1
|
Ranes M, Zaleska M, Sakalas S, Knight R, Guettler S. Reconstitution of the destruction complex defines roles of AXIN polymers and APC in β-catenin capture, phosphorylation, and ubiquitylation. Mol Cell 2021; 81:3246-3261.e11. [PMID: 34352208 PMCID: PMC8403986 DOI: 10.1016/j.molcel.2021.07.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 05/18/2021] [Accepted: 07/13/2021] [Indexed: 12/24/2022]
Abstract
The Wnt/β-catenin pathway is a highly conserved, frequently mutated developmental and cancer pathway. Its output is defined mainly by β-catenin's phosphorylation- and ubiquitylation-dependent proteasomal degradation, initiated by the multi-protein β-catenin destruction complex. The precise mechanisms underlying destruction complex function have remained unknown, largely because of the lack of suitable in vitro systems. Here we describe the in vitro reconstitution of an active human β-catenin destruction complex from purified components, recapitulating complex assembly, β-catenin modification, and degradation. We reveal that AXIN1 polymerization and APC promote β-catenin capture, phosphorylation, and ubiquitylation. APC facilitates β-catenin's flux through the complex by limiting ubiquitylation processivity and directly interacts with the SCFβ-TrCP E3 ligase complex in a β-TrCP-dependent manner. Oncogenic APC truncation variants, although part of the complex, are functionally impaired. Nonetheless, even the most severely truncated APC variant promotes β-catenin recruitment. These findings exemplify the power of biochemical reconstitution to interrogate the molecular mechanisms of Wnt/β-catenin signaling.
Collapse
Affiliation(s)
- Michael Ranes
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Mariola Zaleska
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Saira Sakalas
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Ruth Knight
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Sebastian Guettler
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK.
| |
Collapse
|
2
|
Gonzalez-Exposito R, Semiannikova M, Griffiths B, Khan K, Barber LJ, Woolston A, Spain G, von Loga K, Challoner B, Patel R, Ranes M, Swain A, Thomas J, Bryant A, Saffery C, Fotiadis N, Guettler S, Mansfield D, Melcher A, Powles T, Rao S, Watkins D, Chau I, Matthews N, Wallberg F, Starling N, Cunningham D, Gerlinger M. CEA expression heterogeneity and plasticity confer resistance to the CEA-targeting bispecific immunotherapy antibody cibisatamab (CEA-TCB) in patient-derived colorectal cancer organoids. J Immunother Cancer 2019; 7:101. [PMID: 30982469 PMCID: PMC6463631 DOI: 10.1186/s40425-019-0575-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/22/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The T cell bispecific antibody cibisatamab (CEA-TCB) binds Carcino-Embryonic Antigen (CEA) on cancer cells and CD3 on T cells, which triggers T cell killing of cancer cell lines expressing moderate to high levels of CEA at the cell surface. Patient derived colorectal cancer organoids (PDOs) may more accurately represent patient tumors than established cell lines which potentially enables more detailed insights into mechanisms of cibisatamab resistance and sensitivity. METHODS We established PDOs from multidrug-resistant metastatic CRCs. CEA expression of PDOs was determined by FACS and sensitivity to cibisatamab immunotherapy was assessed by co-culture of PDOs and allogeneic CD8 T cells. RESULTS PDOs could be categorized into 3 groups based on CEA cell-surface expression: CEAhi (n = 3), CEAlo (n = 1) and CEAmixed PDOs (n = 4), that stably maintained populations of CEAhi and CEAlo cells, which has not previously been described in CRC cell lines. CEAhi PDOs were sensitive whereas CEAlo PDOs showed resistance to cibisatamab. PDOs with mixed expression showed low sensitivity to cibisatamab, suggesting that CEAlo cells maintain cancer cell growth. Culture of FACS-sorted CEAhi and CEAlo cells from PDOs with mixed CEA expression demonstrated high plasticity of CEA expression, contributing to resistance acquisition through CEA antigen loss. RNA-sequencing revealed increased WNT/β-catenin pathway activity in CEAlo cells. Cell surface CEA expression was up-regulated by inhibitors of the WNT/β-catenin pathway. CONCLUSIONS Based on these preclinical findings, heterogeneity and plasticity of CEA expression appear to confer low cibisatamab sensitivity in PDOs, supporting further clinical evaluation of their predictive effect in CRC. Pharmacological inhibition of the WNT/β-catenin pathway may be a rational combination to sensitize CRCs to cibisatamab. Our novel PDO and T cell co-culture immunotherapy models enable pre-clinical discovery of candidate biomarkers and combination therapies that may inform and accelerate the development of immuno-oncology agents in the clinic.
