasts depleted of miR-103a/107 often failed to extend cilia or developed shorter cilia, indicating functional conservation between species. We identified arl6, araf and foxH1 as direct targets of miR-103/107 providing a mechanistic link to cilia development and nodal signal titration. We describe a new microRNA family controlling KV development and hence influencing establishment of internal organ asymmetry.
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Affiliation(s)
- Jana Heigwer
- Department of Internal Medicine III, Cardiology, Heidelberg University Hospital, 69120, Heidelberg, Germany and DZHK (German Centre for Cardiovascular Research), Partner Site, Heidelberg, Mannheim, Germany; Department of Pediatrics I, University Children's Hospital Heidelberg, 69120, Heidelberg, Germany.
| | - Juliane Kutzner
- Department of Internal Medicine III, Cardiology, Heidelberg University Hospital, 69120, Heidelberg, Germany and DZHK (German Centre for Cardiovascular Research), Partner Site, Heidelberg, Mannheim, Germany
| | - Monika Haeussler
- Institute of Biochemistry and Molecular Biology (iBMB), Ulm University, 89081, Ulm, Germany
| | - Martin D Burkhalter
- Institute of Biochemistry and Molecular Biology (iBMB), Ulm University, 89081, Ulm, Germany; Department of Experimental and Clinical Pharmacology and Pharmacogenomics, University Hospital Tübingen, 72074, Tübingen, Germany
| | - Thomas Draebing
- Department of Internal Medicine III, Cardiology, Heidelberg University Hospital, 69120, Heidelberg, Germany and DZHK (German Centre for Cardiovascular Research), Partner Site, Heidelberg, Mannheim, Germany
| | - Lonny Juergensen
- Department of Internal Medicine III, Cardiology, Heidelberg University Hospital, 69120, Heidelberg, Germany and DZHK (German Centre for Cardiovascular Research), Partner Site, Heidelberg, Mannheim, Germany
| | - Hugo A Katus
- Department of Internal Medicine III, Cardiology, Heidelberg University Hospital, 69120, Heidelberg, Germany and DZHK (German Centre for Cardiovascular Research), Partner Site, Heidelberg, Mannheim, Germany
| | - Melanie Philipp
- Institute of Biochemistry and Molecular Biology (iBMB), Ulm University, 89081, Ulm, Germany; Department of Experimental and Clinical Pharmacology and Pharmacogenomics, University Hospital Tübingen, 72074, Tübingen, Germany
| | - Jens H Westhoff
- Department of Pediatrics I, University Children's Hospital Heidelberg, 69120, Heidelberg, Germany
| | - David Hassel
- Department of Internal Medicine III, Cardiology, Heidelberg University Hospital, 69120, Heidelberg, Germany and DZHK (German Centre for Cardiovascular Research), Partner Site, Heidelberg, Mannheim, Germany
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Alfieri M, Iaconis D, Tammaro R, Perone L, Calì G, Nitsch L, Dougherty GW, Ragnini-Wilson A, Franco B. The centrosomal/basal body protein OFD1 is required for microtubule organization and cell cycle progression. Tissue Cell 2020; 64:101369. [PMID: 32473706 DOI: 10.1016/j.tice.2020.101369] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/28/2022]
Abstract
Oral-Facial-Digital type I (OFD1) is a rare inherited form of renal cystic disease associated with ciliary dysfunction. This disorder is due to mutations in the OFD1 gene that encodes a protein localized to centrosomes and basal bodies in different cell types. Immunofluorescence analysis demonstrated that OFD1 displays a dynamic distribution during cell cycle. High-content microscopy analysis of Ofd1-depleted fibroblasts revealed impaired cell cycle progression. Immunofluorescence analysis and cell proliferation assays also indicated the presence of a variety of defects such as centrosome accumulation, nuclear abnormalities and aneuploidy. In addition, Ofd1-depleted cells displayed an abnormal microtubule network that may underlie these defects. All together our results suggest that OFD1 contributes to the function of the microtubule organizing center (MTOC) in the cell, controlling cell cycle progression both in vitro and in vivo.
