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Hong DS, Van Tine BA, Biswas S, McAlpine C, Johnson ML, Olszanski AJ, Clarke JM, Araujo D, Blumenschein GR, Kebriaei P, Lin Q, Tipping AJ, Sanderson JP, Wang R, Trivedi T, Annareddy T, Bai J, Rafail S, Sun A, Fernandes L, Navenot JM, Bushman FD, Everett JK, Karadeniz D, Broad R, Isabelle M, Naidoo R, Bath N, Betts G, Wolchinsky Z, Batrakou DG, Van Winkle E, Elefant E, Ghobadi A, Cashen A, Grand'Maison A, McCarthy P, Fracasso PM, Norry E, Williams D, Druta M, Liebner DA, Odunsi K, Butler MO. Autologous T cell therapy for MAGE-A4 + solid cancers in HLA-A*02 + patients: a phase 1 trial. Nat Med 2023; 29:104-114. [PMID: 36624315 PMCID: PMC9873554 DOI: 10.1038/s41591-022-02128-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 11/09/2022] [Indexed: 01/11/2023]
Abstract
Affinity-optimized T cell receptors can enhance the potency of adoptive T cell therapy. Afamitresgene autoleucel (afami-cel) is a human leukocyte antigen-restricted autologous T cell therapy targeting melanoma-associated antigen A4 (MAGE-A4), a cancer/testis antigen expressed at varying levels in multiple solid tumors. We conducted a multicenter, dose-escalation, phase 1 trial in patients with relapsed/refractory metastatic solid tumors expressing MAGE-A4, including synovial sarcoma (SS), ovarian cancer and head and neck cancer ( NCT03132922 ). The primary endpoint was safety, and the secondary efficacy endpoints included overall response rate (ORR) and duration of response. All patients (N = 38, nine tumor types) experienced Grade ≥3 hematologic toxicities; 55% of patients (90% Grade ≤2) experienced cytokine release syndrome. ORR (all partial response) was 24% (9/38), 7/16 (44%) for SS and 2/22 (9%) for all other cancers. Median duration of response was 25.6 weeks (95% confidence interval (CI): 12.286, not reached) and 28.1 weeks (95% CI: 12.286, not reached) overall and for SS, respectively. Exploratory analyses showed that afami-cel infiltrates tumors, has an interferon-γ-driven mechanism of action and triggers adaptive immune responses. In addition, afami-cel has an acceptable benefit-risk profile, with early and durable responses, especially in patients with metastatic SS. Although the small trial size limits conclusions that can be drawn, the results warrant further testing in larger studies.
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Affiliation(s)
- David S Hong
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Brian A Van Tine
- Section of Medical Oncology, Division of Oncology, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Melissa L Johnson
- Sarah Cannon Cancer Institute, Tennessee Oncology/One Oncology, Nashville, TN, USA
| | - Anthony J Olszanski
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Dejka Araujo
- Department of Sarcoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George R Blumenschein
- Department of Thoracic-Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Partow Kebriaei
- Department of Stem Cell Transplantation and Cellular Therapy, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Quan Lin
- Adaptimmue, Philadelphia, PA, USA
| | | | | | | | | | | | - Jane Bai
- Adaptimmue, Philadelphia, PA, USA
| | | | - Amy Sun
- Adaptimmue, Philadelphia, PA, USA
| | | | | | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - John K Everett
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Derin Karadeniz
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | | | | | - Armin Ghobadi
- Section of Medical Oncology, Division of Oncology, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Amanda Cashen
- Section of Medical Oncology, Division of Oncology, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne Grand'Maison