Collapse
Affiliation(s)
- Reyes Gonzalez-Exposito
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Maria Semiannikova
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Beatrice Griffiths
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Khurum Khan
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Louise J. Barber
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Andrew Woolston
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Georgia Spain
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Katharina von Loga
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Ben Challoner
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Radhika Patel
- Flow Cytometry and Light Microscopy Core Facility, The Institute of Cancer Research, London, UK
| | - Michael Ranes
- Structural Biology of Cell Signalling Laboratory, The Institute of Cancer Research, London, UK
| | - Amanda Swain
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Janet Thomas
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Annette Bryant
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Claire Saffery
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Nicos Fotiadis
- Department of Radiology, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Sebastian Guettler
- Structural Biology of Cell Signalling Laboratory, The Institute of Cancer Research, London, UK
| | - David Mansfield
- Translational Immunotherapy Laboratory, The Institute of Cancer Research, London, UK
| | - Alan Melcher
- Translational Immunotherapy Laboratory, The Institute of Cancer Research, London, UK
| | - Thomas Powles
- Barts Cancer Institute, Queen Mary University, London, UK
| | - Sheela Rao
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - David Watkins
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Ian Chau
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Nik Matthews
- Tumour Profiling Unit, The Institute of Cancer Research, London, UK
| | - Fredrik Wallberg
- Flow Cytometry and Light Microscopy Core Facility, The Institute of Cancer Research, London, UK
| | - Naureen Starling
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - David Cunningham
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Marco Gerlinger
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
- Gastrointestinal Cancer Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| |
Collapse
|
3
|
Pettitt SJ, Krastev DB, Brandsma I, Dréan A, Song F, Aleksandrov R, Harrell MI, Menon M, Brough R, Campbell J, Frankum J, Ranes M, Pemberton HN, Rafiq R, Fenwick K, Swain A, Guettler S, Lee JM, Swisher EM, Stoynov S, Yusa K, Ashworth A, Lord CJ. Genome-wide and high-density CRISPR-Cas9 screens identify point mutations in PARP1 causing PARP inhibitor resistance. Nat Commun 2018; 9:1849. [PMID: 29748565 PMCID: PMC5945626 DOI: 10.1038/s41467-018-03917-2] [Citation(s) in RCA: 280] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 03/22/2018] [Indexed: 12/21/2022] Open
Abstract
Although PARP inhibitors (PARPi) target homologous recombination defective tumours, drug resistance frequently emerges, often via poorly understood mechanisms. Here, using genome-wide and high-density CRISPR-Cas9 "tag-mutate-enrich" mutagenesis screens, we identify close to full-length mutant forms of PARP1 that cause in vitro and in vivo PARPi resistance. Mutations both within and outside of the PARP1 DNA-binding zinc-finger domains cause PARPi resistance and alter PARP1 trapping, as does a PARP1 mutation found in a clinical case of PARPi resistance. This reinforces the importance of trapped PARP1 as a cytotoxic DNA lesion and suggests that PARP1 intramolecular interactions might influence PARPi-mediated cytotoxicity. PARP1 mutations are also tolerated in cells with a pathogenic BRCA1 mutation where they result in distinct sensitivities to chemotherapeutic drugs compared to other mechanisms of PARPi resistance (BRCA1 reversion, 53BP1, REV7 (MAD2L2) mutation), suggesting that the underlying mechanism of PARPi resistance that emerges could influence the success of subsequent therapies.
Collapse
Affiliation(s)
- Stephen J Pettitt
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Dragomir B Krastev
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Inger Brandsma
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Amy Dréan
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Feifei Song
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Radoslav Aleksandrov
- Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
| | - Maria I Harrell
- University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA, 98195, USA
| | - Malini Menon
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - James Campbell
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Jessica Frankum
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Michael Ranes
- Divison of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Helen N Pemberton
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rumana Rafiq
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Amanda Swain
- Tumour Profiling Unit, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Sebastian Guettler
- Divison of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Jung-Min Lee
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Elizabeth M Swisher
- University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA, 98195, USA
| | - Stoyno Stoynov
- Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
| | - Kosuke Yusa
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, 1450 3rd St, San Francisco, CA, 94158, USA.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK.