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Affiliation(s)
- Mariaevelina Alfieri
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy
| | - Daniela Iaconis
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy
| | - Roberta Tammaro
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy
| | - Lucia Perone
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy
| | - Gaetano Calì
- National Research Council - Institute of Experimental Endocrinology and Oncology, Naples, Italy
| | - Lucio Nitsch
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Gerard W Dougherty
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy; Department of General Pediatrics, University Hospital Muenster, 48149, Muenster, Germany
| | | | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy; Medical Genetics, Department of Translational Medicine, University of Naples "Federico II", Via Sergio Pansini, 80131, Naples, Italy.
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10
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Che L, Song JY, Lou Y, Li GY. Analysis from the perspective of cilia: the protective effect of PARP inhibitors on visual function during light-induced damage. Int Ophthalmol 2019; 40:1017-1027. [PMID: 31802371 DOI: 10.1007/s10792-019-01245-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/23/2019] [Indexed: 12/26/2022]
Abstract
PURPOSE To analyze the protective effect of PARP inhibitors on light-damaged retina and explore its possible mechanism from the perspective of ciliopathy. METHODS A systematic review of the literature was performed to investigate the protection of PARP inhibition on light-damaged cilia. PubMed database was retrieved to find the relevant studies and 119 literatures were involved in the review. RESULTS In retina, the outer segment of photoreceptor is regarded as a special type of primary cilium, so various retinal diseases actually belong to a type of ciliopathy. The retina is the only central nervous tissue exposed to light, but poly (ADP-ribose) polymerase (PARP), as a nuclear enzyme repairing DNA breaks, is overactivated during the light-induced DNA damage, and is involved in the cell death cascade. Studies show that both ATR and phosphorylated Akt colocalize with cilium and play an important role in regulating ciliary function. PARP may function at ATR or PI3K/Akt signal to exert protective effect on cilia. CONCLUSION PARP inhibitors may protect the cilia/OS of photoreceptor during light-induced damage, which the possible mechanism may be involved in the activation of ATR and PI3K/Akt signal.
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Affiliation(s)
- Lin Che
- Department of Ophthalmology, Second Hospital of Jilin University, Changchun, 130041, China
| | - Jing-Yao Song
- Department of Ophthalmology, Second Hospital of Jilin University, Changchun, 130041, China
| | - Yan Lou
- Department of Nephropathy, Second Hospital of Jilin University, Changchun, 130041, China
| | - Guang-Yu Li
- Department of Ophthalmology, Second Hospital of Jilin University, Changchun, 130041, China.
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Abstract
Primary cilia project in a single copy from the surface of most vertebrate cell types; they detect and transmit extracellular cues to regulate diverse cellular processes during development and to maintain tissue homeostasis. The sensory capacity of primary cilia relies on the coordinated trafficking and temporal localization of specific receptors and associated signal transduction modules in the cilium. The canonical Hedgehog (HH) pathway, for example, is a bona fide ciliary signalling system that regulates cell fate and self-renewal in development and tissue homeostasis. Specific receptors and associated signal transduction proteins can also localize to primary cilia in a cell type-dependent manner; available evidence suggests that the ciliary constellation of these proteins can temporally change to allow the cell to adapt to specific developmental and homeostatic cues. Consistent with important roles for primary cilia in signalling, mutations that lead to their dysfunction underlie a pleiotropic group of diseases and syndromic disorders termed ciliopathies, which affect many different tissues and organs of the body. In this Review, we highlight central mechanisms by which primary cilia coordinate HH, G protein-coupled receptor, WNT, receptor tyrosine kinase and transforming growth factor-β (TGFβ)/bone morphogenetic protein (BMP) signalling and illustrate how defects in the balanced output of ciliary signalling events are coupled to developmental disorders and disease progression.