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Philip McCarthy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | | | | | | | - Mihaela Druta
- Sarcoma Medical Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - David A Liebner
- Department of Internal Medicine, Division of Medical Oncology, and Department of Biomedical Informatics, Division of Computational Biology and Bioinformatics, Ohio State University, Columbus, OH, USA
| | - Kunle Odunsi
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA
| | - Marcus O Butler
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
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Hong DS, Butler MO, Pachynski RK, Sullivan R, Kebriaei P, Boross-Harmer S, Ghobadi A, Frigault MJ, Dumbrava EE, Sauer A, Brophy F, Navenot JM, Fayngerts S, Wolchinsky Z, Broad R, Batrakou DG, Wang R, Solis LM, Duose DY, Sanderson JP, Gerry AB, Marks D, Bai J, Norry E, Fracasso PM. Phase 1 Clinical Trial Evaluating the Safety and Anti-Tumor Activity of ADP-A2M10 SPEAR T-Cells in Patients With MAGE-A10+ Head and Neck, Melanoma, or Urothelial Tumors. Front Oncol 2022; 12:818679. [PMID: 35372008 PMCID: PMC8972123 DOI: 10.3389/fonc.2022.818679] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/18/2022] [Indexed: 02/02/2023] Open
Abstract
Background ADP-A2M10 specific peptide enhanced affinity receptor (SPEAR) T-cells are genetically engineered autologous T-cells that express a high-affinity melanoma-associated antigen (MAGE)-A10-specific T-cell receptor (TCR) targeting MAGE-A10-positive tumors in the context of human leukocyte antigen (HLA)-A*02. ADP-0022-004 is a phase 1, dose-escalation trial to evaluate the safety and anti-tumor activity of ADP-A2M10 in three malignancies (https://clinicaltrials.gov: NCT02989064). Methods Eligible patients were HLA-A*02 positive with advanced head and neck squamous cell carcinoma (HNSCC), melanoma, or urothelial carcinoma (UC) expressing MAGE-A10. Patients underwent apheresis; T-cells were isolated, transduced with a lentiviral vector containing the MAGE-A10 TCR, and expanded. Patients underwent lymphodepletion with fludarabine and cyclophosphamide prior to receiving ADP-A2M10. ADP-A2M10 was administered in two dose groups receiving 0.1×109 and >1.2 to 6×109 transduced cells, respectively, and an expansion group receiving 1.2 to 15×109 transduced cells. Results Ten patients (eight male and two female) with HNSCC (four), melanoma (three), and UC (three) were treated. Three patients were treated in each of the two dose groups, and four patients were treated in the expansion group. The most frequently reported adverse events grade ≥3 were leukopenia (10), lymphopenia (10), neutropenia (10), anemia (nine), and thrombocytopenia (five). Two patients reported cytokine release syndrome (one each with grade 1 and grade 3), with resolution. Best response included stable disease in four patients, progressive disease in five patients, and not evaluable in one patient. ADP-A2M10 cells were detectable in peripheral blood from patients in each dose group and the expansion group and in tumor tissues from patients in the higher dose group and the expansion group. Peak persistence was greater in patients from the higher dose group and the expansion group compared with the lower dose group. Conclusions ADP-A2M10 has shown an acceptable safety profile with no evidence of toxicity related to off-target binding or alloreactivity in these malignancies. Persistence of ADP-A2M10 in the peripheral blood and trafficking of ADP-A2M10 into the tumor was demonstrated. Because MAGE-A10 expression frequently overlaps with MAGE-A4 expression in tumors and responses were observed in the MAGE-A4 trial (NCT03132922), this clinical program closed, and trials with SPEAR T-cells targeting the MAGE-A4 antigen are ongoing.