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
| |
Collapse
|
4
|
Abstract
The poly(ADP-ribose)polymerase (PARP) enzyme tankyrase (TNKS/ARTD5, TNKS2/ARTD6) uses its ankyrin repeat clusters (ARCs) to recognize degenerate peptide motifs in a wide range of proteins, thereby recruiting such proteins and their complexes for scaffolding and/or poly(ADP-ribosyl)ation. Here, we provide guidance for predicting putative tankyrase-binding motifs, based on the previously delineated peptide sequence rules and existing structural information. We present a general method for the expression and purification of tankyrase ARCs from Escherichia coli and outline a fluorescence polarization assay to quantitatively assess direct ARC-TBM peptide interactions. We provide a basic protocol for evaluating binding and poly(ADP-ribosyl)ation of full-length candidate interacting proteins by full-length tankyrase in mammalian cells.
Collapse
Affiliation(s)
- Katie Pollock
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Cancer Biology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Cancer Therapeutics, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Michael Ranes
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Cancer Biology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ian Collins
- Division of Cancer Therapeutics, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Sebastian Guettler
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK.
- Division of Cancer Biology, The Institute of Cancer Research, London, SW7 3RP, UK.
| |
Collapse
|
5
|
Mariotti L, Templeton CM, Ranes M, Paracuellos P, Cronin N, Beuron F, Morris E, Guettler S. Tankyrase Requires SAM Domain-Dependent Polymerization to Support Wnt-β-Catenin Signaling. Mol Cell 2016; 63:498-513. [PMID: 27494558 PMCID: PMC4980433 DOI: 10.1016/j.molcel.2016.06.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 05/13/2016] [Accepted: 06/13/2016] [Indexed: 01/14/2023]
Abstract
The poly(ADP-ribose) polymerase (PARP) Tankyrase (TNKS and TNKS2) is paramount to Wnt-β-catenin signaling and a promising therapeutic target in Wnt-dependent cancers. The pool of active β-catenin is normally limited by destruction complexes, whose assembly depends on the polymeric master scaffolding protein AXIN. Tankyrase, which poly(ADP-ribosyl)ates and thereby destabilizes AXIN, also can polymerize, but the relevance of these polymers has remained unclear. We report crystal structures of the polymerizing TNKS and TNKS2 sterile alpha motif (SAM) domains, revealing versatile head-to-tail interactions. Biochemical studies informed by these structures demonstrate that polymerization is required for Tankyrase to drive β-catenin-dependent transcription. We show that the polymeric state supports PARP activity and allows Tankyrase to effectively access destruction complexes through enabling avidity-dependent AXIN binding. This study provides an example for regulated signal transduction in non-membrane-enclosed compartments (signalosomes), and it points to novel potential strategies to inhibit Tankyrase function in oncogenic Wnt signaling.
Collapse
Affiliation(s)
- Laura Mariotti
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Catherine M Templeton
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Michael Ranes
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Patricia Paracuellos
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Nora Cronin
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Edward Morris
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Sebastian Guettler
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK.