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12
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Potter H, Chial HJ, Caneus J, Elos M, Elder N, Borysov S, Granic A. Chromosome Instability and Mosaic Aneuploidy in Neurodegenerative and Neurodevelopmental Disorders. Front Genet 2019; 10:1092. [PMID: 31788001 PMCID: PMC6855267 DOI: 10.3389/fgene.2019.01092] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/09/2019] [Indexed: 12/15/2022] Open
Abstract
Evidence from multiple laboratories has accumulated to show that mosaic neuronal aneuploidy and consequent apoptosis characterizes and may underlie neuronal loss in many neurodegenerative diseases, particularly Alzheimer’s disease and frontotemporal dementia. Furthermore, several neurodevelopmental disorders, including Seckel syndrome, ataxia telangiectasia, Nijmegen breakage syndrome, Niemann–Pick type C, and Down syndrome, have been shown to also exhibit mosaic aneuploidy in neurons in the brain and in other cells throughout the body. Together, these results indicate that both neurodegenerative and neurodevelopmental disorders with apparently different pathogenic causes share a cell cycle defect that leads to mosaic aneuploidy in many cell types. When such mosaic aneuploidy arises in neurons in the brain, it promotes apoptosis and may at least partly underlie the cognitive deficits that characterize the neurological symptoms of these disorders. These findings have implications for both diagnosis and treatment/prevention.
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Affiliation(s)
- Huntington Potter
- Department of Neurology, Rocky Mountain Alzheimer's Disease Center, University of Colorado, Aurora, CO, United States.,Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, United States
| | - Heidi J Chial
- Department of Neurology, Rocky Mountain Alzheimer's Disease Center, University of Colorado, Aurora, CO, United States.,Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, United States
| | - Julbert Caneus
- NanoScience Technology Center, University of Central Florida, Orlando, FL, United States
| | - Mihret Elos
- Department of Neurology, Rocky Mountain Alzheimer's Disease Center, University of Colorado, Aurora, CO, United States.,Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, United States
| | - Nina Elder
- Department of Neurology, Rocky Mountain Alzheimer's Disease Center, University of Colorado, Aurora, CO, United States.,Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, United States
| | - Sergiy Borysov
- Department of Math and Science, Saint Leo University, Saint Leo, FL, United States
| | - Antoneta Granic
- AGE Research Group, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom.,Newcastle University Institute for Ageing, NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne, United Kingdom.,Newcastle upon Tyne Hospitals, NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
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13
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Casar Tena T, Maerz LD, Szafranski K, Groth M, Blätte TJ, Donow C, Matysik S, Walther P, Jeggo PA, Burkhalter MD, Philipp M. Resting cells rely on the DNA helicase component MCM2 to build cilia. Nucleic Acids Res 2019; 47:134-151. [PMID: 30329080 PMCID: PMC6326816 DOI: 10.1093/nar/gky945] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 10/04/2018] [Indexed: 12/24/2022] Open
Abstract
Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding the DNA double strand. Interestingly, the number of MCM hexamers greatly exceeds the number of firing origins suggesting additional roles of MCMs. Here we show a hitherto unanticipated function of MCM2 in cilia formation in human cells and zebrafish that is uncoupled from replication. Zebrafish depleted of MCM2 develop ciliopathy-phenotypes including microcephaly and aberrant heart looping due to malformed cilia. In non-cycling human fibroblasts, loss of MCM2 promotes transcription of a subset of genes, which cause cilia shortening and centriole overduplication. Chromatin immunoprecipitation experiments show that MCM2 binds to transcription start sites of cilia inhibiting genes. We propose that such binding may block RNA polymerase II-mediated transcription. Depletion of a second MCM (MCM7), which functions in complex with MCM2 during its canonical functions, reveals an overlapping cilia-deficiency phenotype likely unconnected to replication, although MCM7 appears to regulate a distinct subset of genes and pathways. Our data suggests that MCM2 and 7 exert a role in ciliogenesis in post-mitotic tissues.