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Affiliation(s)
- David S. Hong
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- *Correspondence: David S. Hong,
| | - Marcus O. Butler
- Princess Margaret Hospital Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Russell K. Pachynski
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Ryan Sullivan
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Partow Kebriaei
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sarah Boross-Harmer
- Princess Margaret Hospital Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Armin Ghobadi
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Matthew J. Frigault
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Ecaterina E. Dumbrava
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Amy Sauer
- Adaptimmune LLC, Philadelphia, PA, United States
| | | | | | | | | | - Robyn Broad
- Adaptimmune Limited, Abingdon, United Kingdom
| | | | - Ruoxi Wang
- Adaptimmune Limited, Abingdon, United Kingdom
| | - Luisa M. Solis
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Dzifa Yawa Duose
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | | | - Diane Marks
- Adaptimmune LLC, Philadelphia, PA, United States
| | - Jane Bai
- Adaptimmune LLC, Philadelphia, PA, United States
| | - Elliot Norry
- Adaptimmune LLC, Philadelphia, PA, United States
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Czapiewski R, Batrakou DG, de Las Heras JI, Carter RN, Sivakumar A, Sliwinska M, Dixon CR, Webb S, Lattanzi G, Morton NM, Schirmer EC. Genomic loci mispositioning in Tmem120a knockout mice yields latent lipodystrophy. Nat Commun 2022; 13:321. [PMID: 35027552 PMCID: PMC8758788 DOI: 10.1038/s41467-021-27869-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 04/15/2021] [Accepted: 12/19/2021] [Indexed: 12/13/2022] Open
Abstract
Little is known about how the observed fat-specific pattern of 3D-spatial genome organisation is established. Here we report that adipocyte-specific knockout of the gene encoding nuclear envelope transmembrane protein Tmem120a disrupts fat genome organisation, thus causing a lipodystrophy syndrome. Tmem120a deficiency broadly suppresses lipid metabolism pathway gene expression and induces myogenic gene expression by repositioning genes, enhancers and miRNA-encoding loci between the nuclear periphery and interior. Tmem120a-/- mice, particularly females, exhibit a lipodystrophy syndrome similar to human familial partial lipodystrophy FPLD2, with profound insulin resistance and metabolic defects that manifest upon exposure to an obesogenic diet. Interestingly, similar genome organisation defects occurred in cells from FPLD2 patients that harbour nuclear envelope protein encoding LMNA mutations. Our data indicate TMEM120A genome organisation functions affect many adipose functions and its loss may yield adiposity spectrum disorders, including a miRNA-based mechanism that could explain muscle hypertrophy in human lipodystrophy.
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Affiliation(s)
- Rafal Czapiewski
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Dzmitry G Batrakou
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | | | - Roderick N Carter
- Molecular Metabolism Group, University/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | | | | | - Charles R Dixon
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Giovanna Lattanzi
- CNR - National Research Council of Italy, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, 40136, Italy
- IRCCS, Istituto Ortopedico Rizzoli, Bologna, 40136, Italy
| | - Nicholas M Morton
- Molecular Metabolism Group, University/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Eric C Schirmer
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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Batrakou DG, Heron ED, Nieduszynski CA. Rapid high-resolution measurement of DNA replication timing by droplet digital PCR. Nucleic Acids Res 2018; 46:e112. [PMID: 29986073 PMCID: PMC6212846 DOI: 10.1093/nar/gky590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 06/11/2018] [Accepted: 06/18/2018] [Indexed: 02/03/2023] Open
Abstract
Genomes are replicated in a reproducible temporal pattern. Current methods for assaying allele replication timing are time consuming and/or expensive. These include high-throughput sequencing which can be used to measure DNA copy number as a proxy for allele replication timing. Here, we use droplet digital PCR to study DNA replication timing at multiple loci in budding yeast and human cells. We establish that the method has temporal and spatial resolutions comparable to the high-throughput sequencing approaches, while being faster than alternative locus-specific methods. Furthermore, the approach is capable of allele discrimination. We apply this method to determine relative replication timing across timing transition zones in cultured human cells. Finally, multiple samples can be analysed in parallel, allowing us to rapidly screen kinetochore mutants for perturbation to centromere replication timing. Therefore, this approach is well suited to the study of locus-specific replication and the screening of cis- and trans-acting mutants to identify mechanisms that regulate local genome replication timing.