| |
Collapse
|
6
|
Ranes M, Boeing S, Wang Y, Wienholz F, Menoni H, Walker J, Encheva V, Chakravarty P, Mari PO, Stewart A, Giglia-Mari G, Snijders AP, Vermeulen W, Svejstrup JQ. A ubiquitylation site in Cockayne syndrome B required for repair of oxidative DNA damage, but not for transcription-coupled nucleotide excision repair. Nucleic Acids Res 2016; 44:5246-55. [PMID: 27060134 PMCID: PMC4914099 DOI: 10.1093/nar/gkw216] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/11/2016] [Accepted: 03/18/2016] [Indexed: 12/23/2022] Open
Abstract
Cockayne syndrome B (CSB), best known for its role in transcription-coupled nucleotide excision repair (TC-NER), contains a ubiquitin-binding domain (UBD), but the functional connection between protein ubiquitylation and this UBD remains unclear. Here, we show that CSB is regulated via site-specific ubiquitylation. Mass spectrometry analysis of CSB identified lysine (K) 991 as a ubiquitylation site. Intriguingly, mutation of this residue (K991R) does not affect CSB's catalytic activity or protein stability, but greatly affects genome stability, even in the absence of induced DNA damage. Moreover, cells expressing CSB K991R are sensitive to oxidative DNA damage, but proficient for TC-NER. K991 becomes ubiquitylated upon oxidative DNA damage, and while CSB K991R is recruited normally to such damage, it fails to dissociate in a timely manner, suggesting a requirement for K991 ubiquitylation in CSB activation. Interestingly, deletion of CSB's UBD gives rise to oxidative damage sensitivity as well, while CSB ΔUBD and CSB K991R affects expression of overlapping groups of genes, further indicating a functional connection. Together, these results shed new light on the regulation of CSB, with K991R representing an important separation-of-function-mutation in this multi-functional protein.
Collapse
Affiliation(s)
- Michael Ranes
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Stefan Boeing
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Yuming Wang
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Franziska Wienholz
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Hervé Menoni
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Jane Walker
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Vesela Encheva
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Probir Chakravarty
- Bioinformatics & Biostatistics Laboratory, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Pierre-Olivier Mari
- Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F-31077 Toulouse, France
| | - Aengus Stewart
- Bioinformatics & Biostatistics Laboratory, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Giuseppina Giglia-Mari
- Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F-31077 Toulouse, France
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Wim Vermeulen
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| |
Collapse
|
7
|
Wang Y, Chakravarty P, Ranes M, Kelly G, Brooks PJ, Neilan E, Stewart A, Schiavo G, Svejstrup JQ. Dysregulation of gene expression as a cause of Cockayne syndrome neurological disease. Proc Natl Acad Sci U S A 2014; 111:14454-9. [PMID: 25249633 PMCID: PMC4210037 DOI: 10.1073/pnas.1412569111] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cockayne syndrome (CS) is a multisystem disorder with severe neurological symptoms. The majority of CS patients carry mutations in Cockayne syndrome group B (CSB), best known for its role in transcription-coupled nucleotide excision repair. Indeed, because various repair pathways are compromised in patient cells, CS is widely considered a genome instability syndrome. Here, we investigate the connection between the neuropathology of CS and dysregulation of gene expression. Transcriptome analysis of human fibroblasts revealed that even in the absence of DNA damage, CSB affects the expression of thousands of genes, many of which are neuronal genes. CSB is present in a significant subset of these genes, suggesting that regulation is direct, at the level of transcription. Importantly, reprogramming of CS fibroblasts to neuron-like cells is defective unless an exogenous CSB gene is introduced. Moreover, neuroblastoma cells from which CSB is depleted show defects in gene expression programs required for neuronal differentiation, and fail to differentiate and extend neurites. Likewise, neuron-like cells cannot be maintained without CSB. Finally, a number of disease symptoms may be explained by marked gene expression changes in the brain of patients with CS. Together, these data point to dysregulation of gene regulatory networks as a cause of the neurological symptoms in CS.
Collapse
Affiliation(s)
- Yuming Wang
- Mechanisms of Transcription Laboratory, Cancer Research UK London Research Institute, South Mimms EN6 3LD, United Kingdom
| | - Probir Chakravarty
- Bioinformatics and Biostatistics Group, Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Michael Ranes
- Mechanisms of Transcription Laboratory, Cancer Research UK London Research Institute, South Mimms EN6 3LD, United Kingdom
| | - Gavin Kelly
- Bioinformatics and Biostatistics Group, Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Philip J Brooks
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism and Office of Rare Diseases Research, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892
| | - Edward Neilan
- Genetics and Metabolism, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115; and
| | - Aengus Stewart
- Bioinformatics and Biostatistics Group, Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Giampietro Schiavo
- Sobell Department of Motor Neuroscience and Movement Disorders, Institute of Neurology, University College London, London WC1N 3BG, United Kingdom
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, Cancer Research UK London Research Institute, South Mimms EN6 3LD, United Kingdom;
| |
Collapse
|
8
|
van Vugt JJFA, Ranes M, Campsteijn C, Logie C. The ins and outs of ATP-dependent chromatin remodeling in budding yeast: biophysical and proteomic perspectives. ACTA ACUST UNITED AC 2007; 1769:153-71. [PMID: 17395283 DOI: 10.1016/j.bbaexp.2007.01.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 01/22/2007] [Accepted: 01/29/2007] [Indexed: 11/30/2022]
Abstract
ATP-dependent chromatin remodeling is performed by multi-subunit protein complexes. Over the last years, the identity of these factors has been unveiled in yeast and many parallels have been drawn with animal and plant systems, indicating that sophisticated chromatin transactions evolved prior to their divergence. Here we review current knowledge pertaining to the molecular mode of action of ATP-dependent chromatin remodeling, from single molecule studies to genome-wide genetic and proteomic studies. We focus on the budding yeast versions of SWI/SNF, RSC, DDM1, ISWI, CHD1, INO80 and SWR1.