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Affiliation(s)
- Teresa Casar Tena
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Lars D Maerz
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Karol Szafranski
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Tamara J Blätte
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Cornelia Donow
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Sabrina Matysik
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany
| | - Penelope A Jeggo
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Martin D Burkhalter
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Melanie Philipp
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
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14
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Halder S, Torrecilla I, Burkhalter MD, Popović M, Fielden J, Vaz B, Oehler J, Pilger D, Lessel D, Wiseman K, Singh AN, Vendrell I, Fischer R, Philipp M, Ramadan K. SPRTN protease and checkpoint kinase 1 cross-activation loop safeguards DNA replication. Nat Commun 2019; 10:3142. [PMID: 31316063 PMCID: PMC6637133 DOI: 10.1038/s41467-019-11095-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/21/2019] [Indexed: 01/07/2023] Open
Abstract
The SPRTN metalloprotease is essential for DNA-protein crosslink (DPC) repair and DNA replication in vertebrate cells. Cells deficient in SPRTN protease exhibit DPC-induced replication stress and genome instability, manifesting as premature ageing and liver cancer. Here, we provide a body of evidence suggesting that SPRTN activates the ATR-CHK1 phosphorylation signalling cascade during physiological DNA replication by proteolysis-dependent eviction of CHK1 from replicative chromatin. During this process, SPRTN proteolyses the C-terminal/inhibitory part of CHK1, liberating N-terminal CHK1 kinase active fragments. Simultaneously, CHK1 full length and its N-terminal fragments phosphorylate SPRTN at the C-terminal regulatory domain, which stimulates SPRTN recruitment to chromatin to promote unperturbed DNA replication fork progression and DPC repair. Our data suggest that a SPRTN-CHK1 cross-activation loop plays a part in DNA replication and protection from DNA replication stress. Finally, our results with purified components of this pathway further support the proposed model of a SPRTN-CHK1 cross-activation loop. Cells deficient in SPRTN protease activity exhibit severe DNA-protein crosslink induced replication stress and genome instability. Here the author reveal a functional link between the SPRTN protease and the CHK1 kinase during physiological DNA replication.
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Affiliation(s)
- Swagata Halder
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Ignacio Torrecilla
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Martin D Burkhalter
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.,Department of Experimental and Clinical Pharmacology and Pharmacogenomics, University of Tübingen, 72074, Tübingen, Germany
| | - Marta Popović
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Institute Ruder Boškovic, Bijenička Cesta 54, 10000, Zagreb, Croatia
| | - John Fielden
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Bruno Vaz
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Judith Oehler
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Domenic Pilger
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Katherine Wiseman
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Abhay Narayan Singh
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Iolanda Vendrell
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK.,TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Roman Fischer
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Melanie Philipp
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.,Department of Experimental and Clinical Pharmacology and Pharmacogenomics, University of Tübingen, 72074, Tübingen, Germany
| | - Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK.
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15
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Verification and rectification of cell type-specific splicing of a Seckel syndrome-associated ATR mutation using iPS cell model. J Hum Genet 2019; 64:445-458. [PMID: 30846821 PMCID: PMC8075875 DOI: 10.1038/s10038-019-0574-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/25/2018] [Accepted: 01/18/2019] [Indexed: 11/08/2022]
Abstract
Seckel syndrome (SS) is a rare spectrum of congenital severe microcephaly and dwarfism. One SS-causative gene is Ataxia Telangiectasia and Rad3-Related Protein (ATR), and ATR (c.2101 A>G) mutation causes skipping of exon 9, resulting in a hypomorphic ATR defect. This mutation is considered the cause of an impaired response to DNA replication stress, the main function of ATR, contributing to the pathogenesis of microcephaly. However, the precise behavior and impact of this splicing defect in human neural progenitor cells (NPCs) is unclear. To address this, we established induced pluripotent stem cells (iPSCs) from fibroblasts carrying the ATR mutation and an isogenic ATR-corrected counterpart iPSC clone. SS-patient-derived iPSCs (SS-iPSCs) exhibited cell type-specific splicing; exon 9 was dominantly skipped in fibroblasts and iPSC-derived NPCs, but it was included in undifferentiated iPSCs and definitive endodermal cells. SS-iPSC-derived NPCs (SS-NPCs) showed distinct expression profiles from ATR non-mutated NPCs with negative enrichment of neuronal genesis-related gene sets. In SS-NPCs, abnormal mitotic spindles occurred more frequently than in gene-corrected counterparts, and the alignment of NPCs in the surface of the neurospheres was perturbed. Finally, we tested several splicing-modifying compounds and found that TG003, a CLK1 inhibitor, could pharmacologically rescue the exon 9 skipping in SS-NPCs. Treatment with TG003 restored the ATR kinase activity in SS-NPCs and decreased the frequency of abnormal mitotic events. In conclusion, our iPSC model revealed a novel effect of the ATR mutation in mitotic processes of NPCs and NPC-specific missplicing, accompanied by the recovery of neuronal defects using a splicing rectifier.