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Affiliation(s)
- Dzmitry G Batrakou
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Emma D Heron
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Conrad A Nieduszynski
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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5
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de Las Heras JI, Zuleger N, Batrakou DG, Czapiewski R, Kerr ARW, Schirmer EC. Tissue-specific NETs alter genome organization and regulation even in a heterologous system. Nucleus 2017; 8:81-97. [PMID: 28045568 PMCID: PMC5287206 DOI: 10.1080/19491034.2016.1261230] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Different cell types exhibit distinct patterns of 3D genome organization that correlate with changes in gene expression in tissue and differentiation systems. Several tissue-specific nuclear envelope transmembrane proteins (NETs) have been found to influence the spatial positioning of genes and chromosomes that normally occurs during tissue differentiation. Here we study 3 such NETs: NET29, NET39, and NET47, which are expressed preferentially in fat, muscle and liver, respectively. We found that even when exogenously expressed in a heterologous system they can specify particular genome organization patterns and alter gene expression. Each NET affected largely different subsets of genes. Notably, the liver-specific NET47 upregulated many genes in HT1080 fibroblast cells that are normally upregulated in hepatogenesis, showing that tissue-specific NETs can favor expression patterns associated with the tissue where the NET is normally expressed. Similarly, global profiling of peripheral chromatin after exogenous expression of these NETs using lamin B1 DamID revealed that each NET affected the nuclear positioning of distinct sets of genomic regions with a significant tissue-specific component. Thus NET influences on genome organization can contribute to gene expression changes associated with differentiation even in the absence of other factors and overt cellular differentiation changes.
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Affiliation(s)
- Jose I de Las Heras
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Nikolaj Zuleger
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Dzmitry G Batrakou
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Rafal Czapiewski
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Alastair R W Kerr
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Eric C Schirmer
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
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6
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Batrakou DG, de las Heras JI, Czapiewski R, Mouras R, Schirmer EC. TMEM120A and B: Nuclear Envelope Transmembrane Proteins Important for Adipocyte Differentiation. PLoS One 2015; 10:e0127712. [PMID: 26024229 PMCID: PMC4449205 DOI: 10.1371/journal.pone.0127712] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [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: 01/12/2015] [Accepted: 04/17/2015] [Indexed: 12/23/2022] Open
Abstract
Recent work indicates that the nuclear envelope is a major signaling node for the cell that can influence tissue differentiation processes. Here we present two nuclear envelope trans-membrane proteins TMEM120A and TMEM120B that are paralogs encoded by the Tmem120A and Tmem120B genes. The TMEM120 proteins are expressed preferentially in fat and both are induced during 3T3-L1 adipocyte differentiation. Knockdown of one or the other protein altered expression of several genes required for adipocyte differentiation, Gata3, Fasn, Glut4, while knockdown of both together additionally affected Pparg and Adipoq. The double knockdown also increased the strength of effects, reducing for example Glut4 levels by 95% compared to control 3T3-L1 cells upon pharmacologically induced differentiation. Accordingly, TMEM120A and B knockdown individually and together impacted on adipocyte differentiation/metabolism as measured by lipid accumulation through binding of Oil Red O and coherent anti-Stokes Raman scattering microscopy (CARS). The nuclear envelope is linked to several lipodystrophies through mutations in lamin A; however, lamin A is widely expressed. Thus it is possible that the TMEM120A and B fat-specific nuclear envelope transmembrane proteins may play a contributory role in the tissue-specific pathology of this disorder or in the wider problem of obesity.