Collapse
Affiliation(s)
- Joke J F A van Vugt
- Department of Molecular Biology, NCMLS, Radboud University, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | | | | | | |
Collapse
|
9
|
Hori T, Paliard X, de Waal Malefijt R, Ranes M, Spits H. Comparative analysis of CD8 expressed on mature CD4+ CD8+ T cell clones cultured with IL-4 and that on CD8+ T cell clones: implication for functional significance of CD8 beta. Int Immunol 1991; 3:737-41. [PMID: 1911543 DOI: 10.1093/intimm/3.7.737] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Interleukin (IL-4) can induce CD8 expression on mature CD4+ T cells. To study this phenomenon in more detail, we characterized CD8 expressed on IL-4-induced CD4+ CD8+ (double positive) T cell clones in comparison with that on CD8+ T cell clones. Using 2ST8-5H7 mAb that detects CD8 beta expression, we found that double positive T cell clones isolated with IL-4 express CD8 alpha but not beta, in contrast to CD8+ CTL cell clones, which express both chains of CD8. Northern blot analysis revealed that these double positive clones expressed CD8 alpha but not beta mRNA, indicating that CD8 alpha and beta are independently regulated at the pre-translational level. Immunoprecipitation experiments showed that CD8 expressed on a representative IL-4-induced double positive T cell clone consists mainly of homodimers of a single 34 kd protein of CD8 alpha. The amount of multimers detected from this clone was much less than that from a CD8+ CTL clone. These results suggest that persistent expression of CD8 beta is specific for the CD8+ lineage and may be involved in polymerization and stabilization of CD8 which enhances the efficiency of class I-restricted antigen recognition.
Collapse
Affiliation(s)
- T Hori
- DNAX Research Institute of Molecular and Cellular Biology, Palo Alto, CA 94304-1104
| | | | | | | | | |
Collapse
|
10
|
Schauer A, Ranes M, Santamaria R, Guijarro J, Lawlor E, Mendez C, Chater K, Losick R. Visualizing gene expression in time and space in the filamentous bacterium Streptomyces coelicolor. Science 1988; 240:768-72. [PMID: 3363358 DOI: 10.1126/science.3363358] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Streptomycetes are prokaryotic microorganisms that exhibit a complex, mycelial fungus-like cycle of morphological differentiation. Development involves at least two spatially separated types of cells: the branching hyphae of the substrate mycelium, which penetrate the stratum upon which the colony feeds, and the upwardly protruding hyphae of the aerial mycelium, which undergo metamorphosis into spores. The luciferase-encoding luxA and luxB operon of the luminescent marine bacterium Vibrio harveyi was used as a promoter probe to visualize gene expression in differentiating colonies of Streptomyces coelicolor. Promoters for developmental genes of several kinds gave distinctive temporal and spatial patterns of light emission.
Collapse
Affiliation(s)
- A Schauer
- Department of Cellular and Developmental Biology, Harvard University, Cambridge, MA 02138
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Abstract
Two forms of RNA polymerase holoenzyme have been identified in the filamentous differentiating bacterium Streptomyces coelicolor. They contain different species of sigma factor and are distinguishable by their ability to recognize different promoter classes. These and other holoenzyme forms may in part determine the selective expression of different gene sets in this morphologically-complex bacterium.
Collapse
|