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16
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Maerz LD, Burkhalter MD, Schilpp C, Wittekindt OH, Frick M, Philipp M. Pharmacological cholesterol depletion disturbs ciliogenesis and ciliary function in developing zebrafish. Commun Biol 2019; 2:31. [PMID: 30729178 PMCID: PMC6351647 DOI: 10.1038/s42003-018-0272-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/20/2018] [Indexed: 12/30/2022] Open
Abstract
Patients with an inherited inability to synthesize sufficient amounts of cholesterol develop congenital malformations of the skull, toes, kidney and heart. As development of these structures depends on functional cilia we investigated whether cholesterol regulates ciliogenesis through inhibition of hydroxymethylglutaryl-Coenzyme A reductase (HMG-CoA-R), the rate-limiting enzyme in cholesterol synthesis. HMG-CoA-R is efficiently inhibited by statins, a standard medication for hyperlipidemia. When zebrafish embryos are treated with statins cilia dysfunction phenotypes including heart defects, left-right asymmetry defects and malformation of ciliated organs develop, which are ameliorated by cholesterol replenishment. HMG-CoA-R inhibition and other means of cholesterol reduction lowered ciliation frequency and cilia length in zebrafish as well as several mammalian cell types. Cholesterol depletion further triggers an inability for ciliary signalling. Because of a reduction of the transition zone component Pi(4,5)P2 we propose that cholesterol governs crucial steps of cilium extension. Taken together, we report that cholesterol abrogation provokes cilia defects.
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Affiliation(s)
- Lars D. Maerz
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Martin D. Burkhalter
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Carolin Schilpp
- Institute of General Physiology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Oliver H. Wittekindt
- Institute of General Physiology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Manfred Frick
- Institute of General Physiology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Melanie Philipp
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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17
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Maerz LD, Casar Tena T, Gerhards J, Donow C, Jeggo PA, Philipp M. Analysis of cilia dysfunction phenotypes in zebrafish embryos depleted of Origin recognition complex factors. Eur J Hum Genet 2019; 27:772-782. [PMID: 30696958 DOI: 10.1038/s41431-019-0338-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 12/26/2018] [Accepted: 01/04/2019] [Indexed: 12/15/2022] Open
Abstract
Meier-Gorlin syndrome (MGS) is a rare, congenital primordial microcephalic dwarfism disorder. MGS is caused by genetic variants of components of the origin recognition complex (ORC) consisting of ORC1-6 and the pre-replication complex, which together enable origin firing and hence genome replication. In addition, ORC1 has previously been shown to play a role in ciliogenesis. Here, we extend this work and investigate the function of ORC1 and two other members of the complex on cilia at an organismal level. Knockdown experiments in zebrafish confirmed the impact of ORC1 on cilia. ORC1-deficiency confers defects anticipated to arise from impaired cilia function such as formation of oedema, kidney cysts, curved bodies and left-right asymmetry defects. We found ORC1 furthermore required for cilium formation in zebrafish and demonstrate that ciliopathy phenotypes in ORC1-depleted zebrafish could not be rescued by reconstitution with ORC1 bearing a genetic variant previously identified in MGS patients. Loss-of-function of Orc4 and Orc6, respectively, conferred similar ciliopathy phenotypes and cilium shortening in zebrafish, suggesting that several, if not all, components of the ORC regulate ciliogenesis downstream to or in addition to their canonical function in replication initiation. This study presents the first in vivo evidence of an influence of the MGS genes of the ORC family on cilia, and consolidates the possibility that cilia dysfunction could contribute to the clinical manifestation of ORC-deficient MGS.
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Affiliation(s)
- Lars D Maerz
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Teresa Casar Tena
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Julian Gerhards
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Cornelia Donow
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Penelope A Jeggo
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Melanie Philipp
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany.