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Affiliation(s)
- Dzmitry G. Batrakou
- Wellcome Trust Center for Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Jose I. de las Heras
- Wellcome Trust Center for Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Rafal Czapiewski
- Wellcome Trust Center for Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Rabah Mouras
- Institute for Materials and Processes, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Eric C. Schirmer
- Wellcome Trust Center for Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- * E-mail:
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7
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de Las Heras JI, Meinke P, Batrakou DG, Srsen V, Zuleger N, Kerr AR, Schirmer EC. Tissue specificity in the nuclear envelope supports its functional complexity. Nucleus 2013; 4:460-77. [PMID: 24213376 PMCID: PMC3925691 DOI: 10.4161/nucl.26872] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Nuclear envelope links to inherited disease gave the conundrum of how mutations in near-ubiquitous proteins can yield many distinct pathologies, each focused in different tissues. One conundrum-resolving hypothesis is that tissue-specific partner proteins mediate these pathologies. Such partner proteins may have now been identified with recent proteome studies determining nuclear envelope composition in different tissues. These studies revealed that the majority of the total nuclear envelope proteins are tissue restricted in their expression. Moreover, functions have been found for a number these tissue-restricted nuclear envelope proteins that fit with mechanisms proposed to explain how the nuclear envelope could mediate disease, including defects in mechanical stability, cell cycle regulation, signaling, genome organization, gene expression, nucleocytoplasmic transport, and differentiation. The wide range of functions to which these proteins contribute is consistent with not only their involvement in tissue-specific nuclear envelope disease pathologies, but also tissue evolution.
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Affiliation(s)
- Jose I de Las Heras
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
| | - Peter Meinke
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
| | - Dzmitry G Batrakou
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
| | - Vlastimil Srsen
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
| | - Nikolaj Zuleger
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
| | - Alastair Rw Kerr
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
| | - Eric C Schirmer
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
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Zuleger N, Boyle S, Kelly DA, de las Heras JI, Lazou V, Korfali N, Batrakou DG, Randles KN, Morris GE, Harrison DJ, Bickmore WA, Schirmer EC. Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery. Genome Biol 2013; 14:R14. [PMID: 23414781 PMCID: PMC4053941 DOI: 10.1186/gb-2013-14-2-r14] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 02/15/2013] [Indexed: 01/04/2023] Open
Abstract
Background Different cell types have distinctive patterns of chromosome positioning in the nucleus. Although ectopic affinity-tethering of specific loci can be used to relocate chromosomes to the nuclear periphery, endogenous nuclear envelope proteins that control such a mechanism in mammalian cells have yet to be widely identified. Results To search for such proteins, 23 nuclear envelope transmembrane proteins were screened for their ability to promote peripheral localization of human chromosomes in HT1080 fibroblasts. Five of these proteins had strong effects on chromosome 5, but individual proteins affected different subsets of chromosomes. The repositioning effects were reversible and the proteins with effects all exhibited highly tissue-restricted patterns of expression. Depletion of two nuclear envelope transmembrane proteins that were preferentially expressed in liver each reduced the normal peripheral positioning of chromosome 5 in liver cells. Conclusions The discovery of nuclear envelope transmembrane proteins that can modulate chromosome position and have restricted patterns of expression may enable dissection of the functional relevance of tissue-specific patterns of radial chromosome positioning.
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Korfali N, Wilkie GS, Swanson SK, Srsen V, de Las Heras J, Batrakou DG, Malik P, Zuleger N, Kerr ARW, Florens L, Schirmer EC. The nuclear envelope proteome differs notably between tissues. Nucleus 2012; 3:552-64. [PMID: 22990521 PMCID: PMC3515538 DOI: 10.4161/nucl.22257] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
One hypothesis to explain how mutations in the same nuclear envelope proteins yield pathologies focused in distinct tissues is that as yet unidentified tissue-specific partners mediate the disease pathologies. The nuclear envelope proteome was recently determined from leukocytes and muscle. Here the same methodology is applied to liver and a direct comparison of the liver, muscle and leukocyte data sets is presented. At least 74 novel transmembrane proteins identified in these studies have been directly confirmed at the nuclear envelope. Within this set, RT-PCR, western blot and staining of tissue cryosections confirms that the protein complement of the nuclear envelope is clearly distinct from one tissue to another. Bioinformatics reveals similar divergence between tissues across the larger data sets. For proteins acting in complexes according to interactome data, the whole complex often exhibited the same tissue-specificity. Other tissue-specific nuclear envelope proteins identified were known proteins with functions in signaling and gene regulation. The high tissue specificity in the nuclear envelope likely underlies the complex disease pathologies and argues that all organelle proteomes warrant re-examination in multiple tissues.