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18
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Ogungbenro YA, Tena TC, Gaboriau D, Lalor P, Dockery P, Philipp M, Morrison CG. Centrobin controls primary ciliogenesis in vertebrates. J Cell Biol 2018; 217:1205-1215. [PMID: 29440264 PMCID: PMC5881496 DOI: 10.1083/jcb.201706095] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/19/2017] [Accepted: 01/17/2018] [Indexed: 12/18/2022] Open
Abstract
The BRCA2 interactor, centrobin, is a centrosomal protein that has been implicated in centriole duplication and microtubule stability. We used genome editing to ablate CNTROB in hTERT-RPE1 cells and observed an increased frequency of monocentriolar and acentriolar cells. Using a novel monoclonal antibody, we found that centrobin primarily localizes to daughter centrioles but also associates with mother centrioles upon serum starvation. Strikingly, centrobin loss abrogated primary ciliation upon serum starvation. Ultrastructural analysis of centrobin nulls revealed defective axonemal extension after mother centriole docking. Ciliogenesis required a C-terminal portion of centrobin that interacts with CP110 and tubulin. We also depleted centrobin in zebrafish embryos to explore its roles in an entire organism. Centrobin-depleted embryos showed microcephaly, with curved and shorter bodies, along with marked defects in laterality control, morphological features that indicate ciliary dysfunction. Our data identify new roles for centrobin as a positive regulator of vertebrate ciliogenesis.
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Affiliation(s)
- Yetunde Adesanya Ogungbenro
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Teresa Casar Tena
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - David Gaboriau
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Facility for Imaging by Light Microscopy, Imperial College London, London, England, UK
| | - Pierce Lalor
- Anatomy, School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Peter Dockery
- Anatomy, School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Melanie Philipp
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Ciaran G Morrison
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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19
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Duerinckx S, Abramowicz M. The genetics of congenitally small brains. Semin Cell Dev Biol 2017; 76:76-85. [PMID: 28912110 DOI: 10.1016/j.semcdb.2017.09.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 12/14/2022]
Abstract
Primary microcephaly (PM) refers to a congenitally small brain, resulting from insufficient prenatal production of neurons, and serves as a model disease for brain volumic development. Known PM genes delineate several cellular pathways, among which the centriole duplication pathway, which provide interesting clues about the cellular mechanisms involved. The general interest of the genetic dissection of PM is illustrated by the convergence of Zika virus infection and PM gene mutations on congenital microcephaly, with CENPJ/CPAP emerging as a key target. Physical (protein-protein) and genetic (digenic inheritance) interactions of Wdr62 and Aspm have been demonstrated in mice, and should now be sought in humans using high throughput parallel sequencing of multiple PM genes in PM patients and control subjects, in order to categorize mutually interacting genes, hence delineating functional pathways in vivo in humans.
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Affiliation(s)
- Sarah Duerinckx
- IRIBHM, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Marc Abramowicz
- IRIBHM, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium; Department of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
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20
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O'Driscoll M. The pathological consequences of impaired genome integrity in humans; disorders of the DNA replication machinery. J Pathol 2017; 241:192-207. [PMID: 27757957 DOI: 10.1002/path.4828] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 12/13/2022]
Abstract
Accurate and efficient replication of the human genome occurs in the context of an array of constitutional barriers, including regional topological constraints imposed by chromatin architecture and processes such as transcription, catenation of the helical polymer and spontaneously generated DNA lesions, including base modifications and strand breaks. DNA replication is fundamentally important for tissue development and homeostasis; differentiation programmes are intimately linked with stem cell division. Unsurprisingly, impairments of the DNA replication machinery can have catastrophic consequences for genome stability and cell division. Functional impacts on DNA replication and genome stability have long been known to play roles in malignant transformation through a variety of complex mechanisms, and significant further insights have been gained from studying model organisms in this context. Congenital hypomorphic defects in components of the DNA replication machinery have been and continue to be identified in humans. These disorders present with a wide range of clinical features. Indeed, in some instances, different mutations in the same gene underlie different clinical presentations. Understanding the origin and molecular basis of these features opens a window onto the range of developmental impacts of suboptimal DNA replication and genome instability in humans. Here, I will briefly overview the basic steps involved in DNA replication and the key concepts that have emerged from this area of research, before switching emphasis to the pathological consequences of defects within the DNA replication network; the human disorders. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Mark O'Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