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Affiliation(s)
- Nadia Korfali
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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de Las Heras JI, Batrakou DG, Schirmer EC. Cancer biology and the nuclear envelope: a convoluted relationship. Semin Cancer Biol 2012; 23:125-37. [PMID: 22311402 DOI: 10.1016/j.semcancer.2012.01.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 01/16/2012] [Accepted: 01/19/2012] [Indexed: 12/23/2022]
Abstract
Although its properties have long been used for both typing and prognosis of various tumors, the nuclear envelope (NE) itself and its potential roles in tumorigenesis are only beginning to be understood. Historically viewed as merely a protective barrier, the nuclear envelope is now linked to a wide range of functions. Nuclear membrane proteins connect the nucleus to the cytoskeleton on one side and to chromatin on the other. Several newly identified nuclear envelope functions associated with these connections intersect with cancer pathways. For example, the nuclear envelope could affect genome stability by tethering chromatin. Some nuclear envelope proteins affect cell cycle regulation by directly binding to the master regulator pRb, others by interacting with TGF-ß and Smad signaling cascades, and others by affecting the mitotic spindle. Finally, the NE directly affects cytoskeletal organization and can also influence cell migration in metastasis. In this review we discuss the link between the nuclear envelope and cellular defects that are common in cancer cells, and we show that NE proteins are often aberrantly expressed in tumors. The NE represents a potential reservoir of diagnostic and prognostic markers in cancer.
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Affiliation(s)
- Jose I de Las Heras
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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11
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Korfali N, Srsen V, Waterfall M, Batrakou DG, Pekovic V, Hutchison CJ, Schirmer EC. A flow cytometry-based screen of nuclear envelope transmembrane proteins identifies NET4/Tmem53 as involved in stress-dependent cell cycle withdrawal. PLoS One 2011; 6:e18762. [PMID: 21533191 PMCID: PMC3077400 DOI: 10.1371/journal.pone.0018762] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [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: 01/07/2011] [Accepted: 03/17/2011] [Indexed: 11/29/2022] Open
Abstract
Disruption of cell cycle regulation is one mechanism proposed for how nuclear envelope protein mutation can cause disease. Thus far only a few nuclear envelope proteins have been tested/found to affect cell cycle progression: to identify others, 39 novel nuclear envelope transmembrane proteins were screened for their ability to alter flow cytometry cell cycle/DNA content profiles when exogenously expressed. Eight had notable effects with seven increasing and one decreasing the 4N∶2N ratio. We subsequently focused on NET4/Tmem53 that lost its effects in p53−/− cells and retinoblastoma protein-deficient cells. NET4/TMEM53 knockdown by siRNA altered flow cytometry cell cycle/DNA content profiles in a similar way as overexpression. NET4/TMEM53 knockdown did not affect total retinoblastoma protein levels, unlike nuclear envelope-associated proteins Lamin A and LAP2α. However, a decrease in phosphorylated retinoblastoma protein was observed along with a doubling of p53 levels and a 7-fold increase in p21. Consequently cells withdrew from the cell cycle, which was confirmed in MRC5 cells by a drop in the percentage of cells expressing Ki-67 antigen and an increase in the number of cells stained for ß-galactosidase. The ß-galactosidase upregulation suggests that cells become prematurely senescent. Finally, the changes in retinoblastoma protein, p53, and p21 resulting from loss of NET4/Tmem53 were dependent upon active p38 MAP kinase. The finding that roughly a fifth of nuclear envelope transmembrane proteins screened yielded alterations in flow cytometry cell cycle/DNA content profiles suggests a much greater influence of the nuclear envelope on the cell cycle than is widely held.