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21
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Abramowicz I, Carpenter G, Alfieri M, Colnaghi R, Outwin E, Parent P, Thauvin-Robinet C, Iaconis D, Franco B, O'Driscoll M. Oral-facial-digital syndrome type I cells exhibit impaired DNA repair; unanticipated consequences of defective OFD1 outside of the cilia network. Hum Mol Genet 2017; 26:19-32. [PMID: 27798113 DOI: 10.1093/hmg/ddw364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/18/2016] [Indexed: 02/11/2024] Open
Abstract
Defects in OFD1 underlie the clinically complex ciliopathy, Oral-Facial-Digital syndrome Type I (OFD Type I). Our understanding of the molecular, cellular and clinical consequences of impaired OFD1 originates from its characterised roles at the centrosome/basal body/cilia network. Nonetheless, the first described OFD1 interactors were components of the TIP60 histone acetyltransferase complex. We find that OFD1 can also localise to chromatin and its reduced expression is associated with mis-localization of TIP60 in patient-derived cell lines. TIP60 plays important roles in controlling DNA repair. OFD Type I cells exhibit reduced histone acetylation and altered chromatin dynamics in response to DNA double strand breaks (DSBs). Furthermore, reduced OFD1 impaired DSB repair via homologous recombination repair (HRR). OFD1 loss also adversely impacted upon the DSB-induced G2-M checkpoint, inducing a hypersensitive and prolonged arrest. Our findings show that OFD Type I patient cells have pronounced defects in the DSB-induced histone modification, chromatin remodelling and DSB-repair via HRR; effectively phenocopying loss of TIP60. These data extend our knowledge of the molecular and cellular consequences of impaired OFD1, demonstrating that loss of OFD1 can negatively impact upon important nuclear events; chromatin plasticity and DNA repair.
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Affiliation(s)
- Iga Abramowicz
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Gillian Carpenter
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | | | - Rita Colnaghi
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Emily Outwin
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Philippe Parent
- Service de Génétique, Centre Hospitalier Universitaire de Brest, France
| | | | | | - Brunella Franco
- Telethon Institute of Genetics and Medicine, Naples, Italy
- Department of Medical Translational Sciences, Federico II University, Naples, Italy
| | - Mark O'Driscoll
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
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22
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Johnson CA, Collis SJ. Ciliogenesis and the DNA damage response: a stressful relationship. Cilia 2016; 5:19. [PMID: 27335639 PMCID: PMC4916530 DOI: 10.1186/s13630-016-0040-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 03/22/2016] [Indexed: 01/27/2023] Open
Abstract
Both inherited and sporadic mutations can give rise to a plethora of human diseases. Through myriad diverse cellular processes, sporadic mutations can arise through a failure to accurately replicate the genetic code or by inaccurate separation of duplicated chromosomes into daughter cells. The human genome has therefore evolved to encode a large number of proteins that work together with regulators of the cell cycle to ensure that it remains error-free. This is collectively known as the DNA damage response (DDR), and genome stability mechanisms involve a complex network of signalling and processing factors that ensure redundancy and adaptability of these systems. The importance of genome stability mechanisms is best illustrated by the dramatic increased risk of cancer in individuals with underlying disruption to genome maintenance mechanisms. Cilia are microtubule-based sensory organelles present on most vertebrate cells, where they facilitate transduction of external signals into the cell. When not embedded within the specialised ciliary membrane, components of the primary cilium's basal body help form the microtubule organising centre that controls cellular trafficking and the mitotic segregation of chromosomes. Ciliopathies are a collection of diseases associated with functional disruption to cilia function through a variety of different mechanisms. Ciliopathy phenotypes can vary widely, and although some cellular overgrowth phenotypes are prevalent in a subset of ciliopathies, an increased risk of cancer is not noted as a clinical feature. However, recent studies have identified surprising genetic and functional links between cilia-associated proteins and genome maintenance factors. The purpose of this mini-review is to therefore highlight some of these discoveries and discuss their implications with regards to functional crosstalk between the DDR and ciliogenesis pathways, and how this may impact on the development of human disease.
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Affiliation(s)
- Colin A. Johnson
- />Section of Ophthalmology and Neurosciences, Wellcome Trust Brenner Building, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Leeds, LS9 7TF UK
| | - Spencer J. Collis
- />Genome Stability Group, Department of Oncology and Metabolism, Academic Unit of Molecular Oncology, Medical School, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX UK
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