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Affiliation(s)
- Nadia Korfali
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Vlastimil Srsen
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Martin Waterfall
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Dzmitry G. Batrakou
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Vanja Pekovic
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
| | | | - Eric C. Schirmer
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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Wilkie GS, Korfali N, Swanson SK, Malik P, Srsen V, Batrakou DG, de las Heras J, Zuleger N, Kerr ARW, Florens L, Schirmer EC. Several novel nuclear envelope transmembrane proteins identified in skeletal muscle have cytoskeletal associations. Mol Cell Proteomics 2010; 10:M110.003129. [PMID: 20876400 PMCID: PMC3016689 DOI: 10.1074/mcp.m110.003129] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Nuclear envelopes from liver and a neuroblastoma cell line have previously been analyzed by proteomics; however, most diseases associated with the nuclear envelope affect muscle. To determine whether muscle has unique nuclear envelope proteins, rat skeletal muscle nuclear envelopes were prepared and analyzed by multidimensional protein identification technology. Many novel muscle-specific proteins were identified that did not appear in previous nuclear envelope data sets. Nuclear envelope residence was confirmed for 11 of these by expression of fusion proteins and by antibody staining of muscle tissue cryosections. Moreover, transcript levels for several of the newly identified nuclear envelope transmembrane proteins increased during muscle differentiation using mouse and human in vitro model systems. Some of these proteins tracked with microtubules at the nuclear surface in interphase cells and accumulated at the base of the microtubule spindle in mitotic cells, suggesting they may associate with complexes that connect the nucleus to the cytoskeleton. The finding of tissue-specific proteins in the skeletal muscle nuclear envelope proteome argues the importance of analyzing nuclear envelopes from all tissues linked to disease and suggests that general investigation of tissue differences in organellar proteomes might yield critical insights.
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Affiliation(s)
- Gavin S Wilkie
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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13
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Korfali N, Wilkie GS, Swanson SK, Srsen V, Batrakou DG, Fairley EAL, Malik P, Zuleger N, Goncharevich A, de Las Heras J, Kelly DA, Kerr ARW, Florens L, Schirmer EC. The leukocyte nuclear envelope proteome varies with cell activation and contains novel transmembrane proteins that affect genome architecture. Mol Cell Proteomics 2010; 9:2571-85. [PMID: 20693407 PMCID: PMC3101955 DOI: 10.1074/mcp.m110.002915] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A favored hypothesis to explain the pathology underlying nuclear envelopathies is that mutations in nuclear envelope proteins alter genome/chromatin organization and thus gene expression. To identify nuclear envelope proteins that play roles in genome organization, we analyzed nuclear envelopes from resting and phytohemagglutinin-activated leukocytes because leukocytes have a particularly high density of peripheral chromatin that undergoes significant reorganization upon such activation. Thus, nuclear envelopes were isolated from leukocytes in the two states and analyzed by multidimensional protein identification technology using an approach that used expected contaminating membranes as subtractive fractions. A total of 3351 proteins were identified between both nuclear envelope data sets among which were 87 putative nuclear envelope transmembrane proteins (NETs) that were not identified in a previous proteomics analysis of liver nuclear envelopes. Nuclear envelope localization was confirmed for 11 new NETs using tagged fusion proteins and antibodies on spleen cryosections. 27% of the new proteins identified were unique to one or the other of the two leukocyte states. Differences in expression between activated and resting leukocytes were confirmed for some NETs by RT-PCR, and most of these proteins appear to only be expressed in certain types of blood cells. Several known proteins identified in both data sets have functions in chromatin organization and gene regulation. To test whether the novel NETs identified might include those that also regulate chromatin, nine were run through two screens for different chromatin effects. One screen found two NETs that can recruit a specific gene locus to the nuclear periphery, and the second found a different NET that promotes chromatin condensation. The variation in the protein milieu with pharmacological activation of the same cell population and consequences for gene regulation suggest that the nuclear envelope is a complex regulatory system with significant influences on genome organization.
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Affiliation(s)
- Nadia Korfali
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH93JR, United Kingdom
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14
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Malik P, Korfali N, Srsen V, Lazou V, Batrakou DG, Zuleger N, Kavanagh DM, Wilkie GS, Goldberg MW, Schirmer EC. Cell-specific and lamin-dependent targeting of novel transmembrane proteins in the nuclear envelope. Cell Mol Life Sci 2010; 67:1353-69. [PMID: 20091084 PMCID: PMC2839517 DOI: 10.1007/s00018-010-0257-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [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: 11/02/2009] [Revised: 12/21/2009] [Accepted: 01/05/2010] [Indexed: 12/20/2022]
Abstract
Nuclear envelope complexity is expanding with respect to identification of protein components. Here we test the validity of proteomics results that identified 67 novel predicted nuclear envelope transmembrane proteins (NETs) from liver by directly comparing 30 as tagged fusions using targeting assays. This confirmed 21 as NETs, but 4 only targeted in certain cell types, underscoring the complexity of interactions that tether NETs to the nuclear envelope. Four NETs accumulated at the nuclear rim in normal fibroblasts but not in fibroblasts lacking lamin A, suggesting involvement of lamin A in tethering them in the nucleus. However, intriguingly, for the NETs tested alternative mechanisms for nuclear envelope retention could be found in Jurkat cells that normally lack lamin A. This study expands by a factor of three the number of liver NETs analyzed, bringing the total confirmed to 31, and shows that several have multiple mechanisms for nuclear envelope retention.
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Affiliation(s)
- Poonam Malik
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh, EH9 3JR UK
| | - Nadia Korfali
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh, EH9 3JR UK
| | - Vlastimil Srsen
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh, EH9 3JR UK
| | - Vassiliki Lazou
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh, EH9 3JR UK
| | - Dzmitry G. Batrakou
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh, EH9 3JR UK
| | - Nikolaj Zuleger
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh, EH9 3JR UK
| | - Deirdre M. Kavanagh
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh, EH9 3JR UK
| | - Gavin S. Wilkie
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh, EH9 3JR UK
| | - Martin W. Goldberg
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
| | - Eric C. Schirmer
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh, EH9 3JR UK
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Batrakou DG, Kerr ARW, Schirmer EC. Comparative proteomic analyses of the nuclear envelope and pore complex suggests a wide range of heretofore unexpected functions. J Proteomics 2008; 72:56-70. [PMID: 18852071 DOI: 10.1016/j.jprot.2008.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 08/26/2008] [Accepted: 09/18/2008] [Indexed: 12/31/2022]
Abstract
Since the discovery of several inherited diseases linked to the nuclear envelope the number of functions ascribed to this subcellular organelle has skyrocketed. However the molecular pathways underlying these functions are not clear in most cases, perhaps because of missing components. Several recent proteomic analyses of the nuclear envelope and nuclear pore complex proteomes have yielded not only enough missing components to potentially elucidate these pathways, but suggest an exponentially greater number of functions at the nuclear periphery than ever imagined. Many of these functions appear to derive from recapitulation of pathways utilized at the plasma membrane and from other membrane systems. Additionally, many proteins identified in the comparative nuclear envelope studies have sequence characteristics suggesting that they might also contribute to nuclear pore complex functions. In particular, the striking enrichment for proteins in the nuclear envelope fractions that carry phenylalanine-glycine (FG) repeats may be significant for the mechanism of nuclear transport. In retrospect, these findings are only surprising in context of the notion held for many years that the nuclear envelope was only a barrier protecting the genome. In fact, it is arguably the most complex membrane organelle in the cell.
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Affiliation(s)
- Dzmitry G Batrakou
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